ArticleGenetics2008
Probabilistic cross-species inference of orthologous genomic regions created by whole-genome duplication in yeast.
Article in Genetics, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed.
- Chromosome-level Streptochaeta genome elucidates the ancestral karyotype and allopolyploid origin of grasses.Nature communications · 2026Article
- Mesopolyploidy as a taxonomic clade marker for Brassica and relatives (tribe Brassiceae).Annals of botany · 2026Article
- A Class of Allopolyploidy Showing High Duplicate Retention and Continued Homoeologous Exchanges.Genome biology and evolution · 2025Article
- Complementing model species with model clades.The Plant cell · 2024Review
- Interlocus Gene Conversion, Natural Selection, and Paralog Homogenization.Molecular biology and evolution · 2023Article
- POInTBMC bioinformatics · 2023Article
- Hybridization order is not the driving factor behind biases in duplicate gene losses among the hexaploid Solanaceae.Proceedings. Biological sciences · 2022Article
- Convergent evolution of polyploid genomes from across the eukaryotic tree of life.G3 (Bethesda, Md.) · 2022Article
- Genomic and transcriptomic analyses of the subterranean termiteProceedings of the National Academy of Sciences of the United States of America · 2022Article
- The contributions from the progenitor genomes of the mesopolyploid Brassiceae are evolutionarily distinct but functionally compatible.Genome research · 2021Article
- Transcriptomic Response toFrontiers in genetics · 2021Article
- A Single, Shared Triploidy in Three Species of Parasitic Nematodes.G3 (Bethesda, Md.) · 2020Article
- Genomic Origin and Diversification of the Glucosinolate MAM Locus.Frontiers in plant science · 2020Article
- Article
- Vertebrate SLRP family evolution and the subfunctionalization of osteoglycin gene duplicates in teleost fish.BMC evolutionary biology · 2018Article
- Preferential retention of genes from one parental genome after polyploidy illustrates the nature and scope of the genomic conflicts induced by hybridization.PLoS genetics · 2018Article
- Natural Selection in Cancer Biology: From Molecular Snowflakes to Trait Hallmarks.Cold Spring Harbor perspectives in medicine · 2017Review
- Evaluating and Characterizing Ancient Whole-Genome Duplications in Plants with Gene Count Data.Genome biology and evolution · 2016Article
- Patterns of Gene Conversion in Duplicated Yeast Histones Suggest Strong Selection on a Coadapted Macromolecular Complex.Genome biology and evolution · 2015Article
- Differential retention and divergent resolution of duplicate genes following whole-genome duplication.Genome research · 2014Article
Corrections and comments
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Authors and funding
2 authors.
Funding
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Abstract
Identification of orthologous genes across species becomes challenging in the presence of a whole-genome duplication (WGD). We present a probabilistic method for identifying orthologs that considers all possible orthology/paralogy assignments for a set of genomes with a shared WGD (here five yeast species). This approach allows us to estimate how confident we can be in the orthology assignments in each genomic region. Two inferences produced by this model are indicative of purifying selection acting to prevent duplicate gene loss. First, our model suggests that there are significant differences (up to a factor of seven) in duplicate gene half-life. Second, we observe differences between the genes that the model infers to have been lost soon after WGD and those lost more recently. Gene losses soon after WGD appear uncorrelated with gene expression level and knockout fitness defect. However, later losses are biased toward genes whose paralogs have high expression and large knockout fitness defects, as well as showing biases toward certain functional groups such as ribosomal proteins. We suggest that while duplicate copies of some genes may be lost neutrally after WGD, another set of genes may be initially preserved in duplicate by natural selection for reasons including dosage.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.