NDLI: Interspecific and Intragenic Differences in Codon Usage Bias Among Vertebrate Myosin Heavy-Chain Genes

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Journal of Molecular Evolution : Volume 73, Issue 1-2, August 2011

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Interspecific and Intragenic Differences in Codon Usage Bias Among Vertebrate Myosin Heavy-Chain Genes

Content Provider	Springer Nature Link
Author	Aoi, Mikio C. Rourke, Bryan C.
Copyright Year	2011
Abstract	Synonymous codon usage bias is a broadly observed phenomenon in bacteria, plants, and invertebrates and may result from selection. However, the role of selective pressures in shaping codon bias is still controversial in vertebrates, particularly for mammals. The myosin heavy-chain (MyHC) gene family comprises multiple isoforms of the major force-producing contractile protein in cardiac and skeletal muscles. Slow and fast genes are tandemly arrayed on separate chromosomes, and have distinct patterns of functionality and expression in muscle. We analyze both full-length MyHC genes (~5400 bp) and a larger collection of partial sequences at the 3′ end (~500 bp). The MyHC isoforms are an interesting system in which to study codon usage bias because of their length, expression, and critical importance to organismal mobility. Codon bias and GC content differs among MyHC genes with regards to functional type, isoform, and position within the gene. Codon bias even varies by isoform within a species. We find evidence in favor of both chromosomal influences on nucleotide composition and selection against nonsense errors (SANE) acting on codon usage in MyHC genes. Intragenic variation in codon bias and elongation rate is significant, with a strong trend for increasing codon bias and elongation rate towards the 3′ end of the gene, although the trend is dependent upon the degeneracy class of the codons. Therefore, patterns of codon usage in MyHC genes are consistent with models supporting SANE as a major force shaping codon usage.
Starting Page	74
Ending Page	93
Page Count	20
File Format	PDF
ISSN	00222844
Journal	Journal of Molecular Evolution
Volume Number	73
Issue Number	3-4
e-ISSN	14321432
Language	English
Publisher	Springer-Verlag
Publisher Date	2011-09-14
Publisher Place	New York
Access Restriction	One Nation One Subscription (ONOS)
Subject Keyword	Myosin heavy-chain Codon usage Muscle Translation selection Sequencing Plant Sciences Microbiology Cell Biology Animal Genetics and Genomics Plant Genetics & Genomics Evolutionary Biology
Content Type	Text
Resource Type	Article
Subject	Genetics Molecular Biology Ecology, Evolution, Behavior and Systematics

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