Reconstruction of Oomycete Genome Evolution Identifies Differences in Evolutionary Trajectories Leading to Present-Day Large Gene Families

Seidl, Michael F.; Van den Ackerveken, Guido; Govers, Francine; Snel, Berend

doi:10.1093/gbe/evs003

Reconstruction of Oomycete Genome Evolution Identifies Differences in Evolutionary Trajectories Leading to Present-Day Large Gene Families

Journal Article · Sun Jan 08 23:00:00 EST 2012 · Genome Biology and Evolution

DOI:https://doi.org/10.1093/gbe/evs003· OSTI ID:1625326

Seidl, Michael F. ^[1]; Van den Ackerveken, Guido ^[2]; Govers, Francine ^[3]; Snel, Berend ^[4]

Univ. of Utrecht (Netherlands). Dept. of Biology. Theoretical Biology and Bioinformatics; Centre for BioSystems Genomics, Wageningen (Netherlands); DOE/OSTI
Centre for BioSystems Genomics, Wageningen (Netherlands); Univ. of Utrecht (Netherlands). Dept. of Biology. Plant-Microbe Interactions
Centre for BioSystems Genomics, Wageningen (Netherlands); Wageningen Univ. (Netherlands)
Univ. of Utrecht (Netherlands). Dept. of Biology. Theoretical Biology and Bioinformatics; Centre for BioSystems Genomics, Wageningen (Netherlands)

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.

View Accepted Manuscript (DOE)

Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science Division

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 1625326

Journal Information:: Genome Biology and Evolution, Journal Name: Genome Biology and Evolution Journal Issue: 3 Vol. 4; ISSN 1759-6653

Publisher:: Society for Molecular Biology and EvolutionCopyright Statement

Country of Publication:: United States

Language:: English

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59 BASIC BIOLOGICAL SCIENCES
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genome reconstruction
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Reconstruction of Oomycete Genome Evolution Identifies Differences in Evolutionary Trajectories Leading to Present-Day Large Gene Families

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