Reconstruction of Oomycete Genome Evolution Identifies Differences in Evolutionary Trajectories Leading to Present-Day Large Gene Families
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 genomesmore »
- Authors:
-
- Univ. of Utrecht (Netherlands). Dept. of Biology. Theoretical Biology and Bioinformatics; Centre for BioSystems Genomics, Wageningen (Netherlands)
- 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)
- Publication Date:
- Research Org.:
- Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science Division
- OSTI Identifier:
- 1625326
- Grant/Contract Number:
- AC02-05CH11231
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Genome Biology and Evolution
- Additional Journal Information:
- Journal Volume: 4; Journal Issue: 3; Journal ID: ISSN 1759-6653
- Publisher:
- Society for Molecular Biology and Evolution
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; evolutionary biology; genetics & heredity; oomycetes, genome reconstruction; evolution; gene families; evolutionary dynamics; tree reconciliation
Citation Formats
Seidl, Michael F., Van den Ackerveken, Guido, Govers, Francine, and Snel, Berend. Reconstruction of Oomycete Genome Evolution Identifies Differences in Evolutionary Trajectories Leading to Present-Day Large Gene Families. United States: N. p., 2012.
Web. doi:10.1093/gbe/evs003.
Seidl, Michael F., Van den Ackerveken, Guido, Govers, Francine, & Snel, Berend. Reconstruction of Oomycete Genome Evolution Identifies Differences in Evolutionary Trajectories Leading to Present-Day Large Gene Families. United States. https://doi.org/10.1093/gbe/evs003
Seidl, Michael F., Van den Ackerveken, Guido, Govers, Francine, and Snel, Berend. Mon .
"Reconstruction of Oomycete Genome Evolution Identifies Differences in Evolutionary Trajectories Leading to Present-Day Large Gene Families". United States. https://doi.org/10.1093/gbe/evs003. https://www.osti.gov/servlets/purl/1625326.
@article{osti_1625326,
title = {Reconstruction of Oomycete Genome Evolution Identifies Differences in Evolutionary Trajectories Leading to Present-Day Large Gene Families},
author = {Seidl, Michael F. and Van den Ackerveken, Guido and Govers, Francine and Snel, Berend},
abstractNote = {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.},
doi = {10.1093/gbe/evs003},
journal = {Genome Biology and Evolution},
number = 3,
volume = 4,
place = {United States},
year = {Mon Jan 09 00:00:00 EST 2012},
month = {Mon Jan 09 00:00:00 EST 2012}
}
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