ArticleGenome research2012
Sequence shortening in the rodent ancestor.
Article in Genome research, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed, 22 citations in OpenAlex.
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- Secondary structure impacts patterns of selection in human lncRNAs.BMC biology · 2016Article
- Lineage-specific genomics: Frequent birth and death in the human genome: The human genome contains many lineage-specific elements created by both sequence and functional turnover.BioEssays : news and reviews in molecular, cellular and developmental biology · 2016Review
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- Key Role of Amino Acid Repeat Expansions in the Functional Diversification of Duplicated Transcription Factors.Molecular biology and evolution · 2015Article
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- Genome-wide analysis of positively selected genes in seasonal and non-seasonal breeding species.PloS one · 2015Article
- Emergence of novel domains in proteins.BMC evolutionary biology · 2013Article
- Improving genome-wide scans of positive selection by using protein isoforms of similar length.Genome biology and evolution · 2013Article
- Dissecting the role of low-complexity regions in the evolution of vertebrate proteins.BMC evolutionary biology · 2012Article
- Slow DNA loss in the gigantic genomes of salamanders.Genome biology and evolution · 2012Article
Corrections and comments
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Authors and funding
4 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Insertions and deletions (indels), together with nucleotide substitutions, are major drivers of sequence evolution. An excess of deletions over insertions in genomic sequences-the so-called deletional bias-has been reported in a wide range of species, including mammals. However, this bias has not been found in the coding sequences of some mammalian species, such as human and mouse. To determine the strength of the deletional bias in mammals, and the influence of mutation and selection, we have quantified indels in both neutrally evolving noncoding sequences and protein-coding sequences, in six mammalian branches: human, macaque, ancestral primate, mouse, rat, and ancestral rodent. The results obtained with an improved algorithm for the placement of insertions in multiple alignments, Prank(+F), indicate that contrary to previous results, the only mammalian branch with a strong deletional bias is the rodent ancestral branch. We estimate that such a bias has resulted in an ~2.5% sequence loss of mammalian syntenic region in the ancestor of the mouse and rat. Further, a comparison of coding and noncoding sequences shows that negative selection is acting more strongly against mutations generating amino acid insertions than against mutations resulting in amino acid deletions. The strength of selection against indels is found to be higher in the rodent branches than in the primate branches, consistent with the larger effective population sizes of the rodents.
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