Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

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    Hoe ver en hoeveel? Verspreiding en infecties van koolluis in Nederland, Thema: Functionele biodiversiteit BO-12.03-004-001a
    Belder, E. den; Smulders, M.J.M. ; Esselink, D. ; Elderson, J. - \ 2011
    brevicoryne brassicae - gewasbescherming - verkeerde liggingen - volgorden - gewasmengsels - gewassen - koolsoorten - brevicoryne brassicae - plant protection - malpositions - sequences - crop mixtures - crops - cabbages
    Informatieposter met de titel "Hoe ver en hoeveel? Verspreiding en infecties van koolluis in Nederland", thema functionele biodiversiteit. De frequenties van bladluisinfecties worden beïnvloed door de ruimtelijke ligging en de opvolging van gewassen. Kan er door wijzigingen in bouwplan en gewasrotatie worden bijgedragen aan bladluisbeheersing?
    SLIDER: A Generic Metaheuristic for the Discovery of Correlated Motifs in Protein-Protein Interaction Networks
    Boyen, P. ; Dyck, D. van; Neven, F. ; Ham, R.C.H.J. van; Dijk, A.D.J. van - \ 2011
    IEEE/ACM Transactions on Computational Biology and Bioinformatics 8 (2011)5. - ISSN 1545-5963 - p. 1344 - 1357.
    sequences - scale - pairs
    Correlated motif mining (CMM) is the problem of finding overrepresented pairs of patterns, called motifs, in sequences of interacting proteins. Algorithmic solutions for CMM thereby provide a computational method for predicting binding sites for protein interaction. In this paper, we adopt a motif-driven approach where the support of candidate motif pairs is evaluated in the network. We experimentally establish the superiority of the Chi-square-based support measure over other support measures. Furthermore, we obtain that CMM is an NP-hard problem for a large class of support measures (including Chi-square) and reformulate the search for correlated motifs as a combinatorial optimization problem. We then present the generic metaheuristic SLIDER which uses steepest ascent with a neighborhood function based on sliding motifs and employs the Chi-square-based support measure. We show that SLIDER outperforms existing motif-driven CMM methods and scales to large protein-protein interaction networks. The SLIDER-implementation and the data used in the experiments are available on
    Genetic Basis of Tetracycline Resistance in Bifidobacterium animalis subsp lactis
    Gueimonde, M. ; Florez, A.B. ; Hoek, A.H.A.M. van; Stuer-Lauridsen, B. ; Stroman, P. ; Reyes-Gavilan, C.G. de los; Margolles, A. - \ 2010
    Applied and Environmental Microbiology 76 (2010)10. - ISSN 0099-2240 - p. 3364 - 3369.
    antibiotic susceptibility - probiotic products - tet(w) - bacteria - bile - lactobacillus - sequences - strains - humans - thermophilum
    All strains of Bifidobacterium animalis subsp. lactis described to date show medium level resistance to tetracycline. Screening of 26 strains from a variety of sources revealed the presence of tet(W) in all isolates. A transposase gene upstream of tet(W) was found in all strains, and both genes were cotranscribed in strain IPLAIC4. Mutants with increased tetracycline resistance as well as tetracycline-sensitive mutants of IPLAIC4 were isolated and genetically characterized. The native tet(W) gene was able to restore the resistance phenotype to a mutant with an alteration in tet(W) by functional complementation, indicating that tet(W) is necessary and sufficient for the tetracycline resistance seen in B. animalis subsp. lactis.
    Novel fungal genera and species associated with the sooty blotch and flyspeck complex on apple in China and the USA
    Yang, H.L. ; Sun, G.Y. ; Batzer, J.C. ; Crous, P.W. ; Groenewald, J.Z. ; Gleason, M.L. - \ 2010
    Persoonia (2010)24. - ISSN 0031-5850 - p. 29 - 37.
    ribosomal dna - sp-nov - sporidesmium - sequences - disease
    Fungi in the sooty blotch and flyspeck (SBFS) complex cause blemishes on apple and pear fruit that result in economic losses for growers. The SBFS fungi colonise the epicuticular wax layer of pomaceous fruit but do not invade the cuticle. Fungi causing fuliginous and punctate mycelial types on apple are particularly difficult to identify based on morphological criteria because many species in the SBFS complex share the same mycelial phenotypes. We compared the morphology and nuclear ribosomal DNA phylogeny (ITS, LSU) of 11 fungal strains isolated from SBFS blemishes on apple obtained from two provinces in China and five states in the USA. Parsimony analysis, supported by cultural characteristics and morphology in vitro, provided support to delimit the isolates into three novel genera, representing five new species. Phaeothecoidiella, with two species, P. missouriensis and P. illinoisensis, is introduced as a new genus with pigmented endoconidia in the Dothideomycetes. Houjia (Capnodiales) is introduced for H. pomigena and H. yanglingensis. Although morphologically similar to Stanjehughesia (Chaetosphaeriaceae), Houjia is distinct in having solitary conidiogenous cells. Sporidesmajora (Capnodiales), based on S. pennsylvaniensis, is distinguished from Sporidesmium (Sordariomycetes) in having long, multiseptate conidiophores that frequently have a subconical, darkly pigmented apical cell, and very long, multi-euseptate conidia
    Microcyclospora and Microcyclosporella: novel genera accommodating epiphytic fungi causing sooty blotch on apple
    Frank, J. ; Crous, P.W. ; Groenewald, J.Z. ; Oertel, B. ; Hyde, K.D. ; Phengsintham, P. ; Schroers, H.J. - \ 2010
    Persoonia 24 (2010). - ISSN 0031-5850 - p. 93 - 105.
    flyspeck complex - ribosomal dna - mycosphaerella - anamorphs - phylogeny - disease - teratosphaeria - proteaceae - morphology - sequences
    Recent studies have found a wide range of ascomycetes to be associated with sooty blotch and flyspeck (SBFS) blemishes on the surfaces of pomaceous fruits, specifically apples. Based on collections of such fungi from apple orchards in Germany and Slovenia we introduce two novel genera according to analyses of morphological characters and nuclear ribosomal DNA sequences (large subunit and internal transcribed spacer regions). Microcyclosporella is represented by a single species, M. mali, and is presently known from Germany and Slovenia. Microcyclosporella is Pseudocercosporella-like in morphology, but genetically and morphologically distinct from Pseudocercosporella s.str., for which an epitype is designated based on a fresh collection of P. bakeri from Laos. Furthermore, Pseudocercosporella is shown to be paraphyletic within the Capnodiales. Microcyclospora gen. nov. is Pseudocercospora-like in morphology, but is genetically and morphologically distinct from Pseudocercospora s.str., which is based on P. vitis. Three species, Microcyclospora malicola, M. pomicola (both collected in Germany), and M. tardicrescens (collected in Slovenia) are described. Finally, a new species of Devriesia, D. pseudoamericana, is described from pome fruit surfaces collected in Germany. Devriesia is shown to be paraphyletic, and to represent several lineages of which only Devriesia s.str. is thermotolerant. Further collections are required, however, before the latter generic complex can be resolved.
    Biochemical and genetical analysis reveal a new clade of biovar 3 Dickeya spp. strains isolated from potato in Europe
    Slawiak, M. ; Beckhoven, J.R.C.M. van; Speksnijder, A.G.C.L. ; Czajkowski, R.L. ; Grabe, G. ; Wolf, J.M. van der - \ 2009
    European Journal of Plant Pathology 125 (2009)2. - ISSN 0929-1873 - p. 245 - 261.
    erwinia-chrysanthemi - xanthomonas - pcr - sequences - hosts - water - fingerprints - genomes - plants
    Sixty-five potato strains of the soft rot-causing plant pathogenic bacterium Dickeya spp., and two strains from hyacinth, were characterised using biochemical assays, REP-PCR genomic finger printing, 16S rDNA and dnaX sequence analysis. These methods were compared with nineteen strains representing six Dickeya species which included the type strains. A group of twenty-two potato strains isolated between 2005-2007 in the Netherlands, Poland, Finland and Israel were characterised as belonging to biovar 3. They were 100% identical in REP-PCR, dnaX and 16S rDNA sequence analysis. In a polyphasic analysis they formed a new clade different from the six Dickeya species previously described, and may therefore constitute a new species. The strains were very similar to a Dutch strain from hyacinth. On the basis of dnaX sequences and biochemical assays, all other potato strains isolated in Europe between 1979 and 1994 were identified as D. dianthicola (biovar 1 and 7), with the exception of two German strains classified as D. dieffenbachia (biovar 2) and D. dadantii (biovar 3), respectively. Potato strains from Peru were classified as D. dadantii, from Australia as D. zeae and from Taiwan as D. chrysanthemi bv. parthenii, indicating that different Dickeya species are found in association with potato.
    Base composition, selection, and phylogenetic significance of indels in the recombination activating gene-1 in vertebrates
    Chiari, Y. ; Meijden, A. van der; Madsen, O. ; Vences, M. ; Meyer, A. - \ 2009
    Frontiers in Zoology 6 (2009). - ISSN 1742-9994 - 15 p.
    nuclear rag-1 gene - v(d)j recombination - mitochondrial-dna - evolution - sequences - diversification - patterns - frogs - amphibians - inference
    Background: The Recombination Activating Proteins, RAG1 and RAG2, play a crucial role in the immune response in vertebrates. Among the nuclear markers currently used for phylogenetic purposes, Rag1 has especially enjoyed enormous popularity, since it successfully contributed to elucidating the relationships among and within a large variety of vertebrate lineages. We here report on a comparative investigation of the genetic variation, base composition, presence of indels, and selection in Rag1 in different vertebrate lineages (Actinopterygii, Amphibia, Aves, Chondrichthyes, Crocodylia, Lepidosauria, Mammalia, and Testudines) through the analysis of 582 sequences obtained from Genbank. We also analyze possible differences between distinct parts of the gene with different type of protein functions. Results: In the vertebrate lineages studied, Rag1 is over 3 kb long. We observed a high level of heterogeneity in base composition at the 3(rd) codon position in some of the studied vertebrate lineages and in some specific taxa. This result is also paralleled by taxonomic differences in the GC content at the same codon position. Moreover, positive selection occurs at some sites in Aves, Lepidosauria and Testudines. Indels, which are often used as phylogenetic characters, are more informative across vertebrates in the 5' than in the 3'-end of the gene. When the entire gene is considered, the use of indels as phylogenetic character only recovers one major vertebrate clade, the Actinopterygii. However, in numerous cases insertions or deletions are specific to a monophyletic group. Conclusions: Rag1 is a phylogenetic marker of undoubted quality. Our study points to the need of carrying out a preliminary investigation on the base composition and the possible existence of sites under selection of this gene within the groups studied to avoid misleading resolution. The gene shows highly heterogeneous base composition, which affects some taxa in particular and contains sites under positive selection in some vertebrate lineages in the 5'-end. The first part of the gene (5'-end) is more variable than the second (3'-end), and less affected by a heterogeneous base composition. However, in some vertebrate lineages the 5'-end of the gene is not yet widely used for phylogenetic studies
    Eukaryotic transcriptomics in silico: Optimizing cDNA-AFLP efficiency
    Stölting, K.N. ; Gort, G. ; Wüst, C. ; Wilson, A.B. - \ 2009
    BMC Genomics 10 (2009). - ISSN 1471-2164 - 15 p.
    full-length cdnas - differential gene-expression - identification - distributions - resistance - sequences - resources - markers - library - plant
    Background - Complementary-DNA based amplified fragment length polymorphism (cDNA-AFLP) is a commonly used tool for assessing the genetic regulation of traits through the correlation of trait expression with cDNA expression profiles. In spite of the frequent application of this method, studies on the optimization of the cDNA-AFLP assay design are rare and have typically been taxonomically restricted. Here, we model cDNA-AFLPs on all 92 eukaryotic species for which cDNA pools are currently available, using all combinations of eight restriction enzymes standard in cDNA-AFLP screens. Results - In silco simulations reveal that cDNA pool coverage is largely determined by the choice of individual restriction enzymes and that, through the choice of optimal enzyme combinations, coverage can be increased from
    Towards a phylogenetic clarification of Lophiostoma / Massarina and morphologically similar genera in the Pleosporales
    Zhang, Y. ; Wang, H.K. ; Fournier, J. ; Crous, P.W. ; Jeewon, R. ; Pointing, S.B. ; Hyde, K.D. - \ 2009
    Fungal Diversity 38 (2009). - ISSN 1560-2745 - p. 225 - 251.
    submerged wood - ribosomal dna - fresh-water - hong-kong - fungi - ascomycota - revision - epitypification - teleomorph - sequences
    Lophiostoma, Lophiotrema and Massarina are similar genera that are difficult to distinguish morphologically. In order to obtain a better understanding of these genera, lectotype material of the generic types, Lophiostoma macrostomun, Lophiotrema nucula and Massarina eburnea were examined and are re-described. The phylogeny of these genera is investigated based oil the analysis of 26 Lophiostoma- and Massarina-like taxa and three genes - 18S, 28S rDNA and RPB2. These taxa formed five well-supported sub-clades in Pleosporales. This Study confirms that both Lophiostoma and Massarina are polyphyletic. Massarina-like taxa can presently be differentiated into two groups - the Lentithecium group and the Massarina group. Of these, the type species M. eburnea together with the Massarina group represents Massarina sensu stricto. Lophiostoma taxa Clustered in two groups - one group, including the type species L. macrostomum, is characterized by fusiform, hyaline one-septate ascospores which are pigmented and 3-septate when senescent, clavate asci, and apical structures which are highly variable, being crest-like in L. macrostomum, all umbilicate pore surrounded by 4-6 radial ridges in L. rugulosum, or papillate in L. glabrotunicatum. The second group comprises Lophiostoma species with heavily pigmented multi-septate ascospores and compressed crests. Lophiotrema species including the type species L. nucula form a monophyletic group. One new genus - Lentithecium with five new species - Lentithecium aquaticum, Lophiostoma glabrotunicatum, L. rugulosum, Lophiotrema brunneosporum and L. lignicola and three new combinations - Lentithecium arundinaceum, L. fluviatile and L. lineare are introduced in this paper.
    Quest for ion–ion correlations in electric double layers and overcharging phenomena
    Lyklema, J. - \ 2009
    Advances in Colloid and Interface Science 147-148 (2009). - ISSN 0001-8686 - p. 205 - 213.
    charge inversion - silver-iodide - adsorption - interface - sequences - stability - reversal - systems - anatase - water
    A discussion is given of the experimental evidence for overcharging, also known as charge reversal. The phenomenon is very common. The most general explanation is specific chemical adsorption. However, overcharging can also be explained on the basis of ion-ion correlations, which is rather a physical type of interpretation, and which can also be specific. Several theories have been developed for that. So, there is the luxury problem that two alternative explanations are available for the same observation. The purpose of this paper is to consider the various approaches critically and try to devise experimental options to discriminate between the two interpretations
    Identification of an ortholog of the eukaryotic RNA polymerase III subunit RPC34 in Crenarchaeota and Thaumarchaeota suggests specialization of RNA polymerases for coding and non-coding RNAs in Archaea
    Blombach, F. ; Makarova, K.S. ; Marrero, J. ; Siebers, B. ; Koonin, E.V. ; Oost, J. van der - \ 2009
    Biology Direct 4 (2009). - ISSN 1745-6150 - p. 39 - 39.
    transcription initiation - structure prediction - evolution - sequences - complexes - proteins - database - search - origin - server
    One of the hallmarks of eukaryotic information processing is the co-existence of 3 distinct, multi-subunit RNA polymerase complexes that are dedicated to the transcription of specific classes of coding or non-coding RNAs. Archaea encode only one RNA polymerase that resembles the eukaryotic RNA polymerase II with respect to the subunit composition. Here we identify archaeal orthologs of the eukaryotic RNA polymerase III subunit RPC34. Genome context analysis supports a function of this archaeal protein in the transcription of non-coding RNAs. These findings suggest that functional separation of RNA polymerases for protein-coding genes and non-coding RNAs might predate the origin of the Eukaryotes
    Phylogenetic relationships in Betula (Betulaceae) based on AFLP markers
    Schenk, M.F. ; Thienpont, C.N. ; Koopman, W.J.M. ; Gilissen, L.J.W.J. ; Smulders, M.J.M. - \ 2008
    Tree Genetics and Genomes 4 (2008)4. - ISSN 1614-2942 - p. 911 - 924.
    multilocus genotype data - birch pollen allergen - population-structure - major allergen - b-pubescens - dna - sequences - inference - evolution - isoforms
    The genus Betula comprises various species in boreal and temperate climate zones of the Northern Hemisphere. The taxonomy of Betula is controversial and complicated by parallel evolution of morphological traits, polyploidization events, and extensive hybridization and introgression among species. Multilocus molecular data from AFLPs were used to provide phylogenetic information. A large number of polymorphic markers (321 variable bands) were produced in 107 Betula accessions from 23 species and 11 hybrids. The AFLP results were largely congruent with the results from previously examined nuclear DNA markers. Four distinct subgenera were identified within the genus Betula. These subgenera were partly in disagreement with the traditional (but disputed) division of the genus. In addition, the results indicated several groups of conspecific taxa. The majority of the species fell within subgenus Betula and shared a high degree of similarity with B. pendula. All hybrids were associated with this group, and the AFLP data contained signals on putative parents for some of the interspecific hybrids. Subgenus Chamaebetula and part of the Neurobetula species should be merged with Betula. The subgenera Betulenta, Betulaster, and the remaining part of Neurobetula are distinct and well supported. Although our results indicate that four major taxonomic groups can be recognized within the genus Betula, the relationship between them remains unclear. This may be due to the occurrence of hybridization and introgression, which would have a homogenizing effect on the relationships between species. Naturally occurring Betula species of hybrid origin may explain the low bootstrap values within the Betula clade.
    HaploSNPer: a web-based allele and SNP detection tool
    Tang, J. ; Leunissen, J.A.M. ; Voorrips, R.E. ; Linden, C.G. van der; Vosman, B. - \ 2008
    BMC Genetics 9 (2008). - ISSN 1471-2156 - 7 p.
    discovery - polymorphisms - sequences - database - genomes
    Background - Single nucleotide polymorphisms (SNPs) and small insertions or deletions (indels) are the most common type of polymorphisms and are frequently used for molecular marker development. Such markers have become very popular for all kinds of genetic analysis, including haplotype reconstruction. Haplotypes can be reconstructed for whole chromosomes but also for specific genes, based on the SNPs present. Haplotypes in the latter context represent the different alleles of a gene. The computational approach to SNP mining is becoming increasingly popular because of the continuously increasing number of sequences deposited in databases, which allows a more accurate identification of SNPs. Several software packages have been developed for SNP mining from databases. From these, QualitySNP is the only tool that combines SNP detection with the reconstruction of alleles, which results in a lower number of false positive SNPs and also works much faster than other programs. We have build a web-based SNP discovery and allele detection tool (HaploSNPer) based on QualitySNP. Results - HaploSNPer is a flexible web-based tool for detecting SNPs and alleles in user-specified input sequences from both diploid and polyploid species. It includes BLAST for finding homologous sequences in public EST databases, CAP3 or PHRAP for aligning them, and QualitySNP for discovering reliable allelic sequences and SNPs. All possible and reliable alleles are detected by a mathematical algorithm using potential SNP information. Reliable SNPs are then identified based on the reconstructed alleles and on sequence redundancy. Conclusion - Thorough testing of HaploSNPer (and the underlying QualitySNP algorithm) has shown that EST information alone is sufficient for the identification of alleles and that reliable SNPs can be found efficiently. Furthermore, HaploSNPer supplies a user friendly interface for visualization of SNP and alleles.
    Conversion of chromosome-specific RAPDs into SCAR-based anchor markers for onion linkage maps and its application to genetic analyses inother Allium species
    Masuzaki, S. ; Miyazaki, T. ; McCallum, J. ; Heusden, A.W. van; Kik, C. ; Yamashita, K. ; Tashiro, Y. - \ 2008
    Scientia Horticulturae 115 (2008)4. - ISSN 0304-4238 - p. 323 - 328.
    amplified polymorphic dna - monosomic addition lines - l. aggregatum group - cepa l. - construction - assignment - sequences - aflp - locations - reveals
    Integration of previously developed Allium cepa linkage maps requires the availability of anchor markers for each of the eight chromosomes of shallot (A. cepa L. common group Aggregatum). To this end, eight RAPD markers originating from our previous research were converted into SCAR markers via cloning and sequencing of RAPD amplicons and designing of 24-mer oligonucleotide primers. Of the eight pairs of SCAR primers, seven resulted in the amplification of single bands of the original RAPDs, and the remaining primer set amplified an additional band. The results of Southern hybridization using RAPD amplicons from genomic DNA of Japanese bunching onion (Allium fistulosum L.)¿shallot monosomic addition lines indicated that five SCAR markers were single shallot chromosome-specific markers and were not detected in genomic DNA of A. fistulosum. The eight SCAR primer pairs were applied to other Allium species and exhibited three types of amplification profiles, namely RAPD amplicons observed only in shallot, in shallot and Allium vavilovii, and in several Allium species. A mapping study using 65 F2 plants generated by the selfing of one interspecific cross A. cepa × Allium roylei individual integrated the SCAR marker SAOE17500 into chromosome 5 as expected. The results of the present study show that the eight SCAR primer sets specific to shallot can facilitate the mapping in A. cepa and can also serve as anchor points between maps of different Allium species
    A ribosomal DNA-based framework for the detection and quantification of stress-sensitive nematode families in terrestrial habitats
    Holterman, M.H.M. ; Rybarczyk-Mydlowska, K.D. ; Elsen, S.J.J. van den; Megen, H.H.B. van; Mooijman, P.J.W. ; Santiago, R.P. ; Bongers, A.M.T. ; Bakker, J. ; Helder, J. - \ 2008
    Molecular Ecology Resources 8 (2008). - ISSN 1755-098X - p. 23 - 34.
    phylogenetic-relationships - maturity index - rna gene - sequences - classification - dorylaimida - evolution - reveals
    Indigenous communities of soil-resident nematodes have a high potential for soil health assessment as nematodes are diverse, abundant, trophically heterogeneous and easily extractable from soil. The conserved morphology of nematodes is the main operational reason for their under-exploitation as soil health indicators, and a user-friendly biosensor system should preferably be based on nonmorphological traits. More than 80% of the most environmental stress-sensitive nematode families belong to the orders Mononchida and Dorylaimida. The phylogenetic resolution offered by full-length small subunit ribosomal DNA (SSU rDNA) sequences within these two orders is highly different. Notwithstanding several discrepancies between morphology and SSU rDNA-based systematics, Mononchida families (indicated here as M1¿M5) are relatively well-supported and, consequently, family-specific DNA sequences signatures could be defined. Apart from Nygolaimidae and Longidoridae, the resolution among Dorylaimida families was poor. Therefore, a part of the more variable large subunit rDNA (¿ 1000 bp from the 5'-end) was sequenced for 72 Dorylaimida species. Sequence analysis revealed a subclade division among Dorylaimida (here defined as D1¿D9, PP1¿PP3) that shows only distant similarity with `classical¿ Dorylaimid systematics. Most subclades were trophically homogeneous, and ¿ in most cases ¿ specific morphological characteristics could be pinpointed that support the proposed division. To illustrate the practicability of the proposed molecular framework, we designed primers for the detection of individual subclades within the order Mononchida in a complex DNA background (viz. in terrestrial or freshwater nematode communities) and tested them in quantitative assays (real-time polymerase chain reaction). Our results constitute proof-of-principle for the concept of DNA sequence signatures-based monitoring of stress sensitive nematode families in environmental samples
    Sonnenberg, A.S.M. - \ 2007
    Paddestoelen : onafhankelijk vakblad voor Nederland en België 2007 (2007)6. - ISSN 1380-359X - p. 8 - 8.
    genetica - genomen - dna - paddestoelen - agaricus bisporus - volgorden - genen - toepassing - onderzoek - genetics - genomes - dna - mushrooms - agaricus bisporus - sequences - genes - application - research
    Eind 2007 zal een begin gemaakt worden met de ontrafeling van het hele genoom van de champignon (Agaricus bisporus). Het karwei zal waarschijnlijk in 2009 geklaard zijn. Dan zal de volgorde van alle 34 miljoen bouwstenen in het DNA (sequentie) van deze paddenstoel bekend zijn en tevens de locatie van alle genen
    Molecular and biological characterization of Tomato chlorotic mottle virus suggests that recombination underlies the evolution and diversity of Brazilian tomato begomoviruses
    Ribeiro, S.G. ; Martin, D.P. ; Lacorte, C. ; Simoes, I.C. ; Orlandini, D.R.S. ; Inoue-Nagata, A.K. - \ 2007
    Phytopathology 97 (2007)6. - ISSN 0031-949X - p. 702 - 711.
    whitefly-transmitted geminiviruses - leaf-curl-virus - abutilon-mosaic-virus - dna-b - nicotiana-benthamiana - replication - emergence - sequences - disease - origin
    Tomato chlorotic mottle virus (ToCMoV) is an emerging begomovirus species widely distributed throughout tomato-growing regions of Brazil. ToCMoV appears to have expanded its geographic range recently, invading tomato-growing areas that were free of begomovirus infection before 2004. We have determined the first complete genome sequence of an infectious ToCMoV genome (isolate BA-Se1), which is the first begomovirus species isolated in the northeast of Brazil. When introduced by particle bombardment into tomato, the cloned ToCMoV-[BA-Se1] DNA-A and DNA-B components caused typical chlorotic mottle symptoms. The cloned virus was whitefly-transmissible and, although it was infectious in hosts such as Nicotiana benthamiana, pepper, tobacco, and Nicandra physaloides, it was unable to infect Arabidopsis thaliana, bean, N. glutinosa, and Datura metel. Sequence and biological analyses indicate that ToCMoV-[BA-Se1] is a typical New World begomovirus sp. requiring both DNA-A and DNA-B components to establish systemic infections. Although evidence of multiple recombination events was detected within the ToCMoV-[BA-Se1] DNA-A, they apparently occurred relatively long ago, implying that recombination probably has not contributed to the recent emergence of this species.
    A new robust diagnostic polymerase chain reaction for determining the mating status of female Anopheles gambiae mosquitoes
    Ng'habi, K.R. ; Horton, A. ; Knols, B.G.J. ; Lanzaro, G.C. - \ 2007
    American Journal of Tropical Medicine and Hygiene 77 (2007)3. - ISSN 0002-9637 - p. 485 - 487.
    y-chromosome - drosophila-melanogaster - neo-y - malaria - genome - degeneration - sequences - evolution - miranda - sex
    The principal malaria vector in Africa, Anopheles gambiae, contains two pairs of autosomes and one pair of sex chromosomes. The Y chromosome is only associated with males and other Y chromosome¿specific DNA sequences, which are transferred to women during mating. A reliable tool to determine the mating status of dried wild An. gambiae females is currently lacking. DNA was extracted from dried virgin and mated females and used to test whether Y chromosome¿specific polymerase chain reaction (PCR) markers can be successfully amplified and used as a predictor of mating. Here we report a new PCR-based method to determine the mating status among successfully inseminated and virgin wild An. gambiae females, using three male-specific primers. This dissection-free method has the potential to facilitate studies of both population demographics and gene flow from dried mosquito samples routinely collected in epidemiologic monitoring and aid existing and new malaria-vector control approaches.
    Hybrid Mitochondrial Plasmids From Senescence Suppressor Isolates of Neurospora intermedia
    Maas, M.F.P.M. ; Hoekstra, R.F. ; Debets, A.J.M. - \ 2007
    Genetics 175 (2007). - ISSN 0016-6731 - p. 785 - 794.
    reverse-transcriptase - podospora-anserina - transfer-rnas - dna - sequences - identification - recombination - evolution - insertion - strains
    We analyzed several natural suppressor isolates of the pKalilo-based fungal senescence syndrome of Neurospora intermedia. The pKalilo plasmid did not increase in titer in these isolates. Nor did it show integration "de novo." In at least two of the senescence suppressor isolates, pKalilo had formed stable recombinants with other mitochondrial elements. pKalilo/mtDNA recombination junctions were complete and appeared to have been formed via a nonhomologous recombination mechanism. Further analysis revealed that pKalilo had recombined a novel, 2.6-kb cryptic mitochondrial retroplasmid, similar to the mitochondrial retroplasmid pTHR1 from Trichoderma harzianum and retroplasmids of the "Varkud" homology group. The recombinant molecules consisted of pKalilo, the novel element, and short intervening stretches of mtDNA. The latter stretches clearly corresponded to "in vivo" mitochondrial cDNA, suggesting that the molecules had formed via the action of a template-switching reverse transcriptase. We discuss how different types of mitochondrial plasmids interact and how their detrimental effect on the host may be suppressed.
    A Natural infrageneric classification for Cicer (Leguminoseae, Cicereae)
    Davies, A.M.R. ; Maxted, N. ; Maesen, L.J.G. van der - \ 2007
    Blumea 52 (2007)2. - ISSN 0006-5196 - p. 379 - 400.
    genetic-relationships - genus cicer - phylogenetic-relationships - isozyme polymorphism - sequences - turkey - rapd - dna - morphology - diversity
    A comprehensive morphological survey and analysis of all taxonomically recognised wild species of Cicer L. (Leguminosae, Cicereae) is presented. The data (104 characters from 152 herbarium specimens representing 34 of the 44 recognised taxa in the genus Cicer with supplementary data for the remaining taxa taken from the literature) were analysed using multivariate statistics (cluster analysis, factor analysis and ordination techniques). The results are discussed in the context of extant classifications and the re-organisation of a novel infrageneric classification also incorporating information from published genetic data. A revised classification with 3 subgenera, 5 sections and 2 series is proposed.
    Hepatitis E Virus RNA in Commercial Porcine Livers in The Netherlands
    Bouwknegt, M. ; Lodder-Verschoor, F. ; Poel, W.H.M. van der; Rutjes, S.A. ; Roda Husman, A.M. de - \ 2007
    Journal of Food Protection 70 (2007)12. - ISSN 0362-028X - p. 2889 - 2895.
    cross-species infection - united-states - phylogenetic analysis - genetic diversity - wild boar - swine - transmission - prevalence - sequences - japan
    Human hepatitis E virus (HEV) infections by genotype 3 strains in industrialized countries are hypothesized to be caused by pigs. To examine this hypothesis, the potential health risks of transmission routes should be examined. Possible foodborne transmission was studied by quantifying the presence and infectivity of HEV in commercial porcine livers in The Netherlands. A comparison of four tissue disruption and seven RNA extraction methods revealed that mechanical disruption followed by silica-based RNA extraction gave the highest RNA yields and was therefore employed on commercial porcine livers. Four (6.5%) of 62 porcine livers were HEV RNA positive by reverse transcriptase PCR and Southern blot hybridization. Each positive liver was estimated to contain ~65 PCR-detectable units per g. Sequences were obtained for three of four positive livers and classified as HEV genotype 3. Ninety-three percent similarity to Dutch human HEV sequences and 97% similarity to Dutch swine HEV sequences were observed. To determine whether positive livers contained infectious HEV particles, extracts from livers with known HEV RNA sequences were inoculated intravenously in pigs. Two control pigs were included: one was inoculated with a high dose known to result in infection (104 PCR-detectable units of HEV RNA), and the other was inoculated with a lower concentration of virus that equaled the concentration of PCR-detectable units in commercial livers (~20 PCR-detectable units). Infection was observed in the high-dose control, but not in other pigs, suggesting a dose-dependent response in pigs. Hence, the implications of HEV RNA in commercial porcine livers in The Netherlands are unknown. However, HEV RNA is present in commercial porcine livers, and sufficient heating of porcine livers before consumption as precautionary measure is recommended.
    Distribution and diversity of root-lesion nematodes (Pratylenchus spp.) associated with Ammophila arenaria in coastal dunes of Western Europe
    Peña, E. de la; Karssen, G. ; Moens, M. - \ 2007
    Nematology 9 (2007)6. - ISSN 1388-5545 - p. 881 - 901.
    ribosomal-rna gene - morphological characterization - molecular characterization - phylogenetic analysis - cyst-nematode - clonal grass - d3 expansion - sequences - rdna - region
    The distribution and diversity of Pratylenchus species associated with Ammophila arenaria was investigated in its natural range of distribution. Twelve localities with vigorous stands of A. arenaria along the European Atlantic and Mediterranean coasts were sampled. The populations were identified based on morphology and morphometrics, and further characterised based on sequences of the rDNA D2D3 region. Pratylenchus spp. were present in all of the sampled sites. A total of 19 populations were detected belonging to Pratylenchus dunensis, P. brzeskii, P. pratensis or P. penetrans. Pratylenchus dunensis was widely distributed from Blakeney Point (UK) to Comporta (Portugal). Pratylenchus brzeskii was found in South European localities along the Atlantic coast and also in the Mediterranean region. Pratylenchus pratensis was found associated with A. arenaria for the first time and occurred at different locations along the Atlantic coast. Pratylenchus penetrans was only detected in Biarritz (France). The P. dunensis populations from the south west Iberian Peninsula differed from the original P. dunensis description and showed two incisures on the lip region instead of one. Pratylenchus brzeskii populations did not vary morphologically from the original descriptions; however, the range of their morphometrical characters was wider than that of the type population. The D2D3 rDNA region revealed large interspecific and low intraspecific variation, supporting the morphological identification. The phylogenetic relationships of the populations with respect to other species of the genus were inferred from partial sequences of the rDNA and positioned P. dunensis within the same group as P. convallariae, P. penetrans and P. fallax.
    Phylogeographic patterns in Leccinum sect. Scabra and the status of the arctic/alpine species L. rotundifoliae
    Bakker, H.C. den; Zuccarello, G.C. ; Kuyper, T.W. ; Noordeloos, M.E. - \ 2007
    Mycological Research 111 (2007)6. - ISSN 0953-7562 - p. 663 - 672.
    evolution - substitutions - phylogeny - sequences - muscaria - region - model - dna
    We investigated inter- and intraspecific phylogenetic relationships in the ectomycorrhizal fungal genus Leccinum section Scabra. Species of this section are exclusively associated with Betula and occur throughout the Northern Hemisphere. We compared the phylogenetic relationships of arctic, alpine, boreal and temperate accessions of section Scabra based on DNA sequences of the single-copy nuclear gene Gapdh and the multiple-copy nuclear region 5.8S-ITS2. Exclusively arctic lineages were not detected in species that occur both in arctic-alpine or boreal regions, except in L. rotundifoliae that was restricted to cold climates. L. scabrum and L. holopus showed an intercontinental phylogeographic pattern, and L. variicolor showed a pattern unrelated to geographical distribution. Molecular clock estimates indicated that L. rotundifoliae is as old as other species in section Scabra. Individual gene trees suggest that interspecific hybridisation occurred several times in the evolution of section Scabra.
    Investigation of microbial communities on reverse osmosis membranes used for process water production
    Bereschenko, L.A. ; Stams, A.J.M. ; Heilig, G.H.J. ; Euverink, G.J.W. ; Nederlof, M.M. ; Loosdrecht, M.C.M. - \ 2007
    Water Science and Technology 55 (2007)8-9. - ISSN 0273-1223 - p. 181 - 190.
    16s ribosomal-rna - systems - sequences - biofilms - genes
    In the present study, the diversity and the phylogenetic affiliation of bacteria in a biofouling layer on reverse osmosis (RO) membranes were determined. Fresh surface water was used as a feed in a membrane-based water purification process. Total DNA was extracted from attached cells from feed spacer, RO membrane and product spacer. Universal primers were used to amplify the bacterial 16S rRNA genes. The biofilm community was analysed by 16S rRNA-gene-targeted denaturing gradient gel electrophoresis (DGGE) and the phylogenetic affiliation was determined by sequence analyses of individual 16S rDNA clones. Using this approach, we found that five distinct bacterial genotypes (Sphingomonas, Beta proteobacterium, Flavobacterium, Nitrosomonas and Sphingobacterium) were dominant genera on surfaces of fouled RO membranes. Moreover, the finding that all five ¿key players¿ could be recovered from the cartridge filters of this RO system, which cartridge filters are positioned before the RO membrane, together with literature information where these bacteria are normally encountered, suggests that these microorganisms originate from the feed water rather than from the RO system itself, and represent the fresh water bacteria present in the feed water, despite the fact that the feed water passes an ultrafiltration (UF) membrane (pore size approximately 40 nm), which is able to remove microorganisms to a large extent.
    Microgeographic evolution of snail shell shape and predator behavior
    Schilthuizen, M. ; Til, A. Van; Salverda, M. ; Liew, T.S. ; James, S. ; Elahan, B. Bin; Vermeulen, J.J. - \ 2006
    Evolution 60 (2006)9. - ISSN 0014-3820 - p. 1851 - 1858.
    land-snails - sexual selection - gene flow - speciation - dna - diversification - biodiversity - population - diversity - sequences
    AbstractGenetic divergence in geographically isolated populations is a prerequisite for allopatric speciation, one of the most common modes of speciation. In ecologically equivalent populations existing within a small, environmentally homogeneous area, an important role for environmentally neutral divergence is often found or inferred. We studied a species complex of conspicuously shaped Opisthostoma land snails on scattered limestone outcrops within a small area of lowland rainforest in Borneo. We used shell morphometrics, mitochondrial and nuclear DNA sequences, and marks of predation to study the factors involved in allopatric divergence. We found that a striking geographic divergence exists in shell morphology, which is partly associated with neutral genetic divergence. We also found geographic differentiation in the behavior of the snails' invertebrate predator and evidence of an evolutionary interaction between aspects of shell shape and predator behavior. Our study shows that adaptation to biotic aspects of the environment may play a more important role in allopatric speciation than previously suspected, even on a geographically very small scale.
    Presumptive horizontal symbiont transmission in the fungus-growing termite Macrotermes natalensis
    Fine Licht, H.H. de; Boomsma, J.J. ; Aanen, D.K. - \ 2006
    Molecular Ecology 15 (2006)11. - ISSN 0962-1083 - p. 3131 - 3138.
    odontotermes-formosanus - phylogenetic inference - population-genetics - isoptera - recombination - comb - sequences - colonies - basidiomycota - establishment
    All colonies of the fungus-growing termite Macrotermes natalensis studied so far are associated with a single genetically variable lineage of Termitomyces symbionts. Such limited genetic variation of symbionts and the absence of sexual fruiting bodies (mushrooms) on M. natalensis mounds would be compatible with clonal vertical transmission, as is known to occur in Macrotermes bellicosus. We investigated this hypothesis by analysing DNA sequence polymorphisms as codominant SNP markers of four single-copy gene fragments of Termitomyces isolates from 31 colonies of M. natalensis. A signature of free recombination was found, indicative of frequent sexual horizontal transmission. First, all 31 strains had unique multilocus genotypes. Second, SNP markers (n = 55) were largely in Hardy-Weinberg equilibrium (90.9%) and almost all possible pairs of SNPs between genetically unlinked loci were in linkage equilibrium (96.7%). Finally, extensive intragenic recombination was found, especially in the EF1 alpha fragment. Substantial genetic variation and a freely recombining population structure can only be explained by frequent horizontal and sexual transmission of Termitomyces. The apparent variation in symbiont transmission mode among Macrotermes species implies that vertical symbiont transmission can evolve rapidly. The unexpected finding of horizontal transmission makes the apparent absence of Termitomyces mushrooms on M. natalensis mounds puzzling. To our knowledge, this is the first detailed study of the genetic population structure of a single lineage of Termitomyces.
    Natural occurence of Wolbachia-infected and uninfected Trichogramma species in tomato fields in Portugal
    Gonçalves, C.I. ; Huigens, M.E. ; Verbaarschot, P.G.H. ; Duarte, S. ; Mexia, A. ; Tavares, J. - \ 2006
    Biological Control 37 (2006)3. - ISSN 1049-9644 - p. 375 - 381.
    sex-ratio chromosome - biological-control - parthenogenesis - sequences - wasps - gene - mass
    Minute egg parasitoids of the genus Trichogramma (Hymenoptera; Trichogrammatidae) are promising candidates for biological control of lepidopteran pests in tomato in Portugal. This certainly applies to native Trichogramma strains that have thelytokous reproduction, i.e., produce only daughters. In Trichogramma wasps, thelytoky is mostly induced by the intracellular bacterium Wolbachia. In this study, we carried out a field survey of native Trichogramma species in four locations in Ribatejo, the main processing tomato region of Portugal, and determined the prevalence of Wolbachia in those species. Five Trichogramma species were found to emerge from lepidopteran eggs collected in the field, namely Trichogramma bourarache, Trichogramma cordubensis, Trichogramma evanescens, Trichogramma pintoi, and Trichogramma turkestanica. T. evanescens and T. pintoi were by far the dominating species representing, respectively, 64.9 and 26.4% of the trichogrammatids collected. Total natural parasitism rates of the collected lepidopteran eggs by Trichogramma wasps ranged from 28.2 to 64.6%. Three Trichogramma species were found to be infected with Wolbachia, namely T. cordubensis, T. evanescens, and T. turkestanica. All the wasp broods belonging to T. cordubensis were infected, whereas low infection rates were found in T. evanescens (0.9% of the broods) and T. turkestanica (4.5% of the broods). The latter represents the first record of a Wolbachia infection in T. turkestanica. Sequencing of the Wolbachia surface protein, wsp, revealed this Wolbachia infection to be related to other Wolbachia infections in Trichogramma wasps. As Wolbachia-infected thelytokous strains exist for T. evanescens, the most abundant Trichogramma species naturally occurring in the tomato fields of the Ribatejo region, this species offers interesting and powerful options for biological control of lepidopteran pests in processing tomato in this region.
    Phylum-wide analysis of SSU rDNA reveals deep phylogenetic relationships among nematodes and accelerated evolution toward Crown Clades
    Holterman, M.H.M. ; Wurff, A.W.G. van der; Elsen, S.J.J. van den; Megen, H.H.B. van; Bongers, A.M.T. ; Holovachov, O.V. ; Bakker, J. ; Helder, J. - \ 2006
    Molecular Biology and Evolution 23 (2006)9. - ISSN 0737-4038 - p. 1792 - 1800.
    relative-rate test - ribosomal-rna - sequences - ultrastructure - confidence - bootstrap
    Inference of evolutionary relationships between nematodes is severely hampered by their conserved morphology, the high frequency of homoplasy, and the scarcity of phylum-wide molecular data. To study the origin of nematode radiation and to unravel the phylogenetic relationships between distantly related species, 339 nearly full-length small-subunit rDNA sequences were analyzed from a diverse range of nematodes. Bayesian inference revealed a backbone comprising 12 consecutive dichotomies that subdivided the phylum Nematoda into 12 clades. The most basal clade is dominated by the subclass Enoplia, and members of the order Triplonchida occupy positions most close to the common ancestor of the nematodes. Crown Clades 8¿12, a group formerly indicated as "Secernentea" that includes Caenorhabditis elegans and virtually all major plant and animal parasites, show significantly higher nucleotide substitution rates than the more basal Clades 1¿7. Accelerated substitution rates are associated with parasitic lifestyles (Clades 8 and 12) or short generation times (Clades 9¿11). The relatively high substitution rates in the distal clades resulted in numerous autapomorphies that allow in most cases DNA barcode¿based species identification. Teratocephalus, a genus comprising terrestrial bacterivores, was shown to be most close to the starting point of Secernentean radiation. Notably, fungal feeding nematodes were exclusively found basal to or as sister taxon next to the 3 groups of plant parasitic nematodes, namely, Trichodoridae, Longidoridae, and Tylenchomorpha. The exclusive common presence of fungivorous and plant parasitic nematodes supports a long-standing hypothesis that states that plant parasitic nematodes arose from fungivorous ancestors
    Plant host range of Verticillium longisporum and microsclerotia density in Swedisch soils
    Johansson, A. ; Goud, J.C. ; Dixelius, C. - \ 2006
    European Journal of Plant Pathology 114 (2006)2. - ISSN 0929-1873 - p. 139 - 149.
    molecular characterization - oilseed rape - dahliae - wilt - sequences - identification - nuclear - barley - crops
    Verticillium longisporum is a soil-borne fungal pathogen causing vascular wilt of Brassica crops. This study was conducted to enhance our knowledge on the host range of V. longisporum. Seven crop species (barley, oat, oilseed rape, pea, red clover, sugar beet and wheat) and five weed species (barren brome, black-grass, charlock, cleavers and scentless mayweed) all common in southern Sweden were evaluated for infection by response to V. longisporum. Oat, spring wheat, oilseed rape, scentless mayweed and charlock inoculated with V. longisporum in a greenhouse showed stunting to various degrees close to the fully ripe stage. Based on the extent of microsclerotia formation, explants were separated into four groups: for pea and wheat, 80%. The results suggest that plant species outside the Brassicaceae can act as reservoirs of V. longisporum inoculum. Soil inoculum densities in nine fields were monitored over a period of 12 months, which ranged from 1 to 48 cfu g¿1 soil. Density of microsclerotia was lowest just after harvest, reaching its maximum six months later. No significant correlation between inoculum density in soil and disease incidence on oilseed rape plants was found. However, the data suggest that a threshold of 1 cfu g¿1 soil is needed to cause disease on oilseed rape. Species identification based on microsclerotia morphology and PCR analysis showed that V. longisporum dominated in soil of seven, and V. dahliae in two of the nine fields studied.
    Reconstructing the early evolution of the fungi using a six gene phylogeny
    James, T.Y. ; Kauff, F. ; Schoch, C.L. ; Matheny, P.B. ; Hofstetter, V. ; Cox, C.J. ; Celio, G. ; Gueidan, C. ; Fraker, E. ; Miadlikowska, J. ; Lumbsch, H.T. ; Rauhut, A. ; Reeb, V. ; Arnold, A.E. ; Amtoft, A. ; Stajich, J.E. ; Hosaka, K. ; Sung, G.H. ; Johnson, D. ; O'Rourke, B. ; Binder, M. ; Curtis, J.M. ; Slot, J.C. ; Wang, Z. ; Wilson, A.W. ; Schüßler, A. ; Longcore, J.E. ; O'Donnell, K. ; Mozley-Standridge, S. ; Porter, D. ; Letcher, P.M. ; Powell, M.J. ; Taylor, J.W. ; White, M.M. ; Griffith, G.W. ; Davies, D.R. ; Sugiyama, J. ; Rossman, A.Y. ; Rogers, J.D. ; Pfister, D.H. ; Hewitt, D. ; Hansen, K. ; Hambleton, S. ; Shoemaker, R.A. ; Kohlmeyer, J. ; Volkmann-Kohlmeyer, B. ; Spotts, R.A. ; Serdani, M. ; Crous, P.W. ; Hughes, K.W. ; Matsuura, K. ; Langer, E. ; Langer, G. ; Untereiner, W.A. ; Lücking, R. ; Büdel, B. ; Geiser, D.M. ; Aptroot, A. ; Diederich, P. ; Schmitt, I. ; Schultz, M. ; Yahr, R. ; Hibbett, D.S. ; Lutzoni, F. ; McLaughlin, D.J. ; Spatafora, J.W. ; Vilgalys, R. - \ 2006
    Nature 443 (2006)7113. - ISSN 0028-0836 - p. 818 - 822.
    arbuscular mycorrhizal fungi - molecular phylogeny - maximum-likelihood - land plants - tree - microsporidia - sequences - animals - chytridiomycota - glomeromycota
    The ancestors of fungi are believed to be simple aquatic forms with flagellated spores, similar to members of the extant phylum Chytridiomycota (chytrids). Current classifications assume that chytrids form an early-diverging clade within the kingdom Fungi and imply a single loss of the spore flagellum, leading to the diversification of terrestrial fungi. Here we develop phylogenetic hypotheses for Fungi using data from six gene regions and nearly 200 species. Our results indicate that there may have been at least four independent losses of the flagellum in the kingdom Fungi. These losses of swimming spores coincided with the evolution of new mechanisms of spore dispersal, such as aerial dispersal in mycelial groups and polar tube eversion in the microsporidia (unicellular forms that lack mitochondria). The enigmatic microsporidia seem to be derived from an endoparasitic chytrid ancestor similar to Rozella allomycis, on the earliest diverging branch of the fungal phylogenetic tree
    Analysis of the SHP2 enhancer for the use of tissue specific activation tagging in Arabidopsis thaliana
    Chalfun Junior, A. ; Mes, J.J. ; Busscher, M. ; Angenent, G.C. - \ 2006
    Genetics and Molecular Biology 29 (2006)2. - ISSN 1415-4757 - p. 401 - 407.
    mads-box genes - transformation - biosynthesis - growth - plants - fruit - transcription - regulator - sequences - promoter
    Activation tagging is a powerful tool to identify new mutants and to obtain information about possible biological functions of the overexpressed genes. The quadruple cauliflower mosaic virus (CaMV) 35S enhancer fragment is a strong enhancer, which is most commonly used for this purpose. However, the constitutive nature of this enhancer may generate lethal mutations or aberrations in different plant organs by the same overexpressed gene. A tissue-specific activation tagging approach may overcome these drawbacks and may also lead more efficiently to the desired phenotype. For this reason the SHATTERPROOF2 (SHP2) promoter fragment was analysed for enhancer activity. The SHP2 gene is involved in dehiscence zone development and expressed during silique development. The aim of the experiments described here was to identify a dehiscence zone specific enhancer that could be used for tissue-specific activation tagging. The chosen SHP2 enhancer fragment was found to be expressed predominantly in the dehiscence zone and showed enhancer activity as well as ectopic expression activity. This activity was not influenced by its orientation towards the promoter and it was still functional at the largest tested distance of 2.0 kb. Based on these results, the SHP2 enhancer fragment can potentially be used in a tissue-specific activation tagging approach to identify new Arabidopsis mutants with an altered dehiscence zone formation.
    Lectin receptor kinases participate in protein-protein interactions to mediate plasma membrane-cell wall adhesions in Arabidopsis
    Gouget, A. ; Senchou, V. ; Govers, F. ; Sanson, A. ; Barre, A. ; Rougé, P. ; Pont-Lezica, R. ; Canut, H. - \ 2006
    Plant Physiology 140 (2006)1. - ISSN 0032-0889 - p. 81 - 90.
    signal-transduction - lathyrus-ochrus - isolectin-i - sequences - binding - plants - expression - alignment - families - database
    Interactions between plant cell walls and plasma membranes are essential for cells to function properly, but the molecules that mediate the structural continuity between wall and membrane are unknown. Some of these interactions, which are visualized upon tissue plasmolysis in Arabidopsis (Arabidopsis thaliana), are disrupted by the RGD (arginine-glycine-aspartic acid) tripeptide sequence, a characteristic cell adhesion motif in mammals. In planta induced-O (IPI-O) is an RGD-containing protein from the plant pathogen Phytophthora infestans that can disrupt cell wall-plasma membrane adhesions through its RGD motif. To identify peptide sequences that specifically bind the RGD motif of the IPI-O protein and potentially play a role in receptor recognition, we screened a heptamer peptide library displayed in a filamentous phage and selected two peptides acting as inhibitors of the plasma membrane RGD-binding activity of Arabidopsis. Moreover, the two peptides also disrupted cell wall-plasma membrane adhesions. Sequence comparison of the RGD-binding peptides with the Arabidopsis proteome revealed 12 proteins containing amino acid sequences in their extracellular domains common with the two RGD-binding peptides. Eight belong to the receptor-like kinase family, four of which have a lectin-like extracellular domain. The lectin domain of one of these, At5g60300, recognized the RGD motif both in peptides and proteins. These results imply that lectin receptor kinases are involved in protein-protein interactions with RGD-containing proteins as potential ligands, and play a structural and signaling role at the plant cell surfaces.
    Phylogeography, population dynamics, and molecular evolution of European bat lyssaviruses
    Davis, P.L. ; Holmes, E.C. ; Larrous, F. ; Poel, W.H.M. van der; Tjornehoj, K. ; Alonso, W.J. ; Bourhy, H. - \ 2005
    Journal of Virology 79 (2005)16. - ISSN 0022-538X - p. 10487 - 10497.
    pteropus-giganteus - immune-response - rabies virus - rna viruses - infection - epidemiology - substitution - chiroptera - diversity - sequences
    European bat lyssaviruses types 1 and 2 (EBLV-1 and EBLV-2) are widespread in Europe, although little is known of their evolutionary history. We undertook a comprehensive sequence analysis to infer the selection pressures, rates of nucleotide substitution, age of genetic diversity, geographical origin, and population growth rates of EBLV-1. Our study encompassed data from 12 countries collected over a time span of 35 years and focused on the glycoprotein (G) and nucleoprotein (N) genes. We show that although the two subtypes of EBLV-1¿EBLV-1a and EBLV-1b¿have both grown at a low exponential rate since their introduction into Europe, they have differing population structures and dispersal patterns. Furthermore, there were strong constraints against amino acid change in both EBLV-1 and EBLV-2, as reflected in a low ratio of nonsynonymous to synonymous substitutions per site, particularly in EBLV-1b. Our inferred rate of nucleotide substitution in EBLV-1, approximately 5 x 10¿5 substitutions per site per year, was also one of the lowest recorded for RNA viruses and implied that the current genetic diversity in the virus arose 500 to 750 years ago. We propose that the slow evolution of EBLVs reflects their distinctive epidemiology in bats, where they occupy a relatively stable fitness peak.
    An obliquity-controlled Early Pleistocene river terrace record from Western Turkey?
    Maddy, D. ; Demir, T. ; Bridgeland, D. ; Veldkamp, A. ; Stemerdink, C. ; Schriek, T. van der; Westaway, R. - \ 2005
    Quaternary Research 63 (2005)3. - ISSN 0033-5894 - p. 339 - 346.
    2-stage extension - gediz graben - uplift - stratigraphy - evolution - sequences - selendi - basins - model
    Investigation of the Pleistocene sequence of the Gediz River, Western Turkey, has revealed a record of Early Pleistocene river terraces. Eleven terraces spanning the interval from 1.67 to 1.245 million years ago (MIS 59-37) are preserved beneath basaltic lava flows. The high number of terraces over this short time period reflects high-frequency sedimentation/incision cycles preserved due to the fortuitous combination of relatively high uplift rates (0.16 mm yr¿1) and progressive southwards valley migration. Comparison of this record with ODP967 from the Eastern Mediterranean Basin suggests a link between the production of terraces and obliquity-driven 41,000 year climate cycles in the Early Pleistocene.
    Preliminary studies on Botryosphaeria species from Southern Hemisphere conifers in Australasia and South Africa
    Slippers, B. ; Summerbell, B.A. ; Crous, P.W. ; Coutinho, T.A. ; Wingfield, B.D. ; Wingfield, M.J. - \ 2005
    Australasian Plant Pathology 34 (2005)2. - ISSN 0815-3191 - p. 213 - 220.
    wollemia-nobilis - genetic-variation - sp-nov - eucalyptus - dothidea - characters - pathogens - sequences - cankers - ribis
    Wollemia nobilis is an ancient coniferous tree species that was recently discovered in eastern Australia. This tree is highly threatened due to its limited distribution. No genetic variation has been detected within the wild populations of ~100 adult plants. A recent study has revealed that a species of Botryosphaeria is highly pathogenic to W. nobilis. The aim of the present study was to identify this fungus, as well as Botryosphaeria isolates of unknown identity from other Southern Hemisphere coniferous hosts, Araucaria from New Zealand and Widdringtonia from South Africa. To facilitate their identification, sequence data for the ITS rDNA, as well as the ß-tubulin and translation elongation factor 1-¿ genes were combined to determine the phylogenetic relationship of these isolates with those of known Botryosphaeria spp. Isolates from W. nobilis included two Botryosphaeria spp. The first is closely related to B. ribis, but also shares some unique sequence polymorphisms with B. parva. One isolate grouped with B. australis, but also varied slightly from this taxon in the gene regions analysed. Additional isolates will be needed to determine whether these sequence variations represent speciation events or merely variation within populations of B. ribis and B. australis. In addition to this, B. parva was identified from Araucaria in New Zealand, and B. australis was found on Widdringtonia trees in South Africa. All three reports of these fungi are new records for their various hosts and could represent important pathogens of these trees
    Phylogenetic and morphological re-evaluation of the Botryosphaeria species causing diseases of Mangifera indica
    Slippers, B. ; Johnson, G.I. ; Crous, P.W. ; Coutinho, T.A. ; Wingfield, B.D. ; Wingfield, M.J. - \ 2005
    Mycologia 97 (2005)1. - ISSN 0027-5514 - p. 99 - 110.
    end rot pathogens - new-zealand - mango - dothidea - fungi - characters - anamorphs - infection - sequences - avocado
    Species of Botryosphaeria are among the most serious pathogens that affect mango trees and fruit. Several species occur on mangoes, and these are identified mainly on the morpholopy of the anamorphs. Common taxa include Dothiorella dominicana, D. mangiferae (= Natrassia mangiferae), D. aromatica and an unidentified species, Dothiorella 'long'. The genus name Dothiorella, however, is acknowledged as a synonym of Diplodia. This study aimed to characterize and name the Botryosphaeria spp. associated with disease symptoms on mangoes. To achieve this isolates representing all four Dothiorella slip. mentioned above were compared with the anamorphs of known Botryosphaeria spp., based on conidial morphology and DNA sequence data. Two genomic regions were analyzed, namely the ITS rDNA and beta-tubulin regions. The morphological and molecular results confirmed that the fungi previously identified front mango as species of Dothiorella belong to Fusicoccum. Dothiorella dominicana isolates were identical to isolates of F. parvum (teleomorph = B. Parva). A new epithet, namely F. mangiferum, is proposed for isolates previously treated as D. maugiferae or N. maugiferae. Isolates of D. aromatica were identified as F. aesculi (telcomorph = B. dothidea). A fourth Fusicoccum sp. also was identified as those isolates previously known as Dothiorella 'long'. A key is provided to distinguish these species based on anamorph morphology in culture. This study provides a basis for the identification of Botryosphaeria species front mango, which is important for disease control and to uphold quarantine regulations.
    Alle genen van Phytophthora op een rij: verschillen, overeenkomsten en gastheerspecificiteit
    Meijer, H.J.G. ; Govers, F. ; Jiang, R.H.Y. - \ 2005
    Gewasbescherming 36 (2005)6. - ISSN 0166-6495 - p. 271 - 271.
    gewasbescherming - genoomanalyse - volgorden - schimmels - phytophthora - phytophthora sojae - plantenziekteverwekkers - waardplanten - eiwitten - enzymen - plantensecreties - plantenziektekunde - genexpressieanalyse - plant protection - genome analysis - sequences - fungi - phytophthora - phytophthora sojae - plant pathogens - host plants - proteins - enzymes - plant secretions - plant pathology - genomics
    Samenvatting van de voordracht te houden op 30 november 2005 tijdens de Najaarsvergadering van de KNPV (Koninklijke Nederlandse Plantenziektekundige Vereniging).
    A transmembrane phospholipase D in Phytophthora; a novel PLD subfamily
    Meijer, H.J.G. ; Latijnhouwers, M. ; Ligterink, W. ; Govers, F. - \ 2005
    Gene 350 (2005)2. - ISSN 0378-1119 - p. 173 - 182.
    phosphatidic-acid - infestans - yeast - motif - phosphoinositides - activation - sequences - beta
    Phospholipase D (PLD) is a ubiquitous enzyme in eukaryotes that participates in various cellular processes. Its catalytic domain is characterized by two HKD motifs in the C-terminal part. Until now, two subfamilies were recognized based on their N-terminal domain structure. The first has a PX domain in combination with a PH domain and is designated as PXPH-PLD. Members of the second subfamily, named C2-PLD, have a C2 domain and have, so far, only been found in plants. Here we describe a novel PLD subfamily that we identified in Phytophthora, a genus belonging to the class oomycetes and comprising many important plant pathogens. We cloned Pipld1 from Phytophthora infestans and retrieved full-length sequences of its homologues from Phytophthora sojae and Phytophthora ramorum genome databases. Their promoters contain two putative regulatory elements, one of which is highly conserved in all three genes. The three Phytophthora pld1 genes encode nearly identical proteins of around 1807 amino acids, with the two characteristic HKD motifs in the C-terminal part. Homology of the predicted proteins with known PLDs however is restricted to the two catalytic HKD motifs and adjacent domains. In the N-terminal part Phytophthora PLD1 has a PX-like domain, but it lacks a PH domain. Instead the N-terminal region contains five putative membrane spanning domains suggesting that Phytophthora PLD1 is a transmembrane protein. Since Phytophthora PLD1 cannot be categorized in one of the two existing subfamilies we propose to create a novel subfamily named PXTM-PLD
    Phylogeny, morphological evolution, and speciation of endemic brassicaceae genera in the cape flora of southern Africa
    Mummenhoff, K. ; Al-Shehbaz, I.A. ; Bakker, F.T. ; Linder, H.P. ; Mühlhausen, A. - \ 2005
    Annals of the Missouri Botanical Garden 92 (2005)3. - ISSN 0026-6493 - p. 400 - 424.
    molecular systematics - family brassicaceae - dna - cruciferae - biogeography - arabidopsis - dispersal - radiation - sequences - regions
    Heliophila (ca. 73 spp.), the ditypic Cycloptychis and Thlaspeocarpa, and the monotypic Schlechteria, Silicularia, Brachycarpaea, and Chamira are endemic to the Cape region of South Africa, where they are the dominant genera of Brassicaceae. They may be regarded as the most diversified Brassicaceae lineage in every aspect of habit, leaf, flower, and fruit morphology. The characters used in the separation of these genera and their species, especially fruit type (silique vs. silicle), dehiscence (dehiscent vs. indehiscent), compression (latiseptate vs. angustiseptate), and cotyledonary type (spirolobal, diplecolobal, twice conduplicate), have been used extensively in the delimitation of tribes. The relationship and taxonomic limits among these genera are unclear and controversial. The present ITS study demonstrates the monophyly of tribe Heliophileae, with Chamira as sister clade. The other five smaller genera above are nested within two of the three main lineages of Heliophila, to which they should be reduced to synonymy. The current study reveals parallel evolution of fruit characters often used heavily in the traditional classification schemes of the family. However, the arrangement of species into three main clades largely corresponds with the distribution of morphological characters (e.g., habit, leaf shape, seed structure, inflorescence type, and presence/absence of basal appendages on the pedicels, petals, and staminal filaments) not adequately accounted for in previous studies. Estimation of divergence times of the main lineages of Heliophila is in agreement with recent estimations in other plant groups, all of which date the diversification against a background of aridification in the Pliocene and Pleistocene. Species of one main clade are perennial, microphyllous shrubs/subshrubs typically restricted to poor sandstone soils in the southwestern and western parts of the Cape Floristic Region of South Africa. Species of the other two clades are predominantly annuals that grow in more arid regions of Namibia and Namaqualand, as well as in the above sandstone areas of the Cape Region. The adaptive significance of various floral structures is discussed in terms of their possible role in the rapid diversification within Heliophila.
    PRECISE: software for prediction of cis-acting regulatory elements
    Trindade, L.M. ; Berloo, R. van; Fiers, M.W.E.J. ; Visser, R.G.F. - \ 2005
    Journal of Heredity 96 (2005)5. - ISSN 0022-1503 - p. 618 - 622.
    abscisic-acid - expression - promoter - discovery - regions - genes - sequences - sites - water
    The regulation of gene expression at the transcription initiation level is highly complex and requires the presence of multiple transcription factors. These transcription factors are often proteins or peptides that bind to the so-called cis-acting elements, which are present in the promoter regions and conserved among different species. In order to predict these cis-acting elements, a computer program called PRECISE (Prediction of REgulatory CIS-acting Elements) was developed. The power of the tool lies in its user-friendly interface and in the possibility of using empirical motif frequency tables to filter through the many discovered motifs. The tools to create the empirical motif frequency table (e.g., from a whole genome sequence) are included in the package. In the first case study, the upstream regions of all the genes in the Arabidopsis genome were used to create an empirical motif frequency table and a set of 64 upstream sequences of genes known to be involved in starch metabolism was subjected to analysis by PRECISE. The 20 motifs with the highest specificity in the selected set were analyzed in more detail. Of these 20 motifs, 15 showed a very high or complete homology to the sequences of known cis-acting elements. These cis-acting elements are regulated by light, auxin, and abscisic acid, and confer specific expression in sink organs such as leaves and seeds. All these factors have been shown to play an important role in starch biosynthesis. In the second case study, the upstream regions of 16 genes whose transcription is induced by gibberellins (GA) in Arabidopsis were analyzed with PRECISE and compared to the motifs present in the PLACE database. Among the most promising motifs found by PRECISE were 6 of the 17 known GA motifs. These results indicate the power of the PRECISE software package in the prediction of regulatory elements
    Genetic spatial structure of European common hamsters (Cricetus cricetus) - a result of repeated range expansion and demographic bottlenecks
    Neumann, K. ; Michaux, R. ; Maak, S. ; Jansman, H.A.H. ; Kayser, A. ; Mundt, G. ; Gattermann, R. - \ 2005
    Molecular Ecology 14 (2005)5. - ISSN 0962-1083 - p. 1473 - 1483.
    voles microtus-agrestis - mitochondrial-dna - postglacial colonization - phylogeography - populations - microsatellites - consequences - evolution - oeconomus - sequences
    The spatial genetic structure of common hamsters (Cricetus cricetus) was investigated using three partial mitochondrial (mt) genes and 11 nuclear microsatellite loci. All marker systems revealed significant population differentiation across Europe. Hamsters in central and western Europe belong largely to two allopatric mitochondrial lineages south and northwest of the Carpathian and Sudetes. The southern group, 'Pannonia', comprises populations inside the Carpathian basin (Czech Republic, Hungary) while the second group, 'North', includes hamsters from Belgium, the Netherlands, France, and Germany. Isolation of the lineages is maintained by a combination of geographical and ecological barriers. Both main phylogeographical groups show signs of further subdivision. North is separated into highly polymorphic central German and less polymorphic western populations, which most likely split during late glacial expansion (15 00010 000 bp). Clock estimates based on haplotype distributions predict a divergence of the two major lineages 85 000147 000 bp. Expansion times fall during the last glaciation (115 00010 000 bp) corroborating fossil data, which identify Cricetus cricetus as characteristic of colder climatic phases. Despite the allopatry of mt haplotypes, there is an overlap of nuclear microsatellite alleles between phylogeographical units. Although there are strong evidence that Pannonian hamsters have persisted inside the Carpathian basin over the last 50 000 years, genetic differentiation among European hamsters has mainly been caused by immigration from different eastern refugia. Possible source populations are likely to be found in the Ukrainian and the southern Russian plains core areas of hamster distribution. From there, hamsters have repeatedly expanded during the Quaternary.
    The highly pathogenic avian influenza A (H7N7) virus epidemic in the Netherlands in 2003 - lessons learned from the first five outbreaks
    Elbers, A.R.W. ; Fabri, T. ; Vries, T.S. ; Wit, J.J. de; Pijpers, A. ; Koch, G. - \ 2004
    Avian Diseases 48 (2004)3. - ISSN 0005-2086 - p. 691 - 705.
    poultry - sequences - birds
    Clinical signs and gross lesions observed in poultry submitted for postmortem examination (PME) from the first five infected poultry flocks preceding the detection of the primary outbreak of highly pathogenic avian influenza (HPAI) of subtype H7N7 during the 2003 epidemic in the Netherlands are described. The absence of HPAI from the Netherlands for more than 75 yr created a situation in which poultry farmers and veterinary practitioners did not think of AI in the differential diagnosis as a possible cause of the clinical problems seen. Increased and progressive mortality was not reported to the governmental authorities by farmers or veterinary practitioners. It took 4 days from the first entry of postmortem material to notify the governmental authorities of a strong suspicion of an AI outbreak on the basis of a positive immunofluoresence test result. The gross lesions observed at PME did not comply with the descriptions in literature, especially the lack of hemorrhagic changes in tissues, and the lack of edema and cyanosis in comb and wattles is noted. The following lessons are learned from this epidemic: a) in the future, increased and progressive mortality should be a signal to exclude AI as cause of disease problems on poultry farms; b) intensive contact between the veterinary practitioner in the field and the veterinarian executing PME is necessary to have all relevant data and developments at one's disposal to come to a conclusive diagnosis; c) in an anamnesis, reporting of high or increased mortality should be quantified in the future (number of dead birds in relation to the number of birds brought to the farm to start production, together with the timing within the production cycle), or else this mortality cannot be interpreted properly; d) if clinical findings such as high mortality indicate the possibility of HPAI, the pathologist should submit clinical samples to the reference laboratory, even if PME gives no specific indications for HPAI; e) the best way to facilitate early detection of an HPAI outbreak is to have the poultry farmer and/or veterinary practitioner immediately report to the syndrome-reporting system currently in operation the occurrence of high mortality, a large decrease in feed or water intake, or a considerable drop in egg production; f) in order to detect low pathogenic avian influenza infections that could possibly change to HPAI, a continuous serologic monitoring system has been set up, in which commercial poultry flocks are screened for antibodies against AI virus of subtypes H5 and H7.
    Speciation and distribution of Botryosphaeria spp. on native and introduced Eucalyptus trees in Australia and South Africa
    Slippers, B. ; Fourie, G. ; Crous, P.W. ; Coutinho, T.A. ; Wingfield, B.D. ; Carnegie, A.J. ; Wingfield, M.J. - \ 2004
    Studies in Mycology 50 (2004)2. - ISSN 0166-0616 - p. 343 - 358.
    multiple gene genealogies - sphaeropsis-sapinea - primer sets - sp-nov - fungi - dothidea - sequences - cankers - ribis - characters
    Botryosphaeria spp. are important canker and die-back pathogens that affect Eucalyptus spp. They also occur endophytically in Eucalyptus leaves and stems. For the purpose of this study, Botryosphaeria strains were isolated from diseased and symptomless Eucalyptus material from Australia and South Africa. These isolates were induced to sporulate in culture, and compared with known species of Botryosphaeria. Selected isolates were also compared with authentic isolates of known Botryosphaeria spp. based on nuclear DNA sequence data of the ITS rDNA, P-tubulin and elongation factor l-alpha regions. Five Botryosphaeria spp. were identified from Eucalyptus plants. The ITS rDNA sequence data were then used to develop a PCR RFLP technique that could distinguish these species. Botryosphaeria eucalyptorum and a new species, B. eucalypticola, were the most common species on Eucalyptus in eastern Australia. These species also occur on Eucalyptus in South Africa, where they have most likely been introduced. Botryosphaeria parva was common on Eucalyptus in exotic environments, but rare on this host in Australia. Although B. dothidea was previously thought to be common on eucalypts, only one isolate of each of B. dothidea and B. australis were found in all the areas surveyed. No isolates of B. ribis, which was also commonly reported from Eucalyptus, were identified during this survey from Eucalyptus. Data from the present study provide the first holistic overview of the species of Botryosphaeria associated with Eucalyptus in both native and exotic environments.
    DNA phylogeny, morphology and pathogenicity of Botryosphaeria species on grapevines
    Niekerk, J.M. van; Crous, P.W. ; Groenewald, J.Z. ; Fourie, P.H. ; Halleen, F. - \ 2004
    Mycologia 96 (2004)4. - ISSN 0027-5514 - p. 781 - 798.
    multiple gene genealogies - fusicoccum - characters - sequences - dothidea - zealand - dieback
    Several species of Botr yosphaeria are known to occur on grapevines, causing a wide range of disorders including bud mortality, dieback, brown wood streaking and bunch rot. In this study the 11 Botryosphaeria spp. associated with grapevines growing in various parts of the world, but primarily in South Africa, are distinguished based on morphology, DNA sequences (ITS-1, 5.8S, ITS-2 and EF1-) and pathological data. Botryosphaeria australis, B. lutea, B. obtusa, B. parva, B. rhodina and a Diplodia sp. are confirmed from grapevines in South Africa, while Diplodia porosum, Fusicoccum viticlavatum and F. vitifusiforme are described as new. Although isolates of B. dothidea and B. stevensii are confirmed from grapevines in Portugal, neither of these species occurred in South Africa, nor were any isolates of B. ribis confirmed from grapevines. All grapevine isolates from Portugal, formerly presumed to be B. ribis, are identified as B. parva based on their EF1- equence data. From artificial inoculations on grapevine shoots, we conclude that B. australis, B. parva, B. ribis and B. stevensii are more virulent than the other species studied. The Diplodia sp. collected from grapevine canes is morphologically similar but phylogenetically distinct from D. sarmentorum. Diplodia sarmentorum is confirmed as anamorph of Otthia spiraeae, the type species of the genus Otthia (Botryosphaeriaceae). A culture identified as O. spiraeae clustered within Botryosphaeria and thus is regarded as probable synonym. These findings confirm earlier suggestions that the generic concept of Botryosphaeria should be expanded to include genera with septate ascospores and Diplodia anamorphs.
    Combined multiple gene genealogies and phenotypic characters differentiate several species previously identified as Botryosphaeria dothidea
    Slippers, B. ; Crous, P.W. ; Denman, S. ; Coutinho, T.A. ; Wingfield, B.D. ; Wingfield, M.J. - \ 2004
    Mycologia 96 (2004)1. - ISSN 0027-5514 - p. 83 - 101.
    south-africa - fusicoccum anamorph - primer sets - fungi - eucalyptus - canker - rdna - reassessment - sequences - zealand
    Botryosphaeria dothidea is one of the most commonly reported species in a genus of important pathogens of woody plants. This taxon generally is accepted to represent a species complex, and hence its identity remains unclear. Previous studies either have treated B. dothidea as the valid name for B. ribis and B. berengeriana or argued for them to be separate entities. To add to the confusion, no ex-type cultures are available for either B. dothidea or B. ribis. The aim of the present study, therefore, was to recollect and characterize these fungi and designate a set of reference cultures that can be used in future studies. To this end, morphological, cultural and multi-allelic DNA sequence datasets from the rDNA (ITS 1, 5.8S, and ITS 2), ß-tubulin and EF1- genes were used to fully characterize these species. Botryosphaeria dothidea was found to be distinct from B. ribis, while B. berengeriana was retained as synonym of the former name. Furthermore, Fusicoccum aesculi is accepted as anamorph of B. dothidea, while the anamorph of B. ribis is newly described as F. ribis sp. nov. Botryosphaeria ribis could be distinguished from B. parva based on ß-tubulin and EF1- sequence data. A combined phylogeny of the three gene regions used in this study also showed that the genus Botryosphaeria represents two distinct phylogenetic assemblages that correspond to species with Diplodia and Fusicoccum anamorphs
    Morphology, phylogeny and evolution of the superfamily Plectoidea Örley, 1880 (Nematoda: Plectida
    Holovachov, O.V. - \ 2004
    Annales zoologici 54 (2004)4. - ISSN 0003-4541 - p. 631 - 672.
    n-sp nematoda - revised taxonomy - phylum nematoda - genus - ultrastructure - classification - araeolaimida - leptolaimidae - rhabditidae - sequences
    The phylogeny and classification of the superfamily Plectoidea Örley, 1880 is revised on the basis of published and updated morphological data for 35 ingroup and 2 outgroup species. The following features are here considered to support the monophyletic origin of the superfamily: 1) stegostom developed and differentiated into two sections; 2) dorsal gland orifice opening into the second stegostom section; 3) pharynx cylindrical, with distinct subdivision into corpus and postcorpus by the orifices of the subventral pharyngeal glands and a discontinuity in the muscular pharyngeal tissue; 4) corpus cylindrical, with subdivision into procorpus and metacorpus homologues; 5) pharyngeal radii of the corpus with prominent pharyngeal tubes along the procorpus; 6) cuticular lumen of the basal part of postcorpus (within basal bulb if latter is present) is modified to form a valvular apparatus. In addition the inner labial sensilla open inside the cheilostom. New data on postembryonic development of Anaplectus grandepapillatus (Ditlevsen, 1928), Plectus parietinus Bastian, 1865, P. decens Andrássy, 1985 and P. communis Bütschli, 1873 are given and supplemented with a discussion of the phylogenetic significance of the ontogeny in Plectoidea. Following the proposal of a phylogeny, some key events in the evolution of Plectidae Örley, 1880 are discussed. It is suggested that the superfamily Plectoidea includes four families: Pakiridae Inglis, 1983, Chronogastridae Gagarin, 1975, Metateratocephalidae Eroshenko, 1973 and Plectidae. Plectolaimus supplementatus Keppner, 1988 is transferred to the genus Caribplectus Andrássy, 1973. The genus Keralanema Siddiqi, 2003 is considered a junior synonim of Chronogaster Cobb, 1913. The genus Chiloplectus Andrássy, 1984 is considered a junior synonim of Plectus Bastian, 1865. The family Anaplectidae Zell, 1993 is downgraded to the subfamily level
    The relationship between global and regional distribution diminishes among phylogenetically basal species
    Prinzing, A. ; Ozinga, W.A. ; Durka, W. - \ 2004
    Evolution 58 (2004)12. - ISSN 0014-3820 - p. 2622 - 2633.
    range size - diversification rates - geographical range - flowering plants - body-size - macroecological patterns - chloroplast ndhf - gene rbcl - phylogeny - sequences
    Phylogenetic legacy and phylogenetic trends affect the ecology of species—except, apparently, for the width of their distribution. As a result, “macroecological” patterns of species distributions emerge constantly in phylogenetically very distinct species assemblages. The width of the global distribution of species, for instance, constantly correlates positively to the width of their regional distribution. However, such patterns primarily reflect the phylogenetically derived species that dominate most assemblages. Basal species, in contrast, might show different macroecological patterns. We tested the hypothesis that the correlation between global and regional distributions of species diminishes among the phylogenetically basal species. We considered central European higher plants and defined global distribution as the occupancy of global floristic zones, regional distribution as the grid occupancy in Eastern Germany, and phylogenetic position as the rank distance to tree base. We also took into account a number of confounding variables. We found that, across all lineages, the global/regional correlation diminished among basal species. We then reanalyzed 19 lineages separately and always found the same pattern. The pattern reflected both increases in global distributions and decreases in regional distributions among basal species. The results indicate that many basal species face a risk of global or at least regional extinction, but have escaped the downward spiral of mutually reinforcing extinction risks at multiple scales. We suggest that many basal species had much time to expand their global ranges but are presently displaced locally by more derived species. Overall, the study shows that macroecological patterns may not be static and universal, but may undergo macroevolutionary trends. Analyses of macroecological patterns across a phylogeny may thus provide insights into macroevolutionary processes.
    A high-resolution radiation hybrid map of chicken chromosome 5 and comparison with human chromosomes
    Pitel, F. ; Abasht, B. ; Morrison, M. ; Crooijmans, R.P.M.A. ; Vignoles, F. ; Leroux, S. ; Feve, K. ; Bardes, S. ; Milan, D. ; Lagarrigue, S. ; Groenen, M.A.M. ; Douaire, M. ; Vignal, A. - \ 2004
    BMC Genomics 5 (2004). - ISSN 1471-2164 - 9 p.
    in-situ hybridization - human genome - genes - assignment - sequences - synteny - panel - pig
    Background - The resolution of radiation hybrid (RH) maps is intermediate between that of the genetic and BAC (Bacterial Artificial Chromosome) contig maps. Moreover, once framework RH maps of a genome have been constructed, a quick location of markers by simple PCR on the RH panel is possible. The chicken ChickRH6 panel recently produced was used here to construct a high resolution RH map of chicken GGA5. To confirm the validity of the map and to provide valuable comparative mapping information, both markers from the genetic map and a high number of ESTs (Expressed Sequence Tags) were used. Finally, this RH map was used for testing the accuracy of the chicken genome assembly for chromosome 5. Results - A total of 169 markers (21 microsatellites and 148 ESTs) were typed on the ChickRH6 RH panel, of which 134 were assigned to GGA5. The final map is composed of 73 framework markers extending over a 1315.6 cR distance. The remaining 61 markers were placed alongside the framework markers within confidence intervals. Conclusion - The high resolution framework map obtained in this study has markers covering the entire chicken chromosome 5 and reveals the existence of a high number of rearrangements when compared to the human genome. Only two discrepancies were observed in relation to the sequence assembly recently reported for this chromosome.
    Downstream targets of the Phytophthora infestans G alpha subunit PiGPA1 revealed by cDNA-AFLP
    Dong, W. ; Latijnhouwers, M. ; Jiang, R.H.Y. ; Meijer, H.J.G. ; Govers, F. - \ 2004
    Molecular Plant Pathology 5 (2004)5. - ISSN 1464-6722 - p. 483 - 494.
    gene-expression profiles - gtp-binding proteins - beta-subunit - sequences - mutations - infection - database
    In many plant pathogens heterotrimeric G-proteins are essential signalling components involved in development and pathogenicity. In the late blight oomycete pathogen Phytophthora infestans the G-protein (x subunit PiGPA1 controls zoospore motility and is required for virulence. To identify G-protein targets and signalling pathways downstream of PiGPA1, we used an optimized cDNA-AFLP protocol for analysing gene expression profiles in hypovirulent P. infestans strains that were previously generated by silencing the Pigpa1 gene. First, expression profiles in sporangia and mycelium of the wild-type strain were compared, and this revealed a substantial number of mycelium- or sporangia-specific transcript derived fragments (TDFs). Subsequently, profiles in sporangia of wild-type, Pigpa1-silenced mutants and of a strain expressing a constitutively active form of PiGPA1 were compared. From a total of 2860 TDFs, 92 were down- and 19 upregulated in the Pigpa1-silenced mutants. A subset of the differential TDFs was cloned and sequenced, and homology searches were carried out against Phytophthora EST and genomic databases and the NCBI database. cDNA-AFLP expression profiles were verified by Northern blot analysis or RT-PCR. The power of cDNA-AFLP for the identification of target genes in knock-down or gain-of-function mutants is discussed.
    Isolation and biodiversity of hitherto undescribed soil bacteria related to Bacillus niacini
    Felske, A. ; Tzeneva, V.A. ; Heyrman, J. ; Langeveld, M.A. ; Akkermans, A.D.L. ; Vos, P. - \ 2004
    Microbial Ecology 48 (2004)1. - ISSN 0095-3628 - p. 111 - 119.
    16s ribosomal-rna - genus bacillus - culturable bacteria - agricultural soil - paddy soil - sp-nov - diversity - sequences - dna - identification
    The hitherto largely not described phylogenetic neighborhood of Bacillus niacini has been explored by a comprehensive cultivation experiment and genomic variety studies. Previous culture-independent studies demonstrated that similar to15% of all Bacillus 16S rDNA directly extracted from soils worldwide was affiliated to B. niacini. Seven different media were inoculated with soil suspensions in serial dilutions and incubated at different temperatures. Then, bacterial colonies were picked and analyzed by sequencing. A mineral medium with acetate as carbon source yielded a B. niacini rate of >3% of all picked colonies. Other media were less efficient but also successful. Applying this culturing approach, we succeeded in obtaining 64 isolates from different Dutch soils. The isolates turned out to be diverse, although closely related to B. niacini as revealed by 16S rDNA sequencing. Close matches with environmental clones were also found, thus demonstrating much more diversity beyond previously known 16S rDNA sequences. The rep-PCR fingerprinting method revealed a high genomic variety, redundancy could not be observed among our isolates. Hence, the hitherto neglected B. niacini lineage, apparently among the most abundant soil Bacillus, was accessible to our cultivation approach.
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