Evolutionary rate variation in two conifer species, taxodium distichum (L.) rich. var. distichum(baldcypress) and cryptomeria Japonica(Thunb. ex L.F.) D. Don (Sugi, Japanese Cedar)

Junko Kusumi, Yoshihiko Tsumura, Hidenori Tachida

Research output: Contribution to journalArticle

3 Citations (Scopus)

Abstract

With the advance of sequencing technologies, large-scale data of expressed sequence tags and full-length cDNA sequences have been reported for several conifer species. Comparative analyses of evolutionary rates among diverse taxa provide insights into taxon-specific molecular evolutionary features and into the origin of variation in evolutionary rates within genomes and between species.Here, we estimated evolutionary rates in two conifer species, Taxodium distichumand Cryptomeria japonica, to illuminate the molecular evolutionary features of these species, using hundreds of genes and employing Chamaecyparis obtusa as an outgroup. Our results show that the mutation rates based on synonymous substitution rates (dS) of T. distichum and C. japonica are approximately 0.67 × 10–9and 0.59 × 10–9/site/year, respectively, which are 15–25 times lower than those of annual angiosperms. We found a significant positive correlation between dS and GC3. This implies that a local mutation bias, such as context dependency of the mutation bias, exists within the genomes of T. distichum and C. japonica, and/or that selection acts on synonymous sites in these species. In addition, the means of the ratios of synonymous to nonsynonymous substitution rate in the two species are almost the same, suggesting that the average intensity of functional constraint is constant between the lineages. Finally, we tested the possibility of positive selection based on the site model, and detected one candidate gene for positive selection.

Original languageEnglish
Pages (from-to)305-315
Number of pages11
JournalGenes and Genetic Systems
Volume90
Issue number5
DOIs
Publication statusPublished - Mar 23 2016

All Science Journal Classification (ASJC) codes

  • Molecular Biology
  • Genetics

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