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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.

    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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    Microbiome dynamics of disease suppresive soils
    Gómez Expósito, Ruth - \ 2017
    Wageningen University. Promotor(en): F.P.M. Govers; J.M. Raaijmakers, co-promotor(en): J. Postma; I. de Bruijn. - Wageningen : Wageningen University - ISBN 9789463431774 - 267
    suppressive soils - soil suppressiveness - plant diseases - thanatephorus cucumeris - microbial ecology - soil microbiology - rhizosphere bacteria - soil bacteria - community ecology - soil fungi - transcriptomics - taxonomy - ziektewerende gronden - bodemweerbaarheid - plantenziekten - thanatephorus cucumeris - microbiële ecologie - bodemmicrobiologie - rizosfeerbacteriën - bodembacteriën - gemeenschapsecologie - bodemschimmels - transcriptomica - taxonomie

    Disease suppressive soils are soils in which plants do not get diseased from plant pathogens due to the presence (and activities) of the microbes present in the soil. Understanding which microbes contribute to confer suppression and through which mechanisms they can protect plants is crucial for a sustainable control of plant diseases. In the research conducted in this thesis, I first examined the role of Lysobacter species, previously associated with disease suppressive soils, in suppressing damping-off disease caused by the soil-borne fungal pathogen Rhizoctonia solani on sugar beet. The majority of the Lysobacter strains tested revealed a broad metabolic potential in producing a variety of enzymes and secondary metabolites able to suppress R. solani in vitro. However, any of these strains could consistently suppress damping-off disease when applied in soil bioassays. Their ability to promote plant growth was also tested for sugar beet, cauliflower, onion or Arabidopsis thaliana. Results indicated that any of the Lysobacter strains could consistently promote plant growth, neither via direct contact nor via volatile production. Second, I investigated whether the antagonistic activity of Lysobacter species could be triggered when applied as bacterial consortia, together with Pseudomonas and Streptomyces species. Although several bacterial combinations showed an increased antagonistic effect towards R. solani in vitro, no consistent effects were observed when these bacterial consortia were applied in vivo. Third, I investigated the dynamical changes in the bacterial community composition and functions occurring during the process of disease suppressiveness induction by performing whole community analyses using next-generation sequencing techniques. Results indicated that suppressiveness induction was most associated with changes in certain bacterial traits rather than changes in the bacteria community composition itself. Among the functions found as more active in suppressive soils were several ‘classic’ mechanisms of disease suppression, including competition for nutrients, iron and space and production of extracellular enzymes, indol-acetic-acid and hydrogen cyanide. Among the enzymes found in higher abundance in suppressive soil were these ones involved in the degradation of oxalic acid, a pathogenicity factor produced by pathogenic fungi to help infecting the host plant. Hence, I finally studied the role of bacteria able to produce enzymes able to degrade oxalic acid in suppressing R. solani disease. Enrichment of native oxalotrophic bacteria existing in soil, their isolation and further application into soil revealed that they could effectively suppress Rhizoctonia disease. Characterization of these oxalotrophic bacteria revealed that members within the Caulobacter and Nocardioides species could suppress R. solani disease by their own. Furthermore, the research done in this thesis highlights the importance of combining different techniques to unravel the mechanisms underlying disease suppression and the importance of studying function-over-phylogeny. Additionally, it also highlights the importance of organic amendments (such as oxalic acid) directly into soils in order to “engineer” the bacterial functions towards the control of diseases caused by R. solani.

    Comparative genomics and trait evolution in Cleomaceae, a model family for ancient polyploidy
    Bergh, Erik van den - \ 2017
    Wageningen University. Promotor(en): M.E. Schranz; Y. van de Peer. - Wageningen : Wageningen University - ISBN 9789463431705 - 106
    capparaceae - genomics - polyploidy - evolution - genomes - reproductive traits - flowers - colour - glucosinolates - genetic variation - biosystematics - taxonomy - identification - capparaceae - genomica - polyploïdie - evolutie - genomen - voortplantingskenmerken - bloemen - kleur - glucosinolaten - genetische variatie - biosystematiek - taxonomie - identificatie

    As more and more species have been sequenced, evidence has been piling up for a fascinating phenomenon that seems to occur in all plant lineages: paleopolyploidy. Polyploidy has historically been a much observed and studied trait, but until recently it was assumed that polyploids were evolutionary dead-ends due to their sterility. However, many studies since the 1990’s have challenged this notion by finding evidence for ancient genome duplications in many genomes of current species. This lead to the observation that all seed plants share at least one ancestral polyploidy event. Another polyploidy event has been proven to lie at the base of all angiosperms, further signifying the notion that ancient polyploidy is widespread and common. These findings have led to questions regarding the apparent disadvantages that can be observed in a first generation polyploid. If these disadvantages can be overcome however, duplication of a genome also presents an enormous potential for evolutionary novelty. Duplicated copies of genes are able to acquire changes that can lead to specialization of the duplicated pair into two functions (subfunctionalization) or the development of one copy towards an entirely new function (neofunctionalization).

    Currently, most research towards polyploidy has focused on the economically and scientifically important Brassicaceae family containing the model plant Arabidopsis thaliana and many crops such as cabbage, rapeseed, broccoli and turnip. In this thesis, I lay the foundations for the expansion of this scope to the Cleomaceae, a widespread cosmopolitan plant family and a sister family of Brassicaceae. The species within Cleomaceae are diverse and exhibit many scientifically interesting traits. They are also in a perfect position phylogenetically to draw comparisons with the much more studied Brassicaceae. I describe the Cleomaceae and their relevance to polyploid research in more detail in the Introduction. I then describe the important first step towards setting up the genetic framework of this family with the sequencing of Tarenaya hassleriana in Chapter 1.

    In Chapter 2, I have studied the effects of polyploidy on the development of C4 photosynthesis by comparing the transcriptome of C3 photosynthesis based species Tarenaya hassleriana with the C4 based Gynandropsis gynandra. C4 photosynthesis is an elaboration of the more common C3 form of photosynthesis that concentrates CO2 in specific cells leading to decreased photorespiration by the RuBisCO and higher photosynthetic efficieny in low CO2 environments. I find that polyploidy has not led to sub- or neofunctionalization towards the development of this trait, but instead find evidence for another important phenomenon in postpolyploid evolution: the dosage balance hypothesis. This hypothesis states that genes which are dependent on specific dosage levels of their products will be maintained in duplicate; any change in their function would lead to dosage imbalance which would have deleterious effects on their pathway. We show that most genes involved in photosynthesis have returned to single copy in G. gynandra and that the changes leading to C4 have mostly taken place at the expression level confirming current assumptions on the development of this trait.

    In Chapter 3, I have studied the effects of polyploidy on an important class of plant defence compounds: glucosinolates. These compounds, sometimes referred to as ‘mustard oils’, play an important role in the defence against herbivores and have radiated widely in Brassicaceae to form many different ‘flavors’ to deter specific herbivores. I show that in Cleomaceae many genes responsible for these compounds have benefited from the three rounds of polyploidy that T. hassleriana has undergone and that many duplicated genes have been retained. We also show that more than 75% is actively expressed in the plant, proving that the majority of these duplications has an active function in the plant.

    Finally, in Chapter 4 I investigate a simple observation made during experiments with T. hassleriana in the greenhouse regarding the variation in flower colour between different individuals: some had pink flowers and some purple. Using LC-PDA mass spectrometry we find that the two colours are caused by different levels of two anthocyanin pigments, with cyanidin dominating in the purple flowers and pelargonidin being more abundant in pink flowers. Through sequence comparison and synteny analysis between A. thaliana and T. hassleriana we find the orthologs of the genes involved in this pathway. Using a Genotyping by Sequencing method on a cross between these two flower colours, we produce a collection of SNP markers on the reference genome. With these SNPs, we find two significant binary trait loci, one of which corresponds to the location of the F3’H ortholog which performs the conversion of a pelargonidin precursor to a cyanidin precursor.

    In the General Conclusion, I combine all findings of the previous chapters and explain how they establish part of a larger species framework to study ancient polyploidy in angiosperms. I then put forth what these findings can mean for possible future research and the directions that are worth to be explored further.

    Concealed diversity : taxonomical, phytogeographical and phytosociological notes on brambles (Rubus L. subgen. Rubus) in north-west Europe
    Haveman, Rense - \ 2017
    Wageningen University. Promotor(en): Joop Schaminee, co-promotor(en): Rienk Jan Bijlsma. - Wageningen : Wageningen University - ISBN 9789463431019 - 200
    rubus - diversity - taxonomy - phytogeography - geographical distribution - biogeography - apomixis - northwestern europe - rubus - diversiteit - taxonomie - plantengeografie - geografische verdeling - biogeografie - apomixis - noordwest-europa

    Rubus subgen. Rubus (bramble) is one of the large plant genera in Europe, consisting of only a few sexual biological species and at least 700 apomictic lineages. In this thesis, it is argued that the stabilised apomict lineages should best be regarded species, even if their distribution area doesn’t meet the requirements of a regional species as defined in several publications by Weber. Included is a checklist of Dutch bramble species, comprising 191 species belonging to Rubus subgen. Rubus. In the Netherlands, 97 of the 191 species are classified as regional species, with a distribution area diameter under 500 km. On the basis of distribution data of bramble species in Ireland, the UK, Denmark, Germany, and the Netherlands, 12 phytogeographical bramble-regions are distinguished. Although ecological factors play a role in the realisation of these regions, it is argued that the found patterns are primarily the result of evolutionary processes. The density and species composition of Rubus scrubs in the Netherlands is studied using landscape transects. At landscape scale, the bramble species in the scrubs are not randomly distributed, causing a spatial clustering of floristically similar bramble scrubs. It was concluded that only a part of the diversity of Rubus scrubs was accounted for in the Dutch national vegetation classification, and a new scrub type (the Rubetum taxandriae) was described on the basis of these findings. Rubus scrubs are an important biotope for rare shrub species and endemic Rubus species. Additionally, scrubs rich in bramble species are important because they provide foraging and nesting habitats for numerous vertebrates and invertebrates. It is recommended to include the apomict Rubus species in biodiversity accounts, for instance in the national standard list of plant species, as well as the Red List.

    The mountain vegetation of South Peru : syntaxonomy, ecology, phytogeography and conservation
    Montesinos-Tubée, D.B. - \ 2016
    Wageningen University. Promotor(en): Karle Sykora; Frank Berendse, co-promotor(en): Antoine Cleef. - Wageningen : Wageningen University - ISBN 9789462576797 - 334
    vegetation - mountains - phytogeography - ecology - taxonomy - nature conservation - andes - peru - vegetatie - gebergten - plantengeografie - ecologie - taxonomie - natuurbescherming - andes - peru

    THE MOUNTAIN VEGETATION OF SOUTH PERU: SYNTAXONOMY, ECOLOGY, PHYTOGEOGRAPHY AND CONSERVATION

    This thesis presents an overview and revision of plant communities from xerophytic and mountain landscapes in the dry Andes of South Peru. The revision is based on comparison of the collected vegetation data with other regional and interregional studies. This phytosociologic overview comprises the arid and semi-arid montane vegetation of the province of Arequipa and besides the plant communities of Moquegua from the prepuna between 3470 and 3700 m, the puna between 3750 and 4500 m and the superpuna between 4450 and 4800 m. The Braun-Blanquet approach and multivariate ordination and classification methods have been applied to classify the different plant communities and to study the relation between plant communities and environmental variables, such as altitude, slope degree and exposition, rock and stone cover percentage, manure cover and grazing. Furthermore the results are presented of a phytogeographical analysis of the Andean puna flora (at vascular genus level) and its relation to other tropicalpine regions in South America. Finally, the descriptions of six recently published new species are included in this thesis. The results provide an important database for nature conservation issues, stressing the significance of protecting the fragile and diverse ecosystems of the Moqueguan Andes. The results of this vegetation survey can be used to prioritize the selection and assignment of nature reserves.

    Restyling Alternaria
    Woudenberg, J.H.C. - \ 2015
    Wageningen University. Promotor(en): Pedro Crous; Pierre de Wit, co-promotor(en): J.Z. Groenewald. - Wageningen : Wageningen University - ISBN 9789462574106 - 250
    alternaria - taxonomie - fylogenie - moleculaire taxonomie - plantenziekteverwekkende schimmels - alternaria - taxonomy - phylogeny - molecular taxonomy - plant pathogenic fungi

    The omnipresent dematiaceous hyphomycete genus Alternaria is associated with a wide variety of substrates including seeds, plants, agricultural products, humans, soil and even the atmosphere. It includes saprophytic, endophytic and pathogenic species, among which multiple plant pathogens, post-harvest pathogens, and human pathogens (causative agents of phaeohyphomycosis and hypersensitivity reactions). Molecular studies reveal that the Alternaria complex comprises nine genera. Within this complex several genera are non-monophyletic and Alternaria species cluster into multiple distinct species clades, which are not always correlated with species-groups based on morphological characteristics. The most commonly reported species in literature and type species of the genus Alternaria, A. alternata, also comprises one such species-group. The small-spored Alternaria species within this group are mainly described based on morphology and / or host-specificity, but are difficult to distinguish based on molecular techniques alone. As A. alternata is considered as one of the most prolific producers of fungal allergens and is reported as pathogen on over 100 host plants, correct species identification is of utmost importance. The research presented in this thesis discusses the taxonomic status of Alternaria and its related genera, with a further focus on the two biggest and most important species complexes; the large-spored A. porri and small-spored A. alternata species complexes. With the phylogenies and classifications presented in this thesis, more robust and understandable taxonomy and nomenclature in Alternaria and allied genera within the Alternaria complex are created.

    Chapter 1 gives a general introduction to the genus Alternaria and related genera. The history of the genus and its economic importance as plant pathogen, post-harvest pathogen, causative agent of phaeohyphomycosis and common allergen causing hypersensitivity reactions are summarized. The introduction of the morphological species complexes, based on characters of the conidia, the pattern of chain formation, and the nature of the apical extensions of conidia are treated. Molecular studies recognise seven Alternaria species-groups within the Alternaria complex. Besides Alternaria, eight other genera are assigned to the Alternaria complex based on molecular and morphological studies.

    Chapter 2 focusses on the relationship of Alternaria and its closely related genera within the broader Alternaria complex. The phylogenetic lineages within the Alternaria complex are delineated based on nucleotide sequence data of parts of the 18S nrDNA (SSU), 28S nrDNA (LSU), the internal transcribed spacer regions 1 and 2 and intervening 5.8S nrDNA (ITS), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), RNA polymerase second largest subunit (RPB2) and translation elongation factor 1-alpha (TEF1) gene regions. The phylogenetic data reveal a Stemphylium clade sister to Embellisia annulata and a big Alternaria clade. The Alternaria clade contains six monotypic lineages and 24 internal clades, which are treated as sections of Alternaria. In order to create a stable phylogenetic taxonomy, and supported by i) a well-supported phylogenetic node in multiple analyses, ii) a high-similarity of clades within Alternaria based on SSU, LSU and ITS data, and iii) variation in the clade order between the different gene phylogenies, 13 genera are placed into synonymy with Alternaria. Embellisia annulata is synonymized with Dendryphiella salina, and together with D. arenariae placed in the new genus Paradendryphiella. The sexual genera Clathrospora and Comoclathris, with asexual forms linked to Alternaria, cluster within the Pleosporaceae, as does Alternaria, but outside Alternaria s. str. The genus Alternariaster, described to accommodate Alternaria helianthi, clusters within the Leptosphaeriaceae.

    Chapter 3 describes the reappraisal of the genus Alternariaster. Alternaria helianthi, the causal agent of leaf spot on Helianthus annuus (sunflower) was segregated from Alternaria based on conidial morphology, and placed in the new genus Alternariaster. A multi-gene phylogeny of parts of the ITS, LSU, RPB2 and GAPDH gene regions placed a fungal pathogen associated with leaf spot on Bidens sulphurea (yellow cosmos) in Brazil in close relation with Al. helianthi. Based on the close phylogenetic relation to Al. helianthi, but distinct morphological and pathogenicity characters, the fungal pathogen associated with leaf spot on B. sulphurea is newly described as Al. bidentis.

    Chapter 4 treats the Alternaria species which form the largest section of Alternaria, sect. Porri. This section contains almost all Alternaria species with medium to large conidia with long beaks, some of which are important plant pathogens. A multi-gene phylogeny on parts of the ITS, GAPDH, RPB2, TEF1 and Alternaria major allergen (Alt a 1) gene regions, supplemented with morphological and cultural studies, forms the basis for species recognition in this section. The polyphasic data reveal 63 species in sect. Porri, of which 10 are newly described, and 27 names are synonymized.

    Chapter 5 treats the small-spored Alternaria species, which reside in sect. Alternaria. A lot of confusion around the naming of species within this section exists, since the naming is mostly based on morphology and host-specificity, although the molecular variation is minimal. Whole genome sequencing, combined with transcriptome profiling and multi-gene sequencing of nine gene regions, SSU, LSU, ITS, GAPDH, RPB2, TEF1, Alt a 1, endopolygalacturonase (endoPG) and an anonymous gene region (OPA10-2), is used to create a clear and stable species classification in this section. The nine sequenced Alternaria genomes range in size from 32.0 - 39.1 Mb. The number of repetitive sequences varies significantly, with a relative low percentage of repeats within sect. Alternaria. The genome identity within sect. Alternaria is high, compared to the genome identity for isolates from other sections to the A. alternata reference genome. Similarly, a relative low percentage of single nucleotide polymorphisms (SNPs) were observed in genomic and transcriptomic sequences between isolates from sect. Alternaria, compared to the percentage of SNP’s found in isolates from different sections compared to the A. alternata reference genome. A set of core proteins was extracted from the genome and transcriptome data, and primers were designed on two eukaryotic orthologous group (KOG) protein loci with a relatively low degree of conservation within section Alternaria. The phylogenies from these two gene regions, KOG1058 and KOG1077, could not distinguish the described morphospecies within sect. Alternaria better than the phylogenies based on the nine commonly used gene regions for Alternaria. Based on genome and transcriptome comparisons and molecular phylogenies, Alternaria sect. Alternaria consists of only 11 phylogenetic species and one species complex. Thirty-five morphospecies are synonymized under A. alternata. The subclades that are formed by these isolates are incongruent between the different gene regions sequenced; no two genes show the same groupings for any of the over 100 isolates. A sequence-based identification guide is provided for the species which are now recognized in sect. Alternaria. None of the genes sequenced in this study can distinguish all of the species recognized here on its own.

    Chapter 6 investigates the molecular diversity of indoor Alternaria isolates in the USA, with the help of a phylogeographic / population genetic approach. Isolates collected throughout the USA were identified using ITS, GAPDH and endoPG gene sequencing, followed by genotyping and population genetic inference of the sect. Alternaria isolates and 37 reference isolates, using five microsatellite markers. Phylogenetic analyses revealed that 98 % (153 isolates) of the indoor isolates consisted of species from Alternaria sect. Alternaria. The remaining 2 % (three isolates) represented one sect. Infectoriae and two sect. Pseudoulocladium isolates. From the 153 isolates that belonged to sect. Alternaria, one could be assigned to A. burnsii, 15 to the A. arborescens species complex and the remaining 137 isolates were identified as A. alternata. Based on the microsatellite data, no specific indoor population could be distinguished. Population assignment analyses of the A. alternata isolates suggested that subpopulations did not exist within the sample, which we thus divided into four artificial subpopulations to represent four quadrants of the USA. Genotypic diversity was extremely high for all quadrants and a test for linkage disequilibrium suggested that A. alternata has a cryptic sexual cycle. The SouthWest-USA population displayed the highest level of uniqueness, based on private alleles. Intriguingly, the highest amount of gene flow, between SouthWest-USA and SouthEast-USA, correlated with the west-to-east movement of the antitrade winds. This suggests that indoor A. alternata isolates, although extremely diverse, have a continental distribution and high levels of gene flow over the continent.

    Chapter 7 discusses the data presented in this thesis. The implications of the performed studies are placed in a broader context, with a focus on the relation between morphology and the new species classification based on molecular tools and the use of genome data in contrast to multi-gene data.

    Systematics, evolution and historical biogeography of the family Ochnaceae with emphasis on the genus Campylospermum
    Bissiengou, P. - \ 2014
    Wageningen University. Promotor(en): Marc Sosef, co-promotor(en): Lars Chatrou; L. Ngok Banak. - Wageningen : Wageningen University - ISBN 9789462572225 - 357
    ochnaceae - biosystematiek - taxonomie - evolutie - biogeografie - plantengeografie - fylogenie - taxonomische revisies - fylogenetica - ochnaceae - biosystematics - taxonomy - evolution - biogeography - phytogeography - phylogeny - taxonomic revisions - phylogenetics

    Abstract

    Ochnaceae s.l. is a family of trees, shrubs or rarely herbs widely distributed in tropical and subtropical forests and savannas of the Old and New World, and has about 500 species in 32 genera. The family is divided into three subfamilies: Medusagynoideae, Quiinoideae and Ochnoideae. We have provided, for the first time, a nearly complete molecular phylogenetic analysis of Ochnaceae s.l. resolving most of the phylogeny backbone of the family using five DNA regions. Based on this, dating analyses were performed using a secondary calibration, and relaxed molecular clock models. The historical biogeography of Ochnaceae s.l. was reconstructed using Dispersal-Vicariance Analysis and Bayesian Binary MCMC. The Neotropics were inferred as being the geographical origin of the family and the Old World was most likely colonized via the North Atlantic Land Bridge during a period when climatic conditions allowed establishment of a boreotropical flora. A full taxonomic revision of the continental African species of the genus Campylospermum has been prepared and additional historical biogeographic analyses were performed with a focus on the genus Campylospermum.

    Phylogeny and DNA-based identification in Phoma and related genera
    Aveskamp, M.M. - \ 2014
    Wageningen University. Promotor(en): Pedro Crous; Pierre de Wit. - Wageningen : Wageningen University - ISBN 9789461739148 - 206
    phoma - fylogenie - taxonomie - moleculaire taxonomie - identificatie - verklarende woordenlijsten - phoma - phylogeny - taxonomy - molecular taxonomy - identification - glossaries

    This thesis treats the taxonomy of a generic complex presently known as PhomaSacc. emend Boerema & Bollen. This group of fungi comprises more than 200 taxa at species or variety level that are characterised by the production of hyaline, non-septate conidial spores in pycnidial conidiomata. The genus is omnipresent in the environment, and exponents can be found on a wide range of host substrates.

    For many years the genus Phomawas the main research topic of a group of mycologists at the Dutch National Plant Protection Service. The studies conducted in the last decennia of the previous century culminated in a handbook that monographed the majority of the species in the above-mentioned generic complex. This handbook marked the end of the era in which the taxonomy of this genus mainly relied on morphological observations and cultural descriptions. However, it can also be regarded as the starting point of the present study. The aim of the present project was to integrate DNA-based identification methods into the taxonomic system established by the previously mentioned group of researchers. The major part of this study therefore deals with the validation of current generic and species concepts.

    An extensive literature review of the biology, taxonomy and identification methods to the species in this genus is provided in Chapter 2, with specific reference to the progress that has been made in Phomataxonomy after the publication of the abovementioned handbook. The advantages and disadvantages of the current taxonomical system are discussed. Furthermore, this chapter describes the general biology of the species in this fungal group, including their life cycles, distribution and host substrates. The importance of the genus for plant health and quarantine issues is illustrated, and the development of a rapid and robust identification technique based on DNA barcodes is advocated.

    Chapter 3treats species in Phomasection Peyronellaea. Species in this section are typified by the production of dictyochlamydospores, and thus have additional morphological characters to use in taxon delineation in comparison with species in the other Phomasections. All species in this group were subjected to a morphological re-examination and phylogenetic analyses employingITS, actin, and β-tubulin nucleotide sequences. Based on multi-gene analyses, Phomasection Peyronellaeacould not be maintained as a taxonomic entity, due to the polyphasic nature of taxa in this section. The morphological study revealed that for five species a taxonomic revision was required. A further five species appeared to be new to science, including Ph. microchlamydospora, Ph. omnivirens, and Ph. schachtii. Also the taxonomic noveltiesPh. coffeae-arabicaeand Ph. sancta are described here, and are allocated to the genus Peyronellaea, re-erected in Chapter 5.

    In Chapter 4the diversity among species and varieties belonging to the Ph. exiguaspecies complex is investigated. The Ph. exiguaspecies complex includes nine taxa at varietal level and four species that have a high morphological similarity both in vivoand in vitro, whilst historical relations with plant hosts cannot be maintained. Among this group, both omnipresent saprobes as well as host-specific plant pathogens are present – including the potato pathogen Ph. foveata.

    The diversity in this complex is studied by means of Internal Transcribed Spacer regions 1 & 2 and intervening 5.8S nrDNA (ITS) and actin nucleotidesequence analyses and a DNA fingerprinting technique rarely used to study fungal diversity. This technique, DNA Amplification Fingerprinting (DAF) employs short, arbitrary primers that form a loop, or a mini-hairpin, under specific temperature conditions and is frequently used in molecular plant breeding. The amplified DNA fragments were isolated and sequenced in order to develop taxon-specific markers and primer combinations based on the SCARs (Sequence Characterised Amplified Regions) and actin sequence data generated. These tools can aid rapid identification of this morphologically highly similar set of taxa.

    Two separate taxa were recognised within the type variety Ph. exiguavar. exigua. In the following chapter these taxa are described and all species and varieties in this complex are recombined into the new genus Boeremia.

    Chapter 5provides further details about the taxonomy and phylogeny of the species of interest, with a special focus on the taxa that are phylogenetically placed with Didymellaceae. In total 206 taxa were treated, of which 159 have affinities with Phoma.

    The genus is circumscribed in the first section of this chapter. The phylogeny was reconstructed using 28S nrDNA (Large Subunit) and 18S nrDNA (Small Subunit) sequence data. It was shown that the currently used Boeremaean subdivision of the phomoid taxa and the phylogeny were inconsistent, as the genus was highly polyphyletic. Species belonging to the form-genus Phomawere retrieved in as much as six distinct clades within Pleosporales. These clades even represent different families. The majority of the phomoid taxa, including the type species Ph. herbarumand most exponents of the sections Macrospora, Peyronellaea, Heterospora, and Phyllostictioides, were found in a single clade that represented the Didymellaceae. Most species that are associated with the Phomasections Plenodomusand Pilosacluster with the Leptosphaeriaceaeand Pleosporaceaeclades. Furthermore, some species were also found to cluster in the Sporormiaceaeand Cucurbitariaceaeclades.

    In the second part of this chapter, the phylogenetic variation of the species and varieties in Didymellaceaeis further assessed, using a phylogenetic reconstruction that is based on DNA sequences of the Large Subunit, ITS, and part of the β-tubulin (TUB) gene region. Besides the teleomorph genus Didymella, members of the teleomorph genera Leptosphaerulinaand Macroventuriawere also found to cluster in this clade. Based on the reconstructed phylogeny, Didymellaceaesegregate into at least 18 distinct clusters, of which many can be associated with specific morphological characters. Furthermore, a number of taxa did not match any of these clusters, suggesting that an evolutionary correct subdivision of the Phomaspecies in Didymellaceaeis even more complex. Taxa in four of these phylogenetic clusters were also defined well enough by means of morphology to elevate these groups to new or reinstalled genera, namely Stagonosporopsis, Epicoccum, Boeremiaand Peyronellaea. A total of 61 taxa were recombined and several new species of Phomawere introduced, namely Ph. brasiliensis, Ph. bulgarica, Ph. dactylidis, Ph. dimorpha, Ph. longicolla, Ph. minor, Ph. pedeiaeand Ph. saxea. Furthermore, two new varieties were described, Boeremia exigua var. gilvescensand B. exigua var. pseudolilacis.

    Finally, the results presented in this dissertation are highlighted and discussed inChapter 6. In total 13 species of Phomaand two taxa at varietal level were newly described during the course of this study. Moreover the taxonomic status of species in the form-genus Phomawere further clarified, and insight provided into the phylogenetic status of Didymellaceae, a fungal family that was recently established, comprising most species of Phoma, Ascochytaand Didymella. All macro- and micromorphological data obtained in this study, as well as the DNA sequences, were placed online in a publicly available polyphasic identification database (www.q-bank.eu). This will enable scientists and institutes involved in plant health to correctly identify phomoid species. Rapid identification of these species based on the tools and data generated in this study, can facilitate swift clearing of plant material and arable products during export and import, and prevent the spread of quarantine organisms.

    Ontwikkelingen in naamgeving en registratie van cultuurplanten
    Hoffman, M.H.A. - \ 2013
    Dendroflora (2013)50. - ISSN 0374-7247 - p. 28 - 45.
    houtachtige planten als sierplanten - boomkwekerijen - gewaskwaliteit - registratie - rassen (planten) - taxonomie - beschrijvingen - fruitgewassen - siergewassen - plantenveredeling - cultivars - handelsmerken - kwekersrecht - nomenclatuur - ornamental woody plants - forest nurseries - crop quality - registration - varieties - taxonomy - descriptions - fruit crops - ornamental crops - plant breeding - cultivars - trade marks - breeders' rights - nomenclature
    Een correcte en eenduidige naamgeving van onze boomkwekerijgewassen is van groot belang voor de groensector. Het is immers een belangrijk middel voor de garantie van soortechtheid en is daarmee een wezenlijk onderdeel van de plantkwaliteit. In dit artikel staan nieuwe ontwikkelingen weergegeven vanuit de wetenschap, de wetgever en het bedrijfsleven. Het bouwt voort op twee eerder geschreven artikelen in Dendroflora over naamgeving van planten (1999) en classificatie van planten (2008). In het eerste deel van dit artikel wordt een aantal items en ontwikkelingen uit enkele voorgaande artikelen genoemd en in een historisch perspectief gezet. In het tweede deel wordt ingegaan op de wettelijke registratie van plantenrassen. Vooral in de registratie van fruitrassen zijn er flinke veranderingen en daarnaast dreigen op termijn soortgelijke ontwikkelingen in de registratie van siergewassen. Dergelijke wetgeving heeft grote invloed op de teelt en handel van tuinbouwgewassen. In het derde deel wordt ingegaan op de ontwikkelingen in de naamgeving van cultuurplanten vanuit de wetenschap. Vorig jaar is een symposium geweest waarin veel zaken besproken en bediscussieerd zijn. Op basis hiervan wordt de regelgeving van de Cultuurplantencode (ICNCP) aangepast. Opgestelde regels of richtlijnen voor nieuwe categorieën zoals de grex, series en zaadmengsels en cultivartypes worden besproken. Tenslotte komen in het vierde deel enkele werkwijzen en voorbeelden uit de praktijk aan de orde. Voorbeelden zijn de intensivering van veredeling, de diversiteit en wildgroei in gebruik van handelsnamen, het niet vermelden van de cultivarnaam, het merkenrechtelijk beschermen van de cultivarnaam en het gebruik van diverse symbolen om verschillende types van bescherming aan te geven
    Phytopathogenic Dothideomycetes
    Crous, P.W. ; Verkley, G.J.M. ; Groenewald, J.Z. - \ 2013
    Utrecht, The Netherlands : CBS-KNAW Fungal Biodiversity Centre (Studies in mycology 75) - ISBN 9789070351960 - 406
    dothideomycetes - plantenziekteverwekkende schimmels - taxonomie - fylogenie - gastheerreeks - alternaria - cercospora - phoma - pseudocercospora - septoria - nieuwe soorten - nieuw geslacht - dothideomycetes - plant pathogenic fungi - taxonomy - phylogeny - host range - alternaria - cercospora - phoma - pseudocercospora - septoria - new species - new genus
    This volume of Studies in Mycology is dedicated to the plant health officers of the world, who are constantly confronted by a range of plant pathogenic fungi that cause devastating diseases of agricultural and forestry crops. Five main groups of fungi are dealt with, namely Alternaria, Cercospora, Phoma, Pseudocercospora and Septoria. In the first paper Phoma sections Plenodomus, Heterospora and Pilosa were reinvestigated, resulting in the introduction of several novel genera and species. The second paper deals with the paraphyletic genus Pseudocercospora; host specificity was considered for 146 species of Pseudocercospora occurring on 115 host genera from 33 countries. From these results we concluded that the application of European and American names to Asian taxa, and vice versa, was often not warranted. The third paper deals with the genus Cercospora, which contains more than 5 000 different species. Isolates used in the molecular phylogeny were obtained from 161 host species, 49 host families and 39 countries. Although some species were found to host-specific, others were isolated from a wide host range. The fourth paper deals with phylogenetic lineages within the genus Alternaria, which was revealed to represent a well-supported node containing 24 internal clades and six monotypic lineages. Several genera were placed in synonymy with Alternaria, for which 16 new sections were proposed. Two papers deal with the genus Septoria, which was shown to be poly- and paraphyletic, leading to the introduction of 15 new genera, and more than 40 new species. Although some species were shown to be highly specific, other taxa were revealed to occur on hosts in more than six different plant families. For all taxa investigated multi-gene DNA data were deposited in GenBank and other databases to expedite future identification of these plant pathogenic fungi. No single locus was found to be the ideal DNA barcode gene for these taxa, and species identification will have to be based on a combination of gene loci and morphological characters.
    Cultivation and diseases of Proteaceae: Leucadendron, Leucospermum and Protea
    Crous, P.W. ; Denman, S. ; Taylor, J.E. ; Swart, L. ; Bezuidenhout, C.M. ; Hoffman, L. ; Palm, M.E. ; Groenewald, J.Z. - \ 2013
    Utrecht, The Netherlands : CBS-KNAW Fungal Biodiversity Centre (CBS biodiversity series 13) - ISBN 9789070351953 - 360
    proteaceae - leucadendron - leucospermum - protea - snijbloemen - teelt - plantenziekten - plantenziekteverwekkende schimmels - taxonomie - identificatie - determinatietabellen - gastheerreeks - plantenziekteverwekkende bacteriën - ziektebestrijding - fytosanitair beleid - verwelkingsziekten - wortelrot - kanker (plantenziektekundig) - proteaceae - leucadendron - leucospermum - protea - cut flowers - cultivation - plant diseases - plant pathogenic fungi - taxonomy - identification - keys - host range - plant pathogenic bacteria - disease control - phytosanitary policies - wilts - root rots - cankers
    Proteaceae represent a prominent family of flowering plants in the Southern Hemisphere. Because of their beauty, unique appearance, and relatively long shelf life, Proteaceae cut-flowers have become a highly desirable crop for the export market. The cultivation of Proteaceae is a thriving industry that provides employment in countries where these flowers are grown, often in areas that are otherwise unproductive agriculturally. Diseases cause a loss in yield, and also limit the export of these flowers due to strict phytosanitary regulations. In this publication the fungi that cause leaf, stem and root diseases on Leucadendron, Leucospermum and Protea are treated. Data are provided pertaining to the taxonomy, identification, host range, distribution, pathogenicity, molecular characteristics and control of these pathogens. Taxonomic descriptions and illustrations are provided and keys are included to distinguish species in genera where a number of species affect Proteaceae. Disease symptoms are described and colour photographs are included. Where known, factors that affect disease epidemiology are discussed. Disease management strategies are also presented that will assist growers and advisors in making appropriate choices for reducing disease in specific areas. Information is also provided relating to crop improvement, cultivation techniques, harvesting and export considerations. Further development and expansion of this industry depends on producing and obtaining disease-free germplasm from countries where these plants are indigenous. For that reason it is important to document the fungi that occur on Proteaceae, and to establish the distribution of these fungi. These data are essential for plant quarantine services for use in risk assessments.
    Loofbomen in Nederland en Vlaanderen : soorten en hybriden
    Goudzwaard, L. - \ 2013
    Zeist : KNNV - ISBN 9789050114325 - 432
    loofhout - bosbomen - bomen - soorten - identificatie - foto's - habitus - vlaanderen - nederland - taxonomie - broadleaves - forest trees - trees - species - identification - photographs - habit - flanders - netherlands - taxonomy
    Loofbomen van Nederland en Vlaanderen beschrijft 268 verschillende boomsoorten en hybriden en 400 verschillende variëteiten waaronder tal van boomgeslachten, zoals Acer (esdoorn), Fagus (beuk), Magnolia, Malus (appel) en Quercus (eik), maar ook minder bekende boomsoorten, zoals venkelhout (Sassafras albidum) en lederboom (Ptelea trifoliata).H erkenning, gebruik en ziektegevoeligheid komen aan bod, maar ook de geschiedenis van het boomgeslacht en de plaatsen waar prachtige exemplaren van de soort te zien zijn. In dit boek leest u waar u complete collecties van boomgeslachten kunt bekijken, evenals monumentale bomen.
    Revised taxonomy of Phoma and allied genera
    Gruyter, J. de - \ 2012
    Wageningen University. Promotor(en): Pedro Crous; Pierre de Wit. - S.l. : s.n. - ISBN 9789461733887 - 180
    phoma - taxonomie - classificatie - pleosporales - moleculaire detectie - moleculaire fylogenetica - moleculaire taxonomie - phoma - taxonomy - classification - pleosporales - molecular detection - molecular phylogenetics - molecular taxonomy

    The anamorphic genus Phoma includes many important plant pathogens. The identification of Phoma species based on studies in pure culture is difficult and time consuming and the in vitro characters are often variable. Moreover, the present classification of Phoma species
    into sections is ambiguous and morphological characters are shared with related genera. In the present study the molecular phylogeny of species of Phoma and allied genera was examined and the results obtained were used to revise the taxonomy. The DNA sequence data obtained provide tools for the development of detection and identification methods.
    Chapter 1 provides a general introduction of the anamorph genus Phoma and the research that has been performed in The Netherlands during the last decades is described. Phoma is characterised by producing hyaline conidia in fruiting bodies called pycnidia. The genus includes
    many important plant pathogens. The taxonomy of Phoma has been studied intensively at the Plant Protection Service in the Netherlands for more than 50 years, resulting in the development of a generic concept in 1997 as an outline for identification of Phoma species. In this concept species of the genus Phoma are classified based on their morphological characters into the nine sections Phoma, Heterospora, Macrospora, Paraphoma, Peyronellaea, Phyllostictoides, Pilosa, Plenodomus and Sclerophomella. The species placed in each of the sections were
    systematically described culminating in the publication of the “Phoma Identification Manual” in 2004, with the descriptions of 223 specific and infra-specific taxa of Phoma, and more than 1000 synonyms in other coelomycetous genera. In the Netherlands the late Gerhard Boerema, former head of the Mycology Department at the Plant Protection Service, has been the driving
    force behind this Phoma research for decades.
    The Phoma Identification Manual is a valuable tool for the morphological identification of isolates, but in vitro studies are very time consuming and need a high level of expertise.
    Moreover, the classification of Phoma species in sections based on morphological characters appeared artificial and several species can be classified in more than one section because of their multiple “section-specific” characters. In addition, distinctive characters of Phoma sections are shared among morphologically related coelomycetous genera including Ascochyta, Asteromella, Microsphaeropsis, Phomopsis, Phyllosticta, Pleurophoma, Pyrenochaeta and Stagonospora. Phoma sections are related to diverse teleomorph genera including Didymella,
    Leptosphaeria, Mycosphaerella and Pleospora. Synanamorphs of Phoma species have been
    recognised amongst the genera Phaeomoniella, Stagonosporopsis, Epicoccum, Phialophora
    and Sclerotium illustrating their heterogeneity.
    A large, well-studied Phoma culture collection established at the Plant Protection Service and the “Centraalbureau voor Schimmelcultures” includes more than 1100 strains of Phoma species. This collection formed the basis of an intensive molecular phylogenetic study of the genus Phoma and morphologically similar genera, which commenced in 2006. Furthermore, a literature study identified sequences of genes that are suitable for phylogenic studies and elucidation of the evolutionary history of the genus Phoma.
    Several potentially informative regions of the genome were sequenced in the first phase
    of the project as has been described in chapters 2–4. The phylogeny and DNA sequence data obtained have provided tools for the development of fast and reliable molecular detection and identification methods. The development of Real-time TaqMan PCR methods for the detection and identification of two important plant pathogenic (quarantine) species formerly described in Phoma, Stagonosporopsis andigena and S. crystalliniformis, is described in Chapter 5.
    In chapter 2 several genes were studied to elucidate the molecular phylogeny of Phoma and allied genera. Sequence data of the 18S nrDNA (SSU) and 28S nrDNA (LSU) regions of the type species of the Phoma sections and morphologically similar coelomycetes and related teleomorphs were compared. The results justified the introduction of the new family Didymellaceae to
    accommodate the generic type species Didymella exigua and Phoma herbarum. The type species of the Phoma sections Phyllostictoides, Sclerophomella, Macrospora and Peyronellaea also grouped in Didymellaceae.
    The generic type species Ascochyta pisi and Microsphaeropsis olivacea also grouped in
    Didymellaceae and it shows that these genera are closely allied to Phoma. The type species of Phoma sections Heterospora, Paraphoma, Pilosa and Plenodomus grouped in various families outside Didymellaceae and were subject of following studies.
    Chapter 3 provides a molecular phylogenetic re-evaluation on Phoma-like species that appeared only distantly related to the generic type species Phoma herbarum and its related Didymella teleomorph (Didymellaceae). Phoma section Paraphoma, characterised by setose pycnidia, resembles species of Pyrenochaeta and Pleurophoma. Sequence data from the SSU and LSU regions of the species classified in Phoma section Paraphoma were compared with those of representative isolates of Pyrenochaeta and Pleurophoma, and with those of the type
    species of the Phoma sections Phoma, Pilosa and Plenodomus. Unnamed, often sterile Phomalike
    strains in the collections were included. The molecular phylogeny of species that were classified in Phoma section Paraphoma appeared to be highly polyphyletic and a thorough reclassification of the species is provided. Paraphoma was reinstalled and grouped with the new
    genera Neosetophoma and Setophoma in Phaeosphaeriaceae. Pyrenochaeta and the new genus
    Pyrenochaetopsis, including mainly taxa formerly described in Phoma section Paraphoma, were closely allied in Cucurbitariaceae.
    In chapter 4 the molecular phylogeny of species of Phoma sections Plenodomus, Pleospora and Heterospora was determined using LSU, SSU and ITS. In a “one species = one name” approach, the species described in Phoma section Plenodomus and its teleomorph Leptosphaeria
    were reclassified in Leptosphaeria, Plenodomus and the new genera Paraleptosphaeria and Subplenodomus in Leptosphaeriaceae. Two species of Phoma section Heterospora, the type species Phoma heteromorphospora and its allied species Ph. dimorphospora, were transferred
    to the new genus Heterospora that also grouped in Leptosphaeriaceae. Leptosphaeria doliolum
    comprises a species complex that was revised based on multilocus sequence data of LSU, ITS,
    SSU, ß-tubulin, and chitin synthase 1. The molecular phylogeny of species classified in Ascochyta
    and Phoma, section Pilosa in Pleosporaceae that produce morphologically similar pilose pycnidia, was determined based on analysis of actin sequence data. Several Phoma-like species
    grouped outside the suborder Pleosporineae in a LSU sequence analysis and were transferred
    to the genera Aposphaeria (Melanommataceae), Paraconiothyrium (Montagnulaceae) and Westerdykella (Sporormiaceae). Coniothyrium palmarum and related species were described in Coniothyriaceae. The new genera Medicopsis (Trematosphaeriaceae) and Nigrograna, of which the family is still unknown, are introduced to accommodate two medically important
    species formerly classified in Pyrenochaeta.
    In chapter 5 specific real-time (TaqMan) PCR assays were developed for the detection of the pathogens Stagonosporopsis andigena and S. crystalliniformis in leaves of potato and tomato.
    The molecular phylogeny with related species of Stagonosporopsis, Boeremia and Phoma based on sequence polymorphisms in the actine gene, was determined. The reliability of the DNA extraction and TaqMan PCRs for the detection of S. andigena and S. crystalliniformis in leaf material was tested in performance studies and demonstrated the specificity, analytical
    sensitivity, reproducibility, repeatability and robustness of both assays.

    Characterization of African Bush Mango trees with emphasis on the differences between sweet and bitter trees in the Dahomey Gap (West Africa)
    Vihotogbe, R. - \ 2012
    Wageningen University. Promotor(en): Marc Sosef; B. Sinsin, co-promotor(en): Ronald van den Berg. - [S.l. : S.n. - ISBN 9789461734129 - 189
    irvingia - domesticatie - bomen - plantenmorfologie - plantengeografie - genetische diversiteit - taxonomie - smaken - benin - west-afrika - irvingia - domestication - trees - plant morphology - phytogeography - genetic diversity - taxonomy - tastes - benin - west africa

     African bush mango trees (ABMTs) are economically the most important species within the family of Irvingiaceae. They are priority trees producing non-timber forest products (NTFPs) and widely distributed in the humid lowland forests of West and Central Africa. To boost their production and develop them towards a major crop for rural communities in Africa, a domestication program was initiated in the 2000s which is being coordinated by the World Agroforestry Centre. ABMTs belong to two taxa, one with sweet and one with bitter fruits which are morphologically difficult to distinguish. The fresh mesocarp of the sweet bush mangoes are consumed, while the seed of both bitter and sweet fruits are an important component of the African diet. The high oil content of this seed further increases their potential use.

     Apart from the overlap of their morphological characters, the ecological and phenological distinction between sweet and bitter ABMTs is unclear due to: (i) the lack of comparative quantitative data and (ii) the lack of centralizing the existing country-level databases. Therefore, their taxonomic status is still not clear. Do they represent distinct species or varieties or are they mere forms within the same gene pool? It is also unclear whether the occurrence of ABMTs in traditional agroforestry systems in the Dahomey Gap, the dry savannah corridor between the Upper and Lower Guinean rain forest blocks, forms part of the natural distribution or not . Moreover, genetic studies addressing ABMTs diversity have been geographically restricted, and conclusions regarding the taxonomic status of sweet and bitter trees were not unanimous.

    This study was conducted in a perspective of developing suitable strategies for the conservation and use of ABMTs, mostly in the Dahomey Gap. First, differences in ethnobotanical knowledge of the major socio-cultural groups in the Dahomey Gap were linked to the agroforestry status of ABMTs. This was used to explain the characteristics of the spatial pattern of ABMTs abundance and the anthropogenic factors that govern this spatial structure as well as population survival in the Dahomey Gap. Second, occurrence data of wild and cultivated ABMTs were used in a species distribution modelling algorithm to calculate the niche space and potential distribution of bitter and sweet trees in Tropical Africa. The differences in the obtained distribution patterns were compared using ENM-Tools. Third, detailed monthly phenological data and morphological characteristics (qualitative as well as quantitative measurements on the leaves, bark, fruits, and seeds) were used to analyse the diversity of ABMTs and to discover differences between them in order to be able to identify bitter and sweet trees in the field. Finally, the molecular markers AFLP and cpSSR were used in order to map the genetic diversity of ABMTs and to discriminate sweet and bitter trees across Togo, Benin, Nigeria and Cameroon.

    The consumption of mesocarp and seed of bush mangoes is widely known throughout the Dahomey Gap. The level of knowledge within local communities of other types of uses (medical, social-cultural) is generally poor and decreases towards the western part of this region. This suggests that ABMTs (mostly the sweet trees) were introduced in this eco-region through the migration of human populations from the Lower Guinean forest block (Southeast Nigeria) to the West. In the Dahomey Gap, bitter trees are confined to the Volta forest region, a small-sized ecological area in south-western Togo. While low densities (< 462 trees per 25 ha) were recorded for wild bitter trees occurring in the Volta forest region, higher densities (up to 1020 trees per 25 ha) were found for sweet trees in human made agro-systems. This implies a clear difference in cultivation methods between bitter and sweet ABMTs. The intensive cultivation of ABMTs in the Dahomey Gap is influenced by farmland status, farmer’s socio-cultural group and type of ABMT. Small and exhausted farmlands are converted into sweet ABMT orchards indicating that their development is a small-scale process lead by individual farmers. Slash and burn agriculture and intensive collection of fruits for seed commercialization jeopardize bitter trees, while traditional fishing systems (using twigs), traditional mass selection strategy, and intensive land commercialization severely threaten sweet trees genetic resources.

    Using species distribution modelling, the potential distribution of wild sweet trees was predicted in the wetter zones of the Guinean-Congolian phytogeographical region, while that of bitter trees extended to drier zones in the Guineo-Congolia/Sudania and Lake Victoria regions. This difference is significant, supporting the idea that bitter and sweet trees belong to two different species. In the Dahomey Gap, bitter trees occur in the wild in the wettest ecological region of the Volta forest region which is a very small part of the Dahomey Gap. This region is ecologically particular among the ecosystems in which wild bitter trees generally occur. We also conclude that in the Dahomey Gap sweet trees occur only in cultivation.

    Within the Dahomey Gap, clear phenological differences exist between sweet and bitter ABMTs, mostly in their reproduction phases. Moreover, their reproductive success significantly depends on the type of ABMT, soil, climate and season and we conclude there is a low probability of hybridization between sweet and bitter trees in the area where they co-occur.

    The qualitative morphological characters, the type of bark, colour of the mature fruit exocarp and mesocarp, and fruit roughness, do not consistently discriminate bitter and sweet trees in the field. We strongly recommend broadening the geographic area of this study by increasing more bitter trees as well as the wild samples of both taxa to validate this conclusion. The bitter trees in the Volta forest region produce the heaviest seeds and this consistently distinguishes them from all the sweet trees sampled in the Dahomey Gap. However, a combination of quantitative morphological characters (from fruits, mesocarp, and seeds) failed to discriminate populations. On the other hand this indicates the presence of a high diversity and thus high potential for selection across all phytogeographical regions. However, domestication and climate appear to be playing a key role in the morphological differentiation of Dahomey Gap populations, and evidence of success in the traditional domestication and selection of sweet trees is proven.

     Low genetic diversity was found for the bitter trees occurring in the Volta forest region in the Dahomey Gap due to the high fragmentation of the small-sized forest ecosystem in which they occur and the continuous reduction of the population size. The higher polymorphism and genetic diversity observed in the sweet tree population in Benin and Togo indicate the effect of domestication of material from different geographical origins as well as a frequent long distance transfer of genetic material. When used separately, the AFLP and cpSSR data failed to consistently discriminate geographical populations and bitter from sweet trees. But a combined dataset of both markers tends to differentiate such populations as well as tree types. Our results also provide evidence that the suitability of AFLPs and cpSSRs to assess genetic diversity patterns in Irvingia material needs to be thoroughly reassessed.

    Finally, although admitting that a broader study remains necessary, based on the presence of a consistent gap between both taxa regarding their reproductive periods, their different ecology and, of course, the consistent difference in taste of the fruit, we advise to treat the sweet and bitter ABMTs as two taxonomically different entities at species level: Irvingia gabonensis (Aubry-LeComte ex O’Rorke) Baill. and I. wombolu Vermoesen, respectively.

    An ecogeographic analysis of Oryza series Sativae in Asia and the Pacific
    Banaticla-Hilario, M.C.N. - \ 2012
    Wageningen University. Promotor(en): Marc Sosef, co-promotor(en): Ronald van den Berg; K.L. McNally. - S.l. : s.n. - ISBN 9789461733788 - 237
    oryza - oryza sativa - oryza nivara - genetische bronnen van plantensoorten - plantengeografie - plantenecologie - diversiteit - in-situ conservering - plantenmorfologie - taxonomie - genetica - genenbanken - azië - oryza - oryza sativa - oryza nivara - plant genetic resources - phytogeography - plant ecology - diversity - in situ conservation - plant morphology - taxonomy - genetics - gene banks - asia

    The non-cultivated speciesof the genus Oryza can provide a genetic arsenal of useful traits for improving the widely cultivated and consumed Asian rice (O. sativa). The diversity of these valuable plant resources must be well understood to ensure their effective in- and ex-situ conservation. In this thesis, we examined the ecogeographic variations within and between the three species of Oryza series Sativae in Asia and the Pacific. We looked at species differentiation from different spatial scales by analysing sympatric accession pairs of O. meridionalis and O. rufipogon and of O. nivara and O. rufipogon.

    We conducted phenotypic analyses in Chapter 2. The strong influence of ecology on species morphology was demonstrated in the ordination and cluster analyses results where O. meridionalis and O. nivara grouped together and were separated from O. rufipogon. We detected greater differentiation of O. nivara and O. rufipogon in South Asia and positive correlations between spatial and intraspecific (interpopulation) morphological distances in continental Asia. We found significant correlations between geoclimatic factors and certain character measurements within species and observed that seedling height, culm number and diameter, leaf size, and anther length exhibit contrasting responses for O. nivara and O. rufipogon. We confirmed significant morphological differences between the three species, between the South and Southeast Asian populations of O. nivara, and between the Australasian and the non-Australasian populations of O. rufipogon and provided botanical descriptions to delineate O. meridionalis, O. nivara and O. rufipogon morphologically.

    In Chapter 3, we genotyped the same set of accessions with 29 SSR markers and applied a variety of methods for genetic diversity analysis. Based on ordination and phylogenetic results, we verified that O. meridionalis is a genetically distinct species and that O. nivara and O. rufipogon overlap genetically across their geographic distribution. However, Bayesian clustering analysis recognized local-scale species separation of O. nivara and O. rufipogon implying stronger interspecific gene flow barriers in smaller spatial units. Concurrently, AMOVA indicated that the bulk (64%) of genetic variation in Asia Pacific series Sativae can be found among accessions and the lesser portions within accessions (26%) and among species (10%). We captured contrasting intraspecific variation patterns for O. nivara and O. rufipogon where the former exhibited low diversity, high population differentiation and isolation by distance mainly in South Asia while the latter displayed high diversity, low population differentiation and isolation by distance primarily in continental Southeast Asia. We established that altitude is correlated negatively to accession diversity and positively to local-scale species differentiation. Using Bayesian inference, we identified eight genetically distinct population groups: C1) Indian and Bangladeshi O. nivara; C2) Cambodian O. nivara; C3) Southeast Asian O. rufipogon; C4) O. meridionalis; C5) Nepalese O. nivara; C6) non-Cambodian Southeast Asian O. nivara; C7) Australasian O. rufipogon; and C8) South Asian O. rufipogon. Cluster analysis grouped the aromatic and japonica cultivar groups of O. sativa with O. rufipogon in South Asia and the indica and aus groups with O. nivara from Thailand and Cambodia, respectively. O. nivara from Nepal seemed genetically isolated from the other population groups. We also detected variation patterns that agreed with the results in Chapter 1 such as the South and Southeast Asian divisions of O. nivara, the divergence of Australasian populations from the rest of O. rufipogon and the greater differentiation of O. nivara and O. rufipogon in South Asia.

    In Chapter 4, we conducted artificial crossing experiments to 15 selected parental accessions of O. meridionalis, O. nivara, and O. rufipogon and assessed the extent of several post-pollination isolating mechanisms in Oryza series Sativae. We observed reproductive incompatibility within and between the inbreeding species O. meridionalis and O. nivara and high intraspecific crossability of the outcrossing O. rufipogon where viable and non-sterile F1 hybrids were produced only by combinations with a parental distance that ranged from 1062 to 3813 kilometers. Insular Southeast Asian and/or Australasian accessions of O. rufipogon were the most reproductively successful parents. O. rufipogon exhibited significant pre-zygotic species isolation (in terms of seed set) and reduced post-zygotic isolation, and seemed symmetrically compatible with O. nivara and asymmetrically compatible with O. meridionalis. We obtained few annual hybrids with relatively high fertilities from crosses between O. rufipogon and O. nivara and numerous perennial hybrids with low fertilities from crosses between O. rufipogon and O. meridionalis. Crossability estimates did not show significant correlations with geographic distance between parents. However, we discerned reduced seed set and F1 fertility in interspecific combinations with sympatric parents compared to crosses with non-sympatric parents, indicative of reinforced species isolation in sympatry. We evaluated the F1 offspring of different cross combinations and found a mixture of intermediate and parental character traits in interspecific hybrids.

    We discussed the taxonomic implications of the research results in Chapter 5 where we specifically dealt with the opposing views of lumping or splitting of O. nivara and O. rufipogon. We concluded that these two taxadeserve to be treated as separate species based on the following biosystematic evidence obtained from the thesis: 1) ecological distinction; 2) considerable prezygotic barriers; 3) opposing patterns of gene flow and genetic variation; 4) local-scale genetic divergence and 5) enhanced reproductive barriers under sympatric conditions. We identified ecogeography as a major driving force in the diversification of Oryza series Sativae in Asia and the Pacific and suggested that ecological speciation gave rise to O. nivara and O. rufipogon. We also presented recognizable geographic races within species.

    Ultimately in Chapter 6, we emphasized the importance of our study in several aspects of rice science and identified results that agreed with prior Oryza diversity studies. At the same time, we presented previously unreported morphological and genetic variation patterns that were established in this thesis. We discussed the possible applications of the research results to wild rice conservation, covering in situ strategies as well as gene bank practices. We also highlighted the potential role of O. nivara in Asian rice domestication where it could have either directly given rise to the indica cultivar group or hybridized/introgressed with migrated japonica cultivars in India, eventually leading to the development of indica.

    The genus Gloriosa (Colchicaceae) : ethnobotany, phylogeny and taxonomy
    Maroyi, A. - \ 2012
    Wageningen University. Promotor(en): Jos van der Maesen, co-promotor(en): Lars Chatrou. - S.l. : s.n. - ISBN 9789461732446 - 190
    gloriosa - taxonomie - fylogenie - etnobotanie - zaden - plantensamenstelling - knollen - colchicine - economische botanie - gloriosa - taxonomy - phylogeny - ethnobotany - seeds - plant composition - tubers - colchicine - economic botany
    This thesis focuses on the ethnobotany, phylogeny and taxonomy of the genus Gloriosa L. over its distributional range. Some Gloriosa species are known to have economic and commercial value, but the genus is also well known for its complex alpha taxonomy. An appropriate taxonomy for this group is of great importance because it includes widely used species as traditional medicine, horticultural plants and sources of industrial and pharmaceutical chemical colchicine. The seeds and tubers of G. superba are valued as a commercial source of colchicine. The genus Gloriosa has considerable horticultural appeal because of the conspicuous inflorescence of its members and the ease with which taxa are propagated, introduced into new areas and hybridise in cultivation. G. carsonii, G. modesta, G. simplex and G. superba have been taken into cultivation as ornamental plants in several countries, including native countries of these species.
    Plant Resources of Tropical Africa 16 Fibres
    Brink, M. ; Achigan-Dako, E.G. - \ 2012
    Wageningen, Netherlands : PROTA Foundation/CTA (Plant resources of tropical Africa 16) - ISBN 9789290814818 - 602
    vezelgewassen - plantenvezels - soorten - genetische bronnen van plantensoorten - plantengeografie - plantenmorfologie - biologische naamgeving - taxonomie - plantenvermeerdering - tropisch afrika - fibre plants - plant fibres - species - plant genetic resources - phytogeography - plant morphology - biological nomenclature - taxonomy - propagation - tropical africa
    This volume deals with the fibres of Tropical Africa. 515 ‘primary use’ fibres are described in 248 review articles. Many of the articles are illustrated with a geographic distribution map and a line drawing of the habit.
    Sortiment Abelia is volop in beweging
    Hoffman, M.H.A. - \ 2012
    De Boomkwekerij 25 (2012)8. - ISSN 0923-2443 - p. 12 - 13.
    houtachtige planten als sierplanten - abelia - rassen (planten) - cultivars - soortendiversiteit - taxonomie - ornamental woody plants - abelia - varieties - cultivars - species diversity - taxonomy
    Binnen het geslacht Abelia vinden veel ontwikkelingen plaats. Op het gebied van taxonomie zijn nieuwe inzichten, waardoor veranderingen in namen komen. Ondertussen zorgt sortimentsvernieuwing ook voor veel nieuwe namen binnen de productgroep. Het Productschap Tuinbouw liet PPO de ontwikkelingen in kaart brengen.
    Systematics of the blackfly subgenus Trichodagmia Enderlein (Diptera: Simuliidae: Simulium) in the new world
    Hernández Triana, L.M. - \ 2011
    Wageningen University. Promotor(en): Marc Sosef; R.J. Post. - s.n. - ISBN 9789085858652 - 536
    simulium - taxonomy - identification - keys - nearctic region - simulium - taxonomie - identificatie - determinatietabellen - nearctisch gebied

    Systematics of the blackfly subgenus Trichodagmia ENDERLEIN (Diptera: Simuliidae:

    Simulium) in the New World

    The systematics of the New World subgenus Trichodagmia has been reassessed by employing an

    integrated taxonomic approach based upon revisionary taxonomy, phylogenetic (cladistics) analysis, and

    DNA barcoding. This subgenus included several species of great medical importance, which are all

    morphologically very similar. The history of the taxonomy and classification of the subgenus

    Trichodagmia has been put into context with other subgenera within New World Simuliidae, while

    descriptions and keys to the identification of species in this subgenus are also given.

    The subgenus Obuchovia is here considered a new junior synonym of Trichodagmia, and all its

    constituents’ species are now placed in the ALBELLUM species group to represent a Palaearctic

    element within this subgenus. Three new junior synonymies are here proposed: Simulium chiriquiense

    FIELD is a synonym of S. ethelae DALMAT n. syn.; S. biuxinisa COSCARÓN & IBÁÑEZ-BERNAL is a

    synonym of S. paynei VARGAS n. syn.; and S. keenani FIELD is a synonym of S. earlei VARGAS, MARTÍNEZ

    PALÁCIOS &DÍAZ NÁJERA n. syn. A neotype is designated for S. lahillei (PATERSON & SHANNON) and a

    lectotype for S. pulverulentum KNAB.1 Simulium falculatum ENDERLEIN is transferred from the

    TARSATUM species group of to the CANADENSE species group based on the morphology of the

    female genitalia. Two species, S. rivasi RAMÍREZ PÉREZ and S. oviedoi RAMÍREZ PÉREZ, are transferred

    from the TARSATUM species group to the subgenus Psilopelmia based on the morphology of the male

    gonostyle and the ventral plate. Keys to separate all species groups and species based on the adults,

    pupae and larvae are also provided.

    The phylogeny and classification of the subgenus Trichodagmia is delineated using a cladistic

    analysis of 63 taxa based on males, females, pupae and larvae, including two species belonging to the

    subgenus Aspathia and two species of the subgenus Simulium s.str. that served as outgroups. Analysis of

    the original full data set [67 taxa and 67 characters] with multistate characters treated as unordered

    under equal weights led to poorly resolved trees, with many polytomies within TARSATUM [= old

    subgenus Hemicnetha] and CANADENSE [= old subgenus Hearlea]. Nonetheless, the ALBELLUM [=

    old subgenus Obuchovia] and PICTIPES [= old subgenus Shewellomyia] species groups, and some clades

    within the CANADENSE species group were well supported. In the most parsimonious cladograms,

    the position of S. falculatum was problematic as it was placed basal to Trichodagmia. The position of S.

    jeteri, albeit within the ORBITALE [= old subgenera Trichodagmia + Thyrsopelma of MIRANDA-ESQUIVEL

    & COSCARÓN, 2001] clade, was also poorly resolved. This was certainly due to the numerous missing

    data in these two taxa. Therefore, they were removed from the data set together with other taxa in

    which three life stages (> 70% of characters) were missing (e.g. S. paracarolinae and S. tarsale). A second

    analysis was then performed with 63 taxa and 67 characters. In this analysis, the Strict Consensus Tree

    was better resolved and certain clades within the expanded concept of Trichodagmia (sensu SHELLEY et al.,

    2010) were recovered as monophyletic with high support values. The ALBELLUM species group is

    monophyletic in a sister-group relationship with the other species groups in Trichodagmia (sensu SHELLEY

    et al., 2010). The ORBITALE species group clade was recovered as monophyletic by a unique

    combination of seven characters with 89% bootstrap support. In this clade, all species close to S.

    guianense s.l. were better diagnosed by a combination of four characters, one of which (male ventral plate

    with a globular median process) was unique to this group. The position of S. hirtipupa is better resolved

    in the latter clade by the presence of black spiniform setae in the frontoclypeus and thorax of the pupa.

    In contrast, the TARSATUM and CANADENSE species groups were diagnosed by only four

    and five characters, respectively. Within the CANADENSE species group only species with larvae

    having sclerotized plates in the posterior region of the abdomen were well resolved. Species in the

    TARSATUM group were homoplastic. The PICTIPES group is only diagnosed by homoplasies, but the

    combination of these characters is unique to this clade (polythetic taxon). In general, this study supports

    some of the taxonomic changes proposed in SHELLEY et al. (2010), in which the subgeneric-names

    Hearlea, Hemicnetha, Shewellomyia, Trichodagmia + Thyrsopelma (sensu MIRANDA-ESQUIVEL & COSCARÓN,

    502

    2001) are treated as species groups within the subgenus Trichodagmia. Moreover, this study also supports

    the proposal of Obuchovia as a junior synonym within the clade Trichodagmia to represent the

    ALBELLUM species group.

    The utility of the COI DNA barcoding methodology for identification of species in the subgenus

    Trichodagmia and related taxa has been tested. In total, 24 morphospecies within the current expanded

    morphological concept of Trichodagmia were analyzed. In addition, three species of the subgenus

    Aspathia and 10 species of the subgenus Simulium s.str. were also included in the analysis because of their

    putative phylogenetic relationship with Trichodagmia. Within the barcoding neighbour-joining tree, most

    of the specimens were grouped together according to morpho-taxon (species groups and species).

    Mean genetic distance amongst groups (morphospecies) averaged 11.2% (ranged 2.8-19.5%), whereas

    intraspecific genetic divergence within morphologically distinct species averaged 0.5% (range 0-1.3%).

    In known species complexes, maximum values of genetic divergence (3.28-3.79%) indicate the probable

    presence of cryptic diversity. DNA barcoding achieved nearly 100% success in identifying all specimens

    of the subgenus Trichodagmia and related taxa.

    The existence of well defined groups within S. piperi, S. duodenicornium, S. canadense and S. rostratum

    highlighted the possible presence of species complexes in these taxa. In addition, the suspected

    presence of a sibling species in S. paynei and S. tarsatum among populations of Belize, Costa Rica, and

    the USA is confirmed. The use of shorter barcodes (midi and minibarcodes) from specimens held in

    collections was problematic with regards to the DNA quality and PCR success. However, in the cases

    that a readable sequence was obtained, they were sufficient for reliable species identification. With

    regards to the different extraction and preservation techniques tested, larvae preserved in diluted

    Carnoy’s (10% acetic acid) provided full DNA barcodes. Furthermore, legs added directly to the PCR

    mix from freshly collected individuals provided full length barcodes sequences. However, specimens of

    more than 10 years old did not yield good PCR products. In short, I conclude that DNA barcoding in

    combination with a morphological benchwork platform is an effective approach for identification and

    delineation of species in the subgenus Trichodagmia, and the discovery of hidden diversity in this taxon. 

    Naamgeving van boomkwekerijgewassen
    Hoffman, M.H.A. - \ 2011
    boomteelt - houtachtige planten als sierplanten - overblijvende planten - biologische naamgeving - taxonomie - onderzoek - arboriculture - ornamental woody plants - perennials - biological nomenclature - taxonomy - research
    Poster met onderzoeksinformatie.
    Naamlijst houtige gewassen en vaste planten belangrijk hulpmiddel in handelsverkeer : nieuwe naamlijsten onmisbare naslagwerken voor iedereen die met boomkwekerijgewassen werkt
    Hoffman, M.H.A. - \ 2011
    houtachtige planten als sierplanten - sierplanten - overblijvende planten - boomteelt - nomenclatuur - taxonomie - sortimenten - ornamental woody plants - ornamental plants - perennials - arboriculture - nomenclature - taxonomy - assortments
    Poster met informatie over de naamlijsten van houtige gewassen en vaste planten.
    Check title to add to marked list
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