ArticleJournal of molecular evolution2006
Nonneutral GC3 and retroelement codon mimicry in Phytophthora.
Article in Journal of molecular evolution, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed, 16 citations in OpenAlex.
- On the Base Composition of Transposable Elements.International journal of molecular sciences · 2022Review
- In silico characterization of molecular factors involved in metabolism and pathogenicity of Phytophthora cinnamomi.Molecular biology reports · 2022Review
- A genomic survey of transposable elements in the choanoflagellateMobile DNA · 2019Article
- Ancient Origin of the U2 Small Nuclear RNA Gene-Targeting Non-LTR Retrotransposons Utopia.PloS one · 2015Article
- Small homologous blocks in phytophthora genomes do not point to an ancient whole-genome duplication.Genome biology and evolution · 2014Article
- RNA-Seq reveals infection-related global gene changes in Phytophthora phaseoli, the causal agent of lima bean downy mildew.Molecular plant pathology · 2012Article
- Genome evolution in filamentous plant pathogens: why bigger can be better.Nature reviews. Microbiology · 2012Review
- The hidden duplication past of the plant pathogen Phytophthora and its consequences for infection.BMC genomics · 2010Article
- Identification and occurrence of the LTR-Copia-like retrotransposon, PSCR and other Copia-like elements in the genome of Phytophthora sojae.Current genetics · 2009Review
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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
Phytophthora is a genus entirely comprised of destructive plant pathogens. It belongs to the Stramenopila, a unique branch of eukaryotes, phylogenetically distinct from plants, animals, or fungi. Phytophthora genes show a strong preference for usage of codons ending with G or C (high GC3). The presence of high GC3 in genes can be utilized to differentiate coding regions from noncoding regions in the genome. We found that both selective pressure and mutation bias drive codon bias in Phytophthora. Indicative for selection pressure is the higher GC3 value of highly expressed genes in different Phytophthora species. Lineage specific GC increase of noncoding regions is reminiscent of whole-genome mutation bias, whereas the elevated Phytophthora GC3 is primarily a result of translation efficiency-driven selection. Heterogeneous retrotransposons exist in Phytophthora genomes and many of them vary in their GC content. Interestingly, the most widespread groups of retroelements in Phytophthora show high GC3 and a codon bias that is similar to host genes. Apparently, selection pressure has been exerted on the retroelement's codon usage, and such mimicry of host codon bias might be beneficial for the propagation of retrotransposons.
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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.