ArticleBMC genomics2010
Origin and fate of pseudogenes in Hemiascomycetes: a comparative analysis.
Article in BMC genomics, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed, 31 citations in OpenAlex.
- Discovering the hidden function in fungal genomes.Nature communications · 2024Review
- Endogenous miRNA Sponges.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Evolutionary patterns of nucleotide substitution rates in plastid genomes ofEcology and evolution · 2021Article
- GENCODE Pseudogenes.Methods in molecular biology (Clifton, N.J.) · 2021Article
- Computational Methods for Pseudogene Annotation Based on Sequence Homology.Methods in molecular biology (Clifton, N.J.) · 2021Review
- A gene graveyard in the genome of the fungus Podospora comata.Molecular genetics and genomics : MGG · 2019Article
- Review
- Role of Ectopic Gene Conversion in the Evolution of aGenetics · 2017Article
- Pseudogenes and Their Genome-Wide Prediction in Plants.International journal of molecular sciences · 2016Review
- Reconstruction of ancestral chromosome architecture and gene repertoire reveals principles of genome evolution in a model yeast genus.Genome research · 2016Article
- HMGA1-pseudogenes and cancer.Oncotarget · 2016Review
- To the beat of a different drum: determinants implicated in the asymmetric sequence divergence of Caenorhabditis elegans paralogs.BMC evolutionary biology · 2013Article
- Genome-wide survey of pseudogenes in 80 fully re-sequenced Arabidopsis thaliana accessions.PloS one · 2012Article
- Massive changes in genome architecture accompany the transition to self-fertility in the filamentous fungus Neurospora tetrasperma.Genetics · 2011Article
- Systematic discovery of unannotated genes in 11 yeast species using a database of orthologous genomic segments.BMC genomics · 2011Article
- Sequence analysis and structural characterization of a glyceraldehyde-3-phosphate dehydrogenase gene from the phytopathogenic fungus Eremothecium ashbyi.Mycopathologia · 2011Article
- Yeast evolutionary genomics.Nature reviews. Genetics · 2010Review
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Authors and funding
2 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundPseudogenes are ubiquitous genetic elements that derive from functional genes after mutational inactivation. Characterization of pseudogenes is important to understand genome dynamics and evolution, and its significance increases when several genomes of related organisms can be compared. Among yeasts, only the genome of the S. cerevisiae reference strain has been analyzed so far for pseudogenes.
resultsWe present here the first comparative analysis of pseudogenes within the fully sequenced and annotated genomes of eight yeast species, spanning the entire phylogenetic range of Hemiascomycetes. A total of 871 pseudogenes were found, out of which mutational degradation patterns and consequences on the genetic repertoire of each species could be identified. We found that most pseudogenes in yeasts originate from mutational degradation of gene copies formed after species-specific duplications but duplications of pseudogenes themselves are also encountered. In all yeasts, except in Y. lipolytica, pseudogenes tend to cluster in subtelomeric regions where they can outnumber the number of functional genes from 3 to 16 times. Pseudogenes are generally not conserved between the yeast species studied (except in two cases), consistent with their large evolutionary distances, but tend to be conserved among S. cerevisiae strains. Reiterated pseudogenization of some genes is often observed in different lineages and may affect functions essential in S. cerevisiae, which are, therefore, lost in other species. Although a variety of functions are affected by pseudogenization, there is a bias towards functions involved in the adaptation of the yeasts to their environment, and towards genes of unknown functions.
conclusionsOur work illustrates for the first time the formation of pseudogenes in different branches of hemiascomycetous yeasts, showing their limited conservation and how they testify for the adaptation of the yeasts functional repertoires.
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