Complete chloroplast genome of Sedum sarmentosum and chloroplast genome evolution in Saxifragales
作 者：Dong WP, Xu C, Cheng T, Zhou SL*
影响因子：3.73
刊物名称：PLoS One
出版年份：2013
卷：8 期：10 页码：e77965
论文摘要：
Comparative chloroplast genome analyses are mostly carried out at lower taxonomic levels, such as the family and genus levels. At higher taxonomic levels, chloroplast genomes are generally used to reconstruct phylogenies. However, little attention has been paid to chloroplast genome evolution within orders. Here, we present the chloroplast genome ofSedum sarmentosumand take advantage of several available (or elucidated) chloroplast genomes to examine the evolution of chloroplast genomes in Saxifragales. The chloroplast genome ofS. sarmentosumis 150,448 bp long and includes 82,212 bp of a large single-copy (LSC) region, 16.670 bp of a small single-copy (SSC) region, and a pair of 25,783 bp sequences of inverted repeats (IRs).The genome contains 131 unique genes, 18 of which are duplicated within the IRs. Based on a comparative analysis of chloroplast genomes from four representative Saxifragales families, we observed two gene losses and two pseudogenes inPaeonia obovata, and the loss of an intron was detected in therps16gene ofPenthorum chinense. Comparisons among the 72 common protein-coding genes confirmed that the chloroplast genomes ofS. sarmentosumandPaeonia obovataexhibit accelerated sequence evolution. Furthermore, a strong correlation was observed between the rates of genome evolution and genome size. The detected genome size variations are predominantly caused by the length of intergenic spacers, rather than losses of genes and introns, gene pseudogenization or IR expansion or contraction. The genome sizes of these species are negatively correlated with nucleotide substitution rates. Species with shorter duration of the life cycle tend to exhibit shorter chloroplast genomes than those with longer life cycles.
