caa a22 4500 445820799 CHVBK 20180317145243.0 cr unu---uuuuu 170323e20111001xx s 000 0 eng 10.1007/s00239-011-9457-0 doi (NATIONALLICENCE)springer-10.1007/s00239-011-9457-0 Interspecific and Intragenic Differences in Codon Usage Bias Among Vertebrate Myosin Heavy-Chain Genes [Elektronische Daten] [Mikio Aoi, Bryan Rourke] 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 (~5400bp) and a larger collection of partial sequences at the 3′ end (~500bp). 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. Springer Science+Business Media, LLC, 2011 Myosin heavy-chain nationallicence Codon usage nationallicence Muscle nationallicence Translation selection nationallicence Sequencing nationallicence MyHC : Myosin heavy-chain nationallicence GC : Total GC content as fraction nationallicence GC3 : Third position GC as fraction nationallicence SANE : Selection against nonsense errors nationallicence RCBS : Relative codon bias score nationallicence SCUO : Synonymous codon usage order nationallicence c : Elongation rate nationallicence c H : Harmonic mean of elongation rate nationallicence ξ Obs : Observed expected cost of nonsense errors nationallicence η Obs : Observed expected cost of translation nationallicence Aoi Mikio Department of Mathematics, North Carolina State University, 27695, Raleigh, NC, USA aut Rourke Bryan Department of Biological Sciences, California State University, 90840, Long Beach, CA, USA aut Journal of Molecular Evolution Springer-Verlag 73/3-4(2011-10-01), 74-93 0022-2844 73:3-4<74 2011 73 239 https://doi.org/10.1007/s00239-011-9457-0 text/html Onlinezugriff via DOI 1 research-article jats NATIONALLICENCE 856 40 https://doi.org/10.1007/s00239-011-9457-0 text/html Onlinezugriff via DOI NATIONALLICENCE 700 1- Aoi Mikio Department of Mathematics, North Carolina State University, 27695, Raleigh, NC, USA aut NATIONALLICENCE 700 1- Rourke Bryan Department of Biological Sciences, California State University, 90840, Long Beach, CA, USA aut NATIONALLICENCE 773 0- Journal of Molecular Evolution Springer-Verlag 73/3-4(2011-10-01), 74-93 0022-2844 73:3-4<74 2011 73 239 Metadata rights reserved Springer special CC-BY-NC licence nationallicence BK010053 XK010053 XK010000 NATIONALLICENCE NATIONALLICENCE NL-springer