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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.

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    The Nesidiocoris tenuis genome manuscript supporting data
    Pannebakker, Bart ; Ferguson, Kimberley - \ 2019
    Wageningen University & Research
    genome - biocontrol - biological control - insect - mirid - Nesidiocoris tenuis - genomics - genome assembly
    In presenting the first mirid genome, Nesidiocoris tenuis, several supporting information is made available. Following the main supplemetary material document (link), the contents are in this database: S1.2. Flow cytometry data for N. tenuis S1.3. Decontamination and potential LGT indentification S1.4. Gene list (UniProtKB list) and DAVID Reports S1.5. Full protein set S1.7. Poolseq results in full
    The Trichogramma brassicae genome, supporting data
    Pannebakker, Bart ; Ferguson, Kimberley - \ 2019
    Wageningen University & Research
    genome - biocontrol - biological control - insect - parasitoid - Trichogramma - Trichogramma brassicae - genome assembly
    In presenting the Trichogramma brassicae genome, supporting information is made available. Following the main supplemetary material document, the contents in this database entry are as follows: S1.2. Contaminated Wolbachia scaffolds from assembly v3.0 (Backbone_1176.fa and Backbone_1392.fa) S1.3. DAVID input gene list S1.5. Full Trichogramma brassicae protein set from annotation.
    The Bracon brevicornis genome, supporting data
    Pannebakker, Bart ; Ferguson, Kimberley - \ 2019
    Wageningen University & Research
    genome - biocontrol - biological control - insect - parasitoid - Trichogramma - Trichogramma brassicae - genome assembly
    In presenting the Bracon brevicornis genome, supporting information is made available. The material available in this database entry are as follows: 1. Contamination scaffolds from decontamination process (note, identified as being neither the carrier DNA of tomato, nor belonging to the group Arthropoda in a BlobTools analysis. For more details, refer to source manuscript. 2. Two sets of pseudohaplotype FASTA files, generated from decontaminated B. brevicornis reads and output from Supernova assembler.
    Genetic variation of biological control relevant traits in natural enemies: a systematic review, supporting data
    Pannebakker, Bart ; Ferguson, Kimberley - \ 2019
    Wageningen University & Research
    genome - biocontrol - biological control - parasitoid - predator - heritability - genetic variation
    This is supplementary material for a systematic review tentatively titled, "Genetic variation of biological control relevant traits in natural enemies: a systematic review" (2019). Three tables are available, and are referenced in the following manner in text: Table S1: Positive control group for search results, based on papers that fit the ideal search returns for the search term. Table S2: Combined search return hits, in unedited format received from CAB Abstracts. Table S3: Articles narrowed down to BCA, with duplicates and unavailable papers removed, prior to assessment for estimation method and traits.
    The red bayberry genome and genetic basis of sex determination
    Jia, Hui Min ; Jia, Hui Juan ; Cai, Qing Le ; Wang, Yan ; Zhao, Hai Bo ; Yang, Wei Fei ; Wang, Guo Yun ; Li, Ying Hui ; Zhan, Dong Liang ; Shen, Yu Tong ; Niu, Qing Feng ; Chang, Le ; Qiu, Jie ; Zhao, Lan ; Xie, Han Bing ; Fu, Wan Yi ; Jin, Jing ; Li, Xiong Wei ; Jiao, Yun ; Zhou, Chao Chao ; Tu, Ting ; Chai, Chun Yan ; Gao, Jin Long ; Fan, Long Jiang ; Weg, Eric van de; Wang, Jun Yi ; Gao, Zhong Shan - \ 2018
    Plant Biotechnology Journal 17 (2018)2. - ISSN 1467-7644 - p. 397 - 409.
    genome - Morella rubra - sex-determining region - sex-linked marker

    Morella rubra, red bayberry, is an economically important fruit tree in south China. Here, we assembled the first high-quality genome for both a female and a male individual of red bayberry. The genome size was 313-Mb, and 90% sequences were assembled into eight pseudo chromosome molecules, with 32 493 predicted genes. By whole-genome comparison between the female and male and association analysis with sequences of bulked and individual DNA samples from female and male, a 59-Kb region determining female was identified and located on distal end of pseudochromosome 8, which contains abundant transposable element and seven putative genes, four of them are related to sex floral development. This 59-Kb female-specific region was likely to be derived from duplication and rearrangement of paralogous genes and retained non-recombinant in the female-specific region. Sex-specific molecular markers developed from candidate genes co-segregated with sex in a genetically diverse female and male germplasm. We propose sex determination follow the ZW model of female heterogamety. The genome sequence of red bayberry provides a valuable resource for plant sex chromosome evolution and also provides important insights for molecular biology, genetics and modern breeding in Myricaceae family.

    Comparative genomics of the genus Desulfitobacterium
    Kruse, Thomas ; Goris, Tobias ; Maillard, Julien ; Woyke, Tanja ; Lechner, Ute ; Vos, Willem de; Smidt, Hauke - \ 2017
    FEMS microbiology ecology 93 (2017)12. - ISSN 0168-6496
    comparative genomics - Desulfitobacterium spp. - genome - metabolic potential - organohalide respiration - rdhA
    The Desulfitobacterium genus comprises anaerobic Gram-positive bacteria, of which the majority are facultative organohalide respirers. We here present the genomes of eight strains of Desulfitobacterium spp., including five strains of Desulfitobacterium hafniense, one strain each from D. dichloroeliminans and D. metallireducens, and one strain that had not been assigned to any species prior to this study. The newly sequenced genomes were compared with four previously published desulfitobacterial genomes. The average genome sizes are 5.5, 4.3 and 3.4 Mbp for D. hafniense, D. dehalogenans and D. dichloroeliminans/metallireducens, respectively. The genomes encode up to seven reductive dehalogenases, the genomes of both D. hafniense DP7 and D. metallireducens 853-15AT did not encode any reductive dehalogenase. The latter result was a surprise as D. metallireducens 853-15AT has been reported to carry out organohalide respiration. Unlike reported for the pceABCT gene cluster, the other reductive dehalogenase gene clusters do not show any signs of being genetically mobile. All analyzed desulfitobacterial genomes encode a complete cobalamin synthesis pathway. A menaquinone synthesis pathway was found in all strains except D. dichloroeliminans DCA1T. The detailed analysis of the genome sequence of 12 desulfitobacteria from four different species confirmed that this genus has an extremely large metabolic repertoire.
    Data from: Genome-wide SNP data unveils the globalization of domesticated pigs
    Yang, Bin ; Cui, Leilei ; Pérez-Enciso, M. ; Traspov, Aleksei ; Crooijmans, R.P.M.A. ; Zinovieva, Natalia ; Schook, Lawrence B. ; Gatphayak, Kesinee ; Knorr, Christophe ; Triantafyllidis, Alex ; Alexandri, Panoraia ; Semiadi, Gono ; Hanotte, Olivier ; Dias, Deodália ; Dovč, Peter ; Uimari, Pekka ; Iacolina, Laura ; Scandura, Massimo ; Groenen, M. ; Huang, L. ; Megens, H.J.W.C. - \ 2017
    pig - domestication - genome - selection
    Background: Pigs were domesticated independently in Eastern and Western Eurasia early during the agricultural revolution, and have since been transported and traded across the globe. Here, we present a worldwide survey on 60K genome-wide single nucleotide polymorphism (SNP) data for 2093 pigs, including 1839 domestic pigs representing 122 local and commercial breeds, 215 wild boars, and 39 out-group suids, from Asia, Europe, America, Oceania and Africa. The aim of this study was to infer global patterns in pig domestication and diversity related to demography, migration, and selection. Results: A deep phylogeographic division reflects the dichotomy between early domestication centers. In the core Eastern and Western domestication regions, Chinese pigs show differentiation between breeds due to geographic isolation, whereas this is less pronounced in European pigs. The inferred European origin of pigs in the Americas, Africa, and Australia reflects European expansion during the sixteenth to nineteenth centuries. Human-mediated introgression, which is due, in particular, to importing Chinese pigs into the UK during the eighteenth and nineteenth centuries, played an important role in the formation of modern pig breeds. Inbreeding levels vary markedly between populations, from almost no runs of homozygosity (ROH) in a number of Asian wild boar populations, to up to 20% of the genome covered by ROH in a number of Southern European breeds. Commercial populations show moderate ROH statistics. For domesticated pigs and wild boars in Asia and Europe, we identified highly differentiated loci that include candidate genes related to muscle and body development, central nervous system, reproduction, and energy balance, which are putatively under artificial selection. Conclusions: Key events related to domestication, dispersal, and mixing of pigs from different regions are reflected in the 60K SNP data, including the globalization that has recently become full circle since Chinese pig breeders in the past decades started selecting Western breeds to improve local Chinese pigs. Furthermore, signatures of ongoing and past selection, acting at different times and on different genetic backgrounds, enhance our insight in the mechanism of domestication and selection. The global diversity statistics presented here highlight concerns for maintaining agrodiversity, but also provide a necessary framework for directing genetic conservation.
    Genetic Characterization of Porcine Circovirus Type 2 (PCV2) in Pigs of Bhutan
    Monger, V.R. ; Loeffen, W.L.A. ; Kus, K. ; Stegeman, J.A. ; Dukpa, K. ; Szymanek, K. ; Podgórska, K. - \ 2017
    Transboundary and Emerging Diseases 64 (2017)2. - ISSN 1865-1674 - p. 442 - 448.
    Bhutan - genome - phylogenetic analysis - pigs - porcine circovirus type 2 - sequence

    Porcine circovirus (PCV) is a small non-enveloped virus with a single-stranded circular DNA with two antigenically and genetically different species, PCV1 and PCV2. Among these two, PCV2 is responsible for multifactorial disease syndromes, the most important disease known as PCV2-systemic disease (PCV2-SD), previously known as post-weaning multisystemic wasting syndrome (PMWS). The epidemiological situation is dynamically changing and new strains including recombinant PCV2 have emerged in Asia. In Bhutan, pigs are important livestock and play a very important role in providing meat and income for rural farmers. Although high rate of pigs seropositive against PCV2 was described in Bhutan, there was no virological evidence for PCV2 infections. This study was conducted to confirm the presence of PCV2 through detection of PCV2 DNA and molecular characterization of PCV2 strains in tissue and blood samples collected from Bhutanese pigs. Porcine circovirus type 2 genome was detected in 16 of 34 tissue samples pigs from the government farm. In 9 pigs, very high level of viral replication indicated that PCV2-SD was detected. Phylogenetic analysis performed with a set of GenBank sequences revealed that the Bhutanese PCV2 strains belonged to the PCV2b genotype and grouped with cluster 1C.

    Quantitative trait locus mapping for bruising sensitivity and cap color of Agaricus bisporus (button mushrooms)
    Gao, W. ; Weijn, A. ; Baars, J.J.P. ; Mes, J.J. ; Visser, R.G.F. ; Sonnenberg, A.S.M. - \ 2015
    Fungal Genetics and Biology 77 (2015). - ISSN 1087-1845 - p. 69 - 81.
    melanin biosynthesis pathway - latent isoform ppo4 - pseudomonas-tolaasii - genetic-analysis - tyrosinase - purification - behavior - strains - genome
    White button mushrooms discolor after mechanical damage of the cap skin. This hampers the development of a mechanical harvest system for the fresh market. To unravel the genetic basis for bruising sensitivity, two haploid populations (single spore cultures) were generated derived from crosses between parental lines differing in discoloration after mechanical damage (bruising sensitivity). The haploids were crossed with different homokaryotic tester lines to generate mushrooms and allow assessment of the bruising sensitivity in different genetic backgrounds. Bruising sensitivity appears to be a polygenic highly heritable trait (H2: 0.88-0.96) and a significant interaction between genotypes and tester lines and genotypes and flushes was found. Using SNP markers evenly spread over all chromosomes, a very low recombination was found between markers allowing only assignment of QTL for bruising sensitivity to chromosomes and not to sub-regions of chromosomes. The cap color of the two parental lines of population 1 is white and brown respectively. A major QTL for bruising sensitivity was assigned to chromosome 8 in population 1 that also harbors the main determinant for cap color (brown versus white). Splitting offspring in white and non-white mushrooms made minor QTL for bruising sensitivity on other chromosomes (e.g. 3 and 10) more prominent. The one on chromosome 10 explained 31% phenotypic variation of bruising sensitivity in flush 2 in the subpopulations of population 1. The two parental lines of population 2 are both white. Major QTL of bruising sensitivity were detected on chromosome 1 and 2, contributing totally more than 44% variation of the bruising sensitivity in flush 1 and 54% variation of that in flush 2. A considerable consistency was found in QTL for bruising sensitivity in the different populations studied across tester lines and flushes indicating that this study will provide a base for breeding cultivars that are less sensitive for bruising allowing the use of mechanical harvest and automatic postharvest handling for produce for the fresh market. The low recombination between homologous chromosomes, however, underlines the need to introduce a normal recombination pattern found in a subspecies of the button mushroom.
    Using RNA-Seq to assemble a rose transcriptome with more than 13,000 full-length expressed genes and to develop the WagRhSNP 68k Axiom SNP array for rose (Rosa L.)
    Koning, C.F.S. ; Esselink, G. ; Vukosavljev, M. ; Westende, W.P.C. van 't; Gitonga, V.W. ; Krens, F.A. ; Voorrips, R.E. ; Weg, W.E. van de; Schulz, D. ; Debener, T. ; Maliepaard, C.A. ; Arens, P.F.P. ; Smulders, M.J.M. - \ 2015
    Frontiers in Plant Science 6 (2015). - ISSN 1664-462X - 10 p.
    powdery mildew - markers - tool - identification - resistance - genome - diversity - sequences - platform - plant
    In order to develop a versatile and large SNP array for rose, we set out to mine ESTs from diverse sets of rose germplasm. For this RNA-Seq libraries containing about 700 million reads were generated from tetraploid cut and garden roses using Illumina paired-end sequencing, and from diploid Rosa multiflora using 454 sequencing. Separate de novo assemblies were performed in order to identify single nucleotide polymorphisms (SNPs) within and between rose varieties. SNPs among tetraploid roses were selected for constructing a genotyping array that can be employed for genetic mapping and marker-trait association discovery in breeding programs based on tetraploid germplasm, both from cut roses and from garden roses. In total 68,893 SNPs were included on the WagRhSNP Axiom array. Next, an orthology-guided assembly was performed for the construction of a non-redundant rose transcriptome database. A total of 21,740 transcripts had significant hits with orthologous genes in the strawberry (Fragaria vesca L.) genome. Of these 13,390 appeared to contain the full-length coding regions. This newly established transcriptome resource adds considerably to the currently available sequence resources for the Rosaceae family in general and the genus Rosa in particular.
    Identification of Spodoptera exigua nucleopolyhedrovirus genes involved in pathogenicity and virulence
    Serrano, A. ; Pijlman, G.P. ; Vlak, J.M. ; Muñoz, D. ; Williams, T. ; Caballero, P. - \ 2015
    Journal of Invertebrate Pathology 126 (2015). - ISSN 0022-2011 - p. 43 - 50.
    in-vitro - multiple nucleopolyhedrovirus - myristoylated proteins - baculovirus - sequence - prediction - deletion - finger - genome - vivo
    Genome sequence analysis of seven different Spodoptera exigua multiple nucleopolyhedrovirus (SeMNPV) isolates that differed in insecticidal phenotype permitted the identification of genes likely to be involved in pathogenicity of occlusion bodies (OBs) and speed of kill (virulence) of this virus: se4 (hoar), se5 (unknown function), se28 (unknown function), se76 (cg30), se87 (p26) and se129 (p26). To study the role of these genes experimentally on the insecticidal phenotype, a bacmid-based recombination system was constructed to delete selected genes from a SeMNPV isolate, VT-SeAL1, designated as SeBacAL1. All of the knockout viruses were viable and the repair viruses behaved like the wild-type control, vSeBacAL1. Deletion of se4, se5, se76 and se129 resulted in decreased OB pathogenicity compared to vSeBacAL1 OBs. In contrast, deletion of se87 did not significantly affect OB pathogenicity, whereas deletion of se28 resulted in significantly increased OB pathogenicity. Deletion of se4, se28, se76, se87 and se129 did not affect speed of kill compared to the bacmid vSeBacAL1, whereas speed of kill was significantly extended following deletion of se5 and in the wild-type isolate (SeAL1), compared to that of the bacmid. Therefore, biological assays confirmed that several genes had effects on virus insecticidal phenotype. Se5 is an attractive candidate gene for further studies, as it affects both biological parameters of this important biocontrol virus.
    Temporal proteomic analysis and label-free quantitation of viral proteins of an invertebrate iridovirus
    Ince, I.A. ; Boeren, S. ; Oers, M.M. van; Vlak, J.M. - \ 2015
    Journal of General Virology 96 (2015)1. - ISSN 0022-1317 - p. 196 - 205.
    chilo-iridescent-virus - polypeptides - identification - type-6 - cells - membrane - genome - civ
    Invertebrate iridescent virus 6 (IIV-6) is a nucleocytoplasmic virus with a 212 kb-long linear double-stranded DNA genome that encodes 215 putative open reading frames. The IIV-6 virion-associated proteins consist of at least 54 virally-encoded proteins. One of our previous findings showed that most of these proteins are encoded by genes from the early transcriptional class. This indicates that these structural proteins may not only function in the formation of the virion, but also in the initial stage of viral infection. In the current study, we followed the protein expression profile of IIV-6 over time in Drosophila S2 cells by label-free quantitation using a proteomic approach. A total of 95 viral encoded proteins were detected in infected cells, of which 37 are virion proteins. The expressed IIV-6 virion proteins could be categorized into three main clusters based on their expression profiles. These clusters were: 1) proteins with stably low or 2) exponentially increasing expression levels during infection, and 3) proteins that were initially highly abundant, but showed slightly reduced levels after 48 hours (h) post infection (p.i.). Here, we provide novel information on the kinetics of virion and infected cell-specific protein levels that assists in understanding gene regulation in this lesser known DNA virus model.
    Ploidy manipulation and introgression breeding in Darwin hybrid tulips
    Marasek-Ciolakowska, A. ; Xie, S.L. ; Arens, P. ; Tuyl, J.M. van - \ 2014
    Euphytica 198 (2014)3. - ISSN 0014-2336 - p. 389 - 400.
    asiatic lilies lilium - gish analysis - sexual polyploidization - interspecific hybrids - garden tulips - genome - recombination - gesneriana - hybridization - fosteriana
    Meiotic polyploidisation via crossing with 2n gamete producing genotypes and interploidy crosses are two of the main methods currently used to obtain polyploid tulips. In our study diploid 2n gamete producing F-1 hybrids of Darwin hybrids (Tulipa gesneriana x Tulipa fosteriana) and triploid hybrid resulting from 'Rhodos' x 'Princeps' cross were used as pollen donor and crossed with cultivars of T. gesneriana in the following combination: 2x x 2x, 3x x 2x, 2x x 3x, and 3x x 3x. The progenies resulting from crosses at diploid level were mostly diploid, whereas a few seedlings were triploid. In 3x x 2x crosses aneuploids with chromosome constitution in between triploid and tetraploid (43-45 chromosomes) were predominant, but also one tetraploid (2n = 4x = 48) and four pentaploids (2n = 5x = 60) were obtained. In 2x x 3x crosses most progenies were triploid with the exception of a few aneuploids (3x + 1 and 3x - 1), whereas in 3x x 3x cross diploid and aneuploid genotypes were recorded with chromosome number varied from 27 to 34. These results indicate that triploid parents produced aneuploid as well as euploid (x, 2x, 3x) gametes and that success in ploidy manipulation in tulip depends to a large degree on the ploidy level of the parental genotypes used for hybridization. Genome constitution of selected population of F1 and BC1 hybrids was analyzed through genomic in situ hybridization (GISH). GISH analysis of the BC1 showed a considerable amount of intergenomic recombination which is desirable for introgression breeding.
    Polycistronic expression of a ß-carotene biosynthetic pathway in Saccharomyces cerevisiae coupled to ß-ionone production
    Beekwilder, J. ; Rossum, H.M. ; Koopman, F. ; Sonntag, F. ; Buchhaupt, M. ; Schrader, J. ; Hall, R.D. ; Bosch, H.J. ; Pronk, J.T. ; Maris, A.J.A. van; Daran, J.M. - \ 2014
    Journal of Biotechnology 192 (2014)partB. - ISSN 0168-1656 - p. 383 - 392.
    cleavage dioxygenase - yeast - genes - sequences - transformation - translation - polyprotein - versatile - genome - strain
    The flavour and fragrance compound ß-ionone, which naturally occurs in raspberry and many other fruits and flowers, is currently produced by synthetic chemistry. This study describes a synthetic biology approach for ß-ionone production from glucose by Saccharomyces cerevisiae that is partially based on polycistronic expression. Experiments with model proteins showed that the T2A sequence of the Thosea asigna virus mediated efficient production of individual proteins from a single transcript in S. cerevisiae. Subsequently, three ß-carotene biosynthesis genes from the carotenoid-producing ascomycete Xanthophyllomyces dendrorhous (crtI, crtE and crtYB) were expressed in S. cerevisiae from a single polycistronic construct. In this construct, the individual crt proteins were separated by T2A sequences. Production of the individual proteins from the polycistronic construct was confirmed by Western blot analysis and by measuring the production of ß-carotene. To enable ß-ionone production, a carotenoid-cleavage dioxygenase from raspberry (RiCCD1) was co-expressed in the ß-carotene producing strain. In glucose-grown cultures with a second phase of dodecane, ß-ionone and geranylacetone accumulated in the organic phase. Thus, by introducing a polycistronic construct encoding a fungal carotenoid pathway and an expression cassette encoding a plant dioxygenase, a novel microbial production system has been established for a fruit flavour compound.
    Genetic variation, heritability and genotype by environment interaction of morphological traits in a tetraploid rose population
    Gitonga, V.W. ; Koning, C.F.S. ; Verlinden, K. ; Dolstra, O. ; Visser, R.G.F. ; Maliepaard, C.A. ; Krens, F.A. - \ 2014
    BMC Genetics 15 (2014). - ISSN 1471-2156 - 23 p.
    x-chromosome - genome - recombination - qtl - snps - pigs
    Background Global trade has ensured that the ornamental horticulture continues to grow worldwide, with rose hybrids being the most economically important genus (Rosa x hybrida). Due to changes in global trade and an increase in energy costs the ornamental industry has seen a shift in the production and sale of flowers from the US and Europe alone to production in Africa and Latin America. As Kenya is a major exporter of roses to Europe we studied the genetic variation and heritability of specific morphological traits in a tetraploid population grown in the Netherlands and in Kenya. The aim was to estimate genotype by environment interaction (G???E) and to investigate the implications of (G???E) for rose breeding. Results A tetraploid rose population (K5) from a cross between two tetraploid parents was field tested over two seasons in the Netherlands (summer and winter) and two locations in Kenya (Nairobi and Njoro). Ten traits were compared per genotype across the four environments. There were differences in trait association across the four environments showing that the traits were partially influenced by the environment.The traits that had a low ratio of ?2 ge/?2 g also showed a high value for heritability. For the traits number of petals, prickles on petioles, prickles on stems the interaction is minimal. For the traits chlorophyll content, stem width and side shoots we observed a much higher interaction ratio of 0.83, 1.43 and 3.13 respectively. The trait number of petals had the highest heritability of 0.96 and the lowest ?2 ge/?2 g ratio (0.08). The trait number of side shoots (SS) with the lowest heritability (0.40) also had the highest ?2 ge/?2 g ratio of 3.13. Conclusion Results attained by this experiment showed that we have different magnitudes of non-crossover G???E interactions. For the traits number of petals, prickles on stems and prickles on petioles with a low interaction and high heritability, selection can be done at any of the environments. Thus, these traits can be confirmed at the breeding site. For the traits stem width, side shoots and chlorophyll content that had a higher interaction selection for or against these traits should be done at the production location or at least be verified there.
    Automated alignment-based curation of gene models in filamentous fungi
    Burgt, A. van der; Severing, E.I. ; Collemare, J.A.R. ; Wit, P.J.G.M. de - \ 2014
    BMC Bioinformatics 15 (2014). - ISSN 1471-2105 - 13 p.
    pathogen fusarium-graminearum - ab-initio - genome - prediction - introns
    Background Automated gene-calling is still an error-prone process, particularly for the highly plastic genomes of fungal species. Improvement through quality control and manual curation of gene models is a time-consuming process that requires skilled biologists and is only marginally performed. The wealth of available fungal genomes has not yet been exploited by an automated method that applies quality control of gene models in order to obtain more accurate genome annotations. Results We provide a novel method named alignment-based fungal gene prediction (ABFGP) that is particularly suitable for plastic genomes like those of fungi. It can assess gene models on a gene-by-gene basis making use of informant gene loci. Its performance was benchmarked on 6,965 gene models confirmed by full-length unigenes from ten different fungi. 79.4% of all gene models were correctly predicted by ABFGP. It improves the output of ab initio gene prediction software due to a higher sensitivity and precision for all gene model components. Applicability of the method was shown by revisiting the annotations of six different fungi, using gene loci from up to 29 fungal genomes as informants. Between 7,231 and 8,337 genes were assessed by ABFGP and for each genome between 1,724 and 3,505 gene model revisions were proposed. The reliability of the proposed gene models is assessed by an a posteriori introspection procedure of each intron and exon in the multiple gene model alignment. The total number and type of proposed gene model revisions in the six fungal genomes is correlated to the quality of the genome assembly, and to sequencing strategies used in the sequencing centre, highlighting different types of errors in different annotation pipelines. The ABFGP method is particularly successful in discovering sequence errors and/or disruptive mutations causing truncated and erroneous gene models. Conclusions The ABFGP method is an accurate and fully automated quality control method for fungal gene catalogues that can be easily implemented into existing annotation pipelines. With the exponential release of new genomes, the ABFGP method will help decreasing the number of gene models that require additional manual curation.
    F1 hybrid of cultivated apple (Malus x domestica) and European pear (Pyrus communis) with fertile F2 offspring
    Fischer, T.C. ; Malnoy, M. ; Hofmann, T. ; Schwab, W. ; Palmieri, L. ; Wehrens, H.R.M.J. ; Schuch, L.A. ; Müller, M. ; Schimmelpfeng, H. ; Velasco, R. ; Martens, S. - \ 2014
    Molecular Breeding 34 (2014)3. - ISSN 1380-3743 - p. 817 - 828.
    nuclear-dna content - genetic-linkage maps - flow-cytometry - japanese pear - s-alleles - borkh. - diversity - rosaceae - markers - genome
    The establishment of intergeneric hybrids for horticultural and agricultural crops is still a demanding task for breeding programmes. The aim of such approaches is to introduce new quality and resistance traits and to enlarge the gene pool. Recently, an F1 hybrid between Malus × domestica and Pyrus communis became available which arose from a breeding approach undertaken in the late 1980s by the breeder Max Zwintzscher (Cologne-Vogelsang). Unlike previous reports, viable and fertile F2 plants were obtained from this F1 hybrid line by author HS, providing a unique perspective not only for genomic, transcriptomic and metabolomic studies but also for advanced breeding strategies. Here, we give the first report on the confirmation and characterization of the F1 hybrid by phenotypic, genetic and biochemical means. The intergeneric hybrid shows an intermediary phenotype of leaves, flowers and fruits, and some disorder of secondary shoot growth. Nuclear DNA content is also intermediary and corresponds to a diploid state. Apple and pear type rDNA as well as SI alleles from each genus were found. At the metabolic level, parallel biosynthesis of the apple dihydrochalcone phloridzin and of arbutin, a p-hydroquinone-glucoside typical for pear, take place leading to considerable concentrations of both in leaves. The overall data allow secure confirmation of the hybrid character and give a first insight into the hybrids genetics and physiology.
    Green genes: bioinformatics and systems-biology innovations drive algal biotechnology
    Reijnders, M.J.M.F. ; Heck, R.G.A. van; Lam, C.M.C. ; Scaife, M.A. ; Martins dos Santos, V.A.P. ; Smith, A.G. ; Schaap, P.J. - \ 2014
    Trends in Biotechnology 32 (2014)12. - ISSN 0167-7799 - p. 617 - 626.
    protein function prediction - subcellular-localization prediction - metabolic network reconstruction - flux balance analysis - chlamydomonas-reinhardtii - lipid-accumulation - expression data - genome - microalgae - sequence
    Many species of microalgae produce hydrocarbons, polysaccharides, and other valuable products in significant amounts. However, large-scale production of algal products is not yet competitive against non-renewable alternatives from fossil fuel. Metabolic engineering approaches will help to improve productivity, but the exact metabolic pathways and the identities of the majority of the genes involved remain unknown. Recent advances in bioinformatics and systems-biology modeling coupled with increasing numbers of algal genome-sequencing projects are providing the means to address this. A multidisciplinary integration of methods will provide synergy for a systems-level understanding of microalgae, and thereby speed up the improvement of industrially valuable strains. In this review we highlight recent advances, challenges, their application in microalgae research, and their potential.
    New insights into domestication of carrot from root transcriptome analyses
    Rong, J. ; Lammers, Y. ; Strasburg, J.L. ; Schidlo, N.S. ; Ariyurek, Y. ; Jong, T.J. de; Klinkhamer, P.G.L. ; Smulders, M.J.M. ; Vrieling, K. - \ 2014
    BMC Genomics 15 (2014). - ISSN 1471-2164 - 15 p.
    daucus-carota l. - nucleotide polymorphism - wild - populations - inference - sativus - genome - diversity - sequences - selection
    Background - Understanding the molecular basis of domestication can provide insights into the processes of rapid evolution and crop improvement. Here we demonstrated the processes of carrot domestication and identified genes under selection based on transcriptome analyses. Results - The root transcriptomes of widely differing cultivated and wild carrots were sequenced. A method accounting for sequencing errors was introduced to optimize SNP (single nucleotide polymorphism) discovery. 11,369 SNPs were identified. Of these, 622 (out of 1000 tested SNPs) were validated and used to genotype a large set of cultivated carrot, wild carrot and other wild Daucus carota subspecies, primarily of European origin. Phylogenetic analysis indicated that eastern carrot may originate from Western Asia and western carrot may be selected from eastern carrot. Different wild D. carota subspecies may have contributed to the domestication of cultivated carrot. Genetic diversity was significantly reduced in western cultivars, probably through bottlenecks and selection. However, a high proportion of genetic diversity (more than 85% of the genetic diversity in wild populations) is currently retained in western cultivars. Model simulation indicated high and asymmetric gene flow from wild to cultivated carrots, spontaneously and/or by introgression breeding. Nevertheless, high genetic differentiation exists between cultivated and wild carrots (Fst =0.295) showing the strong effects of selection. Expression patterns differed radically for some genes between cultivated and wild carrot roots which may be related to changes in root traits. The up-regulation of water-channel-protein gene expression in cultivars might be involved in changing water content and transport in roots. The activated expression of carotenoid-binding-protein genes in cultivars could be related to the high carotenoid accumulation in roots. The silencing of allergen-protein-like genes in cultivated carrot roots suggested strong human selection to reduce allergy. These results suggest that regulatory changes of gene expressions may have played a predominant role in domestication. Conclusions - Western carrots may originate from eastern carrots. The reduction in genetic diversity in western cultivars due to domestication bottleneck/selection may have been offset by introgression from wild carrot. Differential gene expression patterns between cultivated and wild carrot roots may be a signature of strong selection for favorable cultivation traits.
    Fine mapping of the gene Rvi18 (V25) for broad-spectrum resistance to apple scab, and development of a linked SSR marker suitable for marker-assisted breeding
    Soriano, J.M. ; Madduri, M. ; Schaart, J. ; Burgh, A.M. van der; Kaauwen, M.P.W. van; Tomic, L. ; Groenwold, R. ; Velasco, R. ; Weg, W.E. van de; Schouten, H.J. - \ 2014
    Molecular Breeding 34 (2014)4. - ISSN 1380-3743 - p. 2021 - 2032.
    malus-x-domestica - venturia-inaequalis - microsatellite markers - cisgenic plants - genome - borkh. - receptors - lectins - race
    Apple scab, caused by the fungal pathogen Venturia inaequalis, is one of the most devastating diseases for the apple growing industry in temperate zones with humid springs and summers. Breeding programs around the world have identified several sources of resistance, of which the Rvi6 (Vf) gene from Malus floribunda 821 has been the most widely used. The appearance of Rvi6-virulent strains of V. inaequalis in several European countries have underlined the necessity of pyramiding different effective resistance genes for durably resistant cultivars. Here we report the mapping of the new apple scab resistance gene Rvi18 (V25) from the selection 1980-015-025 of the apple breeding program at Wageningen University and Research Centre, The Netherlands. This gene was fine mapped on the proximal part of LG11 to a region of 34 Kb in the apple genome sequence of ‘Golden Delicious’, using 894 progeny plants, and SSR, DArT, AFLP, and SNP markers. One gene on the ‘Golden Delicious’ reference genome was identified as the potential susceptibility allele of the resistance gene. Moreover, an SSR marker has been developed of which one of its amplicons sizes is highly specific for Rvi18, thus facilitating the directed pyramiding of resistance genes through marker assisted breeding.
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