15 results on '"Seidl, M.F."'
Search Results
2. Segmental Duplications Drive the Evolution of Accessory Regions in a Major Crop Pathogen
- Author
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van Westerhoven, A.C., primary, Aguilera-Galvez, C., additional, Nakasato-Tagami, G., additional, Shi-Kunne, X., additional, Martinez de la Parte, E., additional, Chavarro Carero, E., additional, Meijer, H.J.G., additional, Feurtey, A., additional, Maryani, N., additional, Ordóñez, N., additional, Schneiders, H., additional, Nijbroek, K., additional, Wittenberg, A. H. J., additional, Hofstede, R., additional, García-Bastidas, F., additional, Sørensen, E.H., additional, Swennen, R., additional, Stukenbrock, E.H., additional, Kema, G.H.J., additional, and Seidl, M.F., additional
- Published
- 2023
- Full Text
- View/download PDF
3. Samenvattingen Fusarium
- Author
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de Nijs, W.C.M., Torres Sanchez, David, Ordonez Roman, N.I., Maryani Martawi, N., Meijer, H.J.G., Seidl, M.F., and Kema, G.H.J.
- Subjects
Biointeractions and Plant Health ,BU Contaminants & Toxins ,Laboratory of Phytopathology ,BU Contaminanten & Toxines ,food and beverages ,EPS ,Laboratorium voor Phytopathologie - Published
- 2020
4. The genome of Peronospora belbahrii reveals high heterozygosity, a low number of canonical effectors and CT-rich promoters
- Author
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Thines, M., Sharma, R., Rodenburg, Y.A., Gogleva, A., Judelson, H.S., Xia, X., van den Hoogen, D.J., Kitner, M., Klein, J., Neilen, M., de Ridder, D., Seidl, M.F., van den Ackerveken, G., Govers, F., Schornack, S., and Studholme, D.J.
- Subjects
Bioinformatics ,Laboratory of Phytopathology ,Bioinformatica ,EPS ,Laboratorium voor Phytopathologie - Abstract
Along with Plasmopara destructor, Peronosopora belbahrii has arguably been the economically most important newly emerging downy mildew pathogen of the past two decades. Originating from Africa, it has started devastating basil production throughout the world, most likely due to the distribution of infested seed material. Here we present the genome of this pathogen and results from comparisons of its genomic features to other oomycetes. The assembly of the nuclear genome was ca. 35.4 Mbp in length, with an N50 scaffold length of ca. 248 kbp and an L50 scaffold count of 46. The circular mitochondrial genome consisted of ca. 40.1 kbp. From the repeat-masked genome 9049 protein-coding genes were predicted, out of which 335 were predicted to have extracellular functions, representing the smallest secretome so far found in peronosporalean oomycetes. About 16 % of the genome consists of repetitive sequences, and based on simple sequence repeat regions, we provide a set of microsatellites that could be used for population genetic studies of Pe. belbahrii. Peronospora belbahrii has undergone a high degree of convergent evolution, reflecting its obligate biotrophic lifestyle. Features of its secretome, signalling networks, and promoters are presented, and some patterns are hypothesised to reflect the high degree of host specificity in Peronospora species. In addition, we suggest the presence of additional virulence factors apart from classical effector classes that are promising candidates for future functional studies.
- Published
- 2019
5. Genome-wide characterization of Phytophthora infestans metabolism : a systems biology approach
- Author
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Rodenburg, Y.A., Seidl, M.F., de Ridder, D., and Govers, F.
- Subjects
Bioinformatics ,Phytophthora infestans ,Laboratory of Phytopathology ,metabolic model ,Bioinformatica ,oomycete ,systems biology ,EPS ,metabolism ,Laboratorium voor Phytopathologie - Abstract
Genome-scale metabolic models (GEMs) provide a functional view of the complex network of biochemical reactions in the living cell. Initially mainly applied to reconstruct the metabolism of model organisms, the availability of increasingly sophisticated reconstruction methods and more extensive biochemical databases now make it possible to reconstruct GEMs for less well-characterized organisms, and have the potential to unravel themetabolism in pathogen–host systems. Here, we present a GEM for the oomycete plant pathogen Phytophthora infestans as a first step towards an integrative model with its host. We predict the biochemical reactions in different cellular compartments and investigate the gene–protein–reaction associations in this model to obtain an impression of the biochemical capabilities ofP. infestans . Furthermore, we generate life stage-specific models to place the transcriptomic changes of the genes encoding metabolic enzymes into a functional context. In sporangia and zoospores, there is an overall down-regulation, most strikingly reflected in the fatty acid biosynthesis pathway. To investigate the robustness of the GEM, we simulate gene deletions to predict which enzymes are essential for in vitro growth. This model is anessential first step towards an understanding of P. infestans and its interactions with plants as a system, which will help to formulate new hypotheses on infection mechanisms and disease prevention.
- Published
- 2018
6. Pseudomonas syringae evades host Immunity by degrading flagellin monomers with alkaline protease AprA
- Author
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Pel, M.J.C., Van Dijken, A.J.H., Bardoel, B.W., Seidl, M.F, Van der Ent, S., and Van Strijp, J.A.G.
- Subjects
Pseudomonas, host immune evasion, plant immunity, flagellin, alkaline protease ,fungi ,Biologie - Abstract
Bacterial flagellin molecules are strong inducers of innate immune responses in both mammals and plants. The opportunistic pathogen Pseudomonas aeruginosa secretes an alkaline protease called AprA that degrades flagellin monomers. Here, we show that AprA is widespread among a wide variety of bacterial species. In addition, we investigated the role of AprA in virulence of the bacterial plant athogen P. syringae pv. tomato DC3000. The AprA-deficient DC3000 ΔaprA knockout mutant was significantly less virulent on both tomato and Arabidopsis thaliana. Moreover, infiltration of A. thaliana Col-0 leaves with DC3000 ΔaprA evoked a significantly higher level of expression of the defenserelated genes FRK1 and PR-1 than did wild-type DC3000. In the flagellin receptor mutant fls2, pathogen virulence and defense-related gene activation did not differ between DC3000 and DC3000 ΔaprA. Together, these results suggest that AprA of DC3000 is important for evasion of recognition by the FLS2 receptor, allowing wild-type DC3000 to be more virulent on its host plant than AprA-deficient DC3000 ΔaprA. To provide further evidence for the role of DC3000 AprA in host immune evasion, we overexpressed the AprA inhibitory peptide AprI of DC3000 in A. thaliana to counteract the immune evasive capacity of DC3000 AprA. Ectopic expression of aprI in A. thaliana resulted in an enhanced level of resistance against wild-type DC3000, while the already elevated level of resistance against DC3000 ΔaprA remained unchanged. Together, these results indicate that evasion of host immunity by the alkaline protease AprA is important for full virulence of strain DC3000 and likely acts by preventing flagellin monomers from beingrecognized by its cognate immune receptor.
- Published
- 2014
7. Exploring Evolution and Biology of Oomycetes: Integrative and Comparative Genomics
- Author
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Seidl, M.F., Plant Microbe Interactions, Theoretical Biology and Bioinformatics, Sub Theoretical Biology & Bioinformatics, Hogeweg, P, Govers, F., Snel, Berend, van den Ackerveken, Guido, and University Utrecht
- Abstract
Diseases that destroy livestock and crops have had catastrophic effects on human civilization, causing starvation and economical losses and continue to be a constant threat to global food production. Pathogenic species occur throughout the tree of life including many bacteria, eukaryotic microorganisms and metazoans. The fascinating taxonomic class of oomycetes unites several important pathogenic eukaryotes of plants and animals. We have witnessed considerable advances characterizing the (molecular) biology of these species, in particular their interactions with the hosts, in the last decades. Nevertheless, our current knowledge still lags behind the possibilities provided by large-scale (gen)omics data which is nowadays easily accessible. Comparative genomics and integrative bioinformatics provide an important framework to accompany and complement classical experimental work to advance our knowledge of these species. This thesis describes four complementary comparative genomic studies focusing on different aspects of cellular function and evolution of pathogenic oomycetes. The analyses presented in this thesis highlight the merit of integrative and comparative genomics as a pivotal tool to explore the biology and evolution of oomycetes. They provide (testable) hypotheses on the evolution, biology and the function of as yet uncharacterized gene products in oomycetes, thereby significantly advancing our knowledge on this intriguing group of organisms.
- Published
- 2013
8. Vergelijkende genoomanalyse geeft inzicht in de evolutie en biologie van pathogene oömyceten
- Author
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Seidl, M.F. and Govers, F.
- Subjects
genomica ,plantenziekteverwekkende schimmels ,biologie ,biology ,pathogens ,bioinformatics ,evolutie ,oomycetes ,plant pathogenic fungi ,evolution ,molecular genetics ,genomics ,moleculaire genetica ,pathogenen ,plantenziekten ,oömyceten ,bio-informatica ,phytophthora infestans ,plant diseases - Abstract
Hoewel oömyceten nog maar kortgeleden het genomica-tijdperk zijn binnengetreden hebben de nieuwe ‘-omics’-technieken al geleid tot een overvloed aan kwantitatieve data. Vergelijkende en geïntegreerde genomica is cruciaal om deze schatkist met data te ontsluiten. In het proefschrift ‘Exploring Evolution and Biology of Oomycetes: Integrative and Comparative Genomics’ zijn met succes de eerste stappen gezet om deze data te gebruiken om zodoende de evolutie en biologie van oömyceten verder te ontrafelen en dit heeft reeds geleid tot waardevole nieuwe inzichten.
- Published
- 2013
9. Distinctive expansions of the potential virulence genes in the genome of the oomycete fish pathogen
- Author
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Jiang, R.H.I., de Bruijn, I., Haas, B.J., Belmonte, R., Löbach, L., Christie, J., van den Ackerveken, A.F.J.M., Bottin, A., Bulone, V., Diaz-Moreno, S.M., Dumas, B., Fan, L., Gaulin, E., Govers, F., Grenville-Briggs, L.J., Horner, N.R., Levin, J.Z., Mammella, M., Meijer, H.J., Morris, P., Nusbaum, C., Oome, S., Phillips, A.J., Rooyen, D., Rzeszutek, E., Saraiva, M., Secombes, C.J., Seidl, M.F., Snel, B., Stassen, J.H.M., Sykes, S., tripathy, S., Van den Berg, H., Vega-Arreguin, J.C., Wawra, S., Young, S.K., Zeng, Q., Dieguez-Uribeondo, J., Russ, C., Tyler, B.M., West, P., Plant Microbe Interactions, Theoretical Biology and Bioinformatics, Sub Plant-Microbe Interactions, Sub Theoretical Biology & Bioinformatics, and Dep Scheikunde
- Subjects
International - Abstract
Oomycetes in the class Saprolegniomycetidae of the Eukaryotic kingdom Stramenopila have evolved as severe pathogens of amphibians, crustaceans, fish and insects, resulting in major losses in aquaculture and damage to aquatic ecosystems. We have sequenced the 63 Mb genome of the fresh water fish pathogen, Saprolegnia parasitica. Approximately 1/3 of the assembled genome exhibits loss of heterozygosity, indicating an efficient mechanism for revealing new variation. Comparison of S. parasitica with plant pathogenic oomycetes suggests that during evolution the host cellular environment has driven distinct patterns of gene expansion and loss in the genomes of plant and animal pathogens. S. parasitica possesses one of the largest repertoires of proteases (270) among eukaryotes that are deployed in waves at different points during infection as determined from RNA-Seq data. In contrast, despite being capable of living saprotrophically, parasitism has led to loss of inorganic nitrogen and sulfur assimilation pathways, strikingly similar to losses in obligate plant pathogenic oomycetes and fungi. The large gene families that are hallmarks of plant pathogenic oomycetes such as Phytophthora appear to be lacking in S. parasitica, including those encoding RXLR effectors, Crinkler's, and Necrosis Inducing-Like Proteins (NLP). S. parasitica also has a very large kinome of 543 kinases, 10% of which is induced upon infection. Moreover, S. parasitica encodes several genes typical of animals or animal-pathogens and lacking from other oomycetes, including disintegrins and galactose-binding lectins, whose expression and evolutionary origins implicate horizontal gene transfer in the evolution of animal pathogenesis in S. parasitica.
- Published
- 2013
10. Distinctive expansions of the potential virulence genes in the genome of the oomycete fish pathogen
- Author
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de Bruijn, I., de Haas, B.J., Belmonte, R., Löbach, L., Christie, J., van den Ackerveken, A.F.J.M., Bottin, A., Bulone, V., Diaz-Moreno, S.M., Dumas, B., Fan, L., Gaulin, E., Govers, F., Grenville-Briggs, L.J., Horner, N.R., Levin, J.Z., Mammella, M., Meijer, H.J., Morris, P., Nusbaum, C., Oome, S., Phillips, A.J., Rooyen, D., Rzeszutek, E., Secombes, C.J., Seidl, M.F., Snel, B., Stassen, J.H., Sykes, S., tripathy, S., van den Berg, H., Vega-Arreguin, J.C., Wawra, S., Young, S.K., Dieguez-Uribeondo, J., Russ, C., Tyler, B.M., West, P., Plant Microbe Interactions, Theoretical Biology and Bioinformatics, Sub Plant-Microbe Interactions, Sub Theoretical Biology & Bioinformatics, and Dep Biologie
- Subjects
International ,fungi - Abstract
Oomycetes in the class Saprolegniomycetidae of the Eukaryotic kingdom Stramenopila have evolved as severe pathogens of amphibians, crustaceans, fish and insects, resulting in major losses in aquaculture and damage to aquatic ecosystems. We have sequenced the 63 Mb genome of the fresh water fish pathogen, Saprolegnia parasitica. Approximately 1/3 of the assembled genome exhibits loss of heterozygosity, indicating an efficient mechanism for revealing new variation. Comparison of S. parasitica with plant pathogenic oomycetes suggests that during evolution the host cellular environment has driven distinct patterns of gene expansion and loss in the genomes of plant and animal pathogens. S. parasitica possesses one of the largest repertoires of proteases (270) among eukaryotes that are deployed in waves at different points during infection as determined from RNA-Seq data. In contrast, despite being capable of living saprotrophically, parasitism has led to loss of inorganic nitrogen and sulfur assimilation pathways, strikingly similar to losses in obligate plant pathogenic oomycetes and fungi. The large gene families that are hallmarks of plant pathogenic oomycetes such as Phytophthora appear to be lacking in S. parasitica, including those encoding RXLR effectors, Crinkler's, and Necrosis Inducing-Like Proteins (NLP). S. parasitica also has a very large kinome of 543 kinases, 10% of which is induced upon infection. Moreover, S. parasitica encodes several genes typical of animals or animal-pathogens and lacking from other oomycetes, including disintegrins and galactose-binding lectins, whose expression and evolutionary origins implicate horizontal gene transfer in the evolution of animal pathogenesis in S. parasitica.
- Published
- 2013
11. Effector identification in the lettuce downy mildew Bremia lactucae by massively parallel transcriptome sequencing
- Author
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Stassen, J.H.M., Seidl, M.F., Vergeer, P.W.J., Nijman, I.J., Snel, B., Cuppen, E., van den Ackerveken, A.F.J.M., Plant Microbe Interactions, Theoretical Biology and Bioinformatics, Sub Plant-Microbe Interactions, and Sub Theoretical Biology & Bioinformatics
- Subjects
Econometric and Statistical Methods: General ,International ,Bescherming en bevordering van de menselijke gezondheid ,Geneeskunde(GENK) ,Medical sciences - Abstract
Lettuce downy mildew (Bremia lactucae) is a rapidly adapting oomycete pathogen affecting commercial lettuce cultivation. Oomycetes are known to use a diverse arsenal of secreted proteins (effectors) to manipulate their hosts. Two classes of effector are known to be translocated by the host: the RXLRs and Crinklers. To gain insight into the repertoire of effectors used by B. lactucae to manipulate its host, we performed massively parallel sequencing of cDNA derived from B. lactucae spores and infected lettuce (Lactuca sativa) seedlings. From over 2.3 million 454 GS FLX reads, 59 618 contigs were assembled representing both plant and pathogen transcripts. Of these, 19 663 contigs were determined to be of B. lactucae origin as they matched pathogen genome sequences (SOLiD) that were obtained from >270 million reads of spore-derived genomic DNA. After correction of cDNA sequencing errors with SOLiD data, translation into protein models and filtering, 16 372 protein models remained, 1023 of which were predicted to be secreted. This secretome included elicitins, necrosis and ethylene-inducing peptide 1-like proteins, glucanase inhibitors and lectins, and was enriched in cysteine-rich proteins. Candidate host-translocated effectors included 78 protein models with RXLR effector features. In addition, we found indications for an unknown number of Crinkler-like sequences. Similarity clustering of secreted proteins revealed additional effector candidates. We provide a first look at the transcriptome of B. lactucae and its encoded effector arsenal.
- Published
- 2012
12. Reconstruction of oomycete genome evolution identifies differences in evolutionary trajectories leading to present-day largegene families
- Author
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Seidl, M.F., van den Ackerveken, A.F.J.M., Govers, F., Snel, B., Plant Microbe Interactions, Theoretical Biology and Bioinformatics, Sub Theoretical Biology & Bioinformatics, and Sub Plant-Microbe Interactions
- Subjects
gene families ,International ,evolution ,genome reconstruction ,evolutionary dynamics ,tree reconciliation ,oomycetes - Abstract
The taxonomic class of oomycetes contains numerous pathogens of plants and animals but is related to nonpathogenic diatoms and brown algae. Oomycetes have flexible genomes comprising large gene families that play roles in pathogenicity. The evolutionary processes that shaped the gene content have not yet been studied by applying systematic tree reconciliation of the phylome of these species. We analyzed evolutionary dynamics of ten Stramenopiles. Gene gains, duplications, and losses were inferred by tree reconciliation of 18,459 gene trees constituting the phylome with a highly supported species phylogeny. We reconstructed a strikingly large last common ancestor of the Stramenopiles that contained ∼10,000 genes. Throughout evolution, the genomes of pathogenic oomycetes have constantly gained and lost genes, though gene gains through duplications outnumber the losses. The branch leading to the plant pathogenic Phytophthora genus was identified as a major transition point characterized by increased frequency of duplication events that has likely driven the speciation within this genus. Large gene families encoding different classes of enzymes associated with pathogenicity such as glycoside hydrolases are formed by complex and distinct patterns of duplications and losses leading to their expansion in extant oomycetes. This study unveils the large-scale evolutionary dynamics that shaped the genomes of pathogenic oomycetes. By the application of phylogenetic based analyses methods, it provides additional insights that shed light on the complex history of oomycete genome evolution and the emergence of large gene families characteristic for this important class of pathogens.
- Published
- 2012
13. Reconstruction of Oomycete Genome Evolution Identifies Differences in Evolutionary Trajectories Leading to Present-Day Large Gene Families
- Author
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Seidl, M.F., van den Ackerveken, A.F.J.M., Govers, F., Snel, B., Plant Microbe Interactions, Theoretical Biology and Bioinformatics, Sub Theoretical Biology & Bioinformatics, and Sub Plant-Microbe Interactions
- Subjects
Genome evolution ,gene families ,phytophthora-infestans ,nonphotosynthetic protists ,Genome ,Evolution, Molecular ,Phylogenetics ,evolution ,Gene duplication ,Genetics ,Gene family ,Evolutionary dynamics ,plant-pathogens ,protein families ,Research Articles ,Phylogeny ,Ecology, Evolution, Behavior and Systematics ,obligate biotrophy ,Oomycete ,mechanisms ,biology ,Phylogenetic tree ,EPS-2 ,genome reconstruction ,tree reconciliation ,biology.organism_classification ,Laboratorium voor Phytopathologie ,duplication ,Oomycetes ,pathogen phytophthora ,International ,Laboratory of Phytopathology ,evolutionary dynamics ,cells ,reveals - Abstract
The taxonomic class of oomycetes contains numerous pathogens of plants and animals but is related to nonpathogenic diatoms and brown algae. Oomycetes have flexible genomes comprising large gene families that play roles in pathogenicity. The evolutionary processes that shaped the gene content have not yet been studied by applying systematic tree reconciliation of the phylome of these species. We analyzed evolutionary dynamics of ten Stramenopiles. Gene gains, duplications, and losses were inferred by tree reconciliation of 18,459 gene trees constituting the phylome with a highly supported species phylogeny. We reconstructed a strikingly large last common ancestor of the Stramenopiles that contained ∼10,000 genes. Throughout evolution, the genomes of pathogenic oomycetes have constantly gained and lost genes, though gene gains through duplications outnumber the losses. The branch leading to the plant pathogenic Phytophthora genus was identified as a major transition point characterized by increased frequency of duplication events that has likely driven the speciation within this genus. Large gene families encoding different classes of enzymes associated with pathogenicity such as glycoside hydrolases are formed by complex and distinct patterns of duplications and losses leading to their expansion in extant oomycetes. This study unveils the large-scale evolutionary dynamics that shaped the genomes of pathogenic oomycetes. By the application of phylogenetic based analyses methods, it provides additional insights that shed light on the complex history of oomycete genome evolution and the emergence of large gene families characteristic for this important class of pathogens.
- Published
- 2012
14. AlternariasectionAlternaria: Species,formae specialesor pathotypes?
- Author
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Woudenberg, J.H.C., primary, Seidl, M.F., additional, Groenewald, J.Z., additional, de Vries, M., additional, Stielow, J.B., additional, Thomma, B.P.H.J., additional, and Crous, P.W., additional
- Published
- 2015
- Full Text
- View/download PDF
15. Alternariasection Alternaria: Species, formae specialesor pathotypes?
- Author
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Woudenberg, J.H.C., Seidl, M.F., Groenewald, J.Z., de Vries, M., Stielow, J.B., Thomma, B.P.H.J., and Crous, P.W.
- Abstract
The cosmopolitan fungal genus Alternariaconsists of multiple saprophytic and pathogenic species. Based on phylogenetic and morphological studies, the genus is currently divided into 26 sections. Alternariasect. Alternariacontains most of the small-spored Alternariaspecies with concatenated conidia, including important plant, human and postharvest pathogens. Species within sect. Alternariahave been mostly described based on morphology and / or host-specificity, yet molecular variation between them is minimal. To investigate whether the described morphospecies within sect. Alternariaare supported by molecular data, whole-genome sequencing of nine Alternariamorphospecies supplemented with transcriptome sequencing of 12 Alternariamorphospecies as well as multi-gene sequencing of 168 Alternariaisolates was performed. The assembled genomes ranged in size from 33.3–35.2 Mb within sect. Alternariaand from 32.0–39.1 Mb for all Alternariagenomes. The number of repetitive sequences differed significantly between the different Alternariagenomes; ranging from 1.4–16.5 %. The repeat content within sect. Alternariawas relatively low with only 1.4–2.7 % of repeats. Whole-genome alignments revealed 96.7–98.2 % genome identity between sect. Alternariaisolates, compared to 85.1–89.3 % genome identity for isolates from other sections to the A. alternatareference genome. Similarly, 1.4–2.8 % and 0.8–1.8 % single nucleotide polymorphisms (SNPs) were observed in genomic and transcriptomic sequences, respectively, between isolates from sect. Alternaria, while the percentage of SNPs found in isolates from different sections compared to the A. alternatareference genome was considerably higher; 8.0–10.3 % and 6.1–8.5 %. The topology of a phylogenetic tree based on the whole-genome and transcriptome reads was congruent with multi-gene phylogenies based on commonly used gene regions. Based on the genome and transcriptome data, a set of core proteins was extracted, and primers were designed on two gene regions with a relatively low degree of conservation within sect. Alternaria(96.8 and 97.3 % conservation). Their potential discriminatory power within sect. Alternariawas tested next to nine commonly used gene regions in sect. Alternaria, namely the SSU, LSU, ITS, gapdh, rpb2, tef1, Alt a 1, endoPGand OPA10-2 gene regions. The phylogenies from the two gene regions with a relatively low conservation, KOG1058 and KOG1077, could not distinguish the described morphospecies within sect. Alternariamore effectively than the phylogenies based on the commonly used gene regions for Alternaria. Based on genome and transcriptome comparisons and molecular phylogenies, Alternariasect. Alternariaconsists of only 11 phylogenetic species and one species complex. Thirty-five morphospecies, which cannot be distinguished based on the multi-gene phylogeny, are synonymised under A. alternata. By providing guidelines for the naming and identification of phylogenetic species in Alternariasect. Alternaria, this manuscript provides a clear and stable species classification in this section.
- Published
- 2015
- Full Text
- View/download PDF
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