Evolutionary rate variation in two conifer species, <i>Taxodium</i> <i>distichum</i> (L.) Rich. var. <i>distichum</i> (baldcypress) and <i>Cryptomeria japonica</i> (Thunb. ex L.f.) D. Don (Sugi, Japanese cedar)

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 distichum and 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 -9 and 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.

A chromosome-level genome assembly of a model conifer plant, the Japanese cedar,Cryptomeria japonicaD. Don

“…We largely followed Ma et al [57]. Briefly, (1) we identified the locations of LTR elements by running EDTA [58], (2) aligned the two LTR copies for each identified LTR retrotransposon; the two copies have exactly the same sequence when it was inserted, and therefore the discrepancies between the two LTR copies can serve as a molecular clock, (3) using the mutation rate of 0.59×10 −9 /site/year previously reported for C. japonica [59], the number of mutations between the two LTR copies is converted to the age of the inserted LTR, and (4) we created the histogram of the age distribution of the LTR retrotransposons for each of Gypsy and Copia superfamilies (Figure 2). To our knowledge, this is the first description of the age distribution of LTR retrotransposons for conifer genomes with N50 contig size of over a megabase.…”

Inferences of population structure and demographic history for Taxodium distichum, a coniferous tree in North America, based on amplicon sequencing analysis

“…Target genes -Th e list of 47 nuclear genes used in this study is shown in Appendix S1 (see Supplemental Data with the online version of this article). Primer pairs for the 44 genes were designed based on the RNA-seq data of T. distichum ( Kusumi et al, 2015 ). From these, 40 genes were randomly selected, and the remaining four genes were selected based on their known functions or molecular genetic characteristics as candidate genes that may be under selection.…”

Inferring the demographic history of Japanese cedar, Cryptomeria japonica, using amplicon sequencing

“…One may be concerned with the constancy of the mutation rate given that the evolutionary rates of C. japonica and T. distichum, which separated 90 MYA (Leslie et al 2012), were used to estimate the mutation rate. However, the synonymous substitution rates in the lineages of the two species are similar (6.7 × 10 −10 and 5.9 × 10 −10 per year, respectively; see Kusumi et al 2015). Although any comparison of the accuracies of inferences among different genetic markers or different statistical methods may not be straightforward, especially when sample sizes are different, we believe that our estimation of the order and the ages of population splits is more reliable than that of the previous study.…”