ArticleGenome biology and evolution2012
Reconstruction of oomycete genome evolution identifies differences in evolutionary trajectories leading to present-day large gene families.
Article in Genome biology and evolution, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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25 citing papers in PubMed, 50 citations in OpenAlex.
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- PcLRR-RK3, an LRR receptor kinase is required for growth andMycology · 2024Article
- Genome ofMicrobiology spectrum · 2022Article
- Mining oomycete proteomes for metalloproteases leads to identification of candidate virulence factors in Phytophthora infestans.Molecular plant pathology · 2021Article
- Comparative analysis ofHeliyon · 2021Article
- Comparative Genomic Analysis Reveals Genetic Variation and Adaptive Evolution in the Pathogenicity-Related Genes ofFrontiers in microbiology · 2021Article
- Genome reconstruction of the non-culturable spinach downy mildew Peronospora effusa by metagenome filtering.PloS one · 2020Article
- Genome-wide sequencing and metabolic annotation of Pythium irregulare CBS 494.86: understanding Eicosapentaenoic acid production.BMC biotechnology · 2019Article
- The Phytophthora cactorum genome provides insights into the adaptation to host defense compounds and fungicides.Scientific reports · 2018Article
- Diversity, evolution and expression profiles of histone acetyltransferases and deacetylases in oomycetes.BMC genomics · 2016Article
- Splice Sites Seldom Slide: Intron Evolution in Oomycetes.Genome biology and evolution · 2016Article
- Genome analyses of the sunflower pathogen Plasmopara halstedii provide insights into effector evolution in downy mildews and Phytophthora.BMC genomics · 2015Article
- Lagenidium giganteum pathogenicity in mammals.Emerging infectious diseases · 2015Article
- The secreted proteins of Achlya hypogyna and Thraustotheca clavata identify the ancestral oomycete secretome and reveal gene acquisitions by horizontal gene transfer.Genome biology and evolution · 2014Article
- Small homologous blocks in phytophthora genomes do not point to an ancient whole-genome duplication.Genome biology and evolution · 2014Article
- Sex or no sex: evolutionary adaptation occurs regardless.BioEssays : news and reviews in molecular, cellular and developmental biology · 2014Article
- A predicted functional gene network for the plant pathogen Phytophthora infestans as a framework for genomic biology.BMC genomics · 2013Article
- Article
- Comparative genomics reveals insight into virulence strategies of plant pathogenic oomycetes.PloS one · 2013Article
Corrections and comments
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Authors and funding
4 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
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.
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