Complete chloroplast genome of Sedum sarmentosum and chloroplast genome evolution in Saxifragales.
Complete chloroplast genome of Sedum sarmentosum and chloroplast genome evolution in Saxifragales.
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DOI：
10.1371/journal.pone.0077965
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发表时间：
2013
期刊：
影响因子：
3.7
通讯作者：
Zhou S
中科院分区：
文献类型：
--
作者：
Dong W;Xu C;Cheng T;Zhou S
比较叶绿体基因组分析大多在较低的分类水平上进行，如科和属水平。在较高的分类水平上，叶绿体基因组通常用于重建系统发育。然而，对目内叶绿体基因组进化的研究却很少。本文介绍了景天（Sedum sarmentosum）的叶绿体基因组，并利用几个可用的（或已阐明的）叶绿体基因组来研究沙盆草属植物叶绿体基因组的进化。sammentosum叶绿体基因组长150,448 bp，包括82,212 bp的大单拷贝（LSC）区，16.670 bp的小单拷贝（SSC）区和一对25,783 bp的反向重复序列（IRs）。基因组包含131个独特的基因，其中18个在IRs内复制。通过对4个代表性沙盆草科植物叶绿体基因组的比较分析，发现芍药（Paeonia obovata）中有2个基因缺失和2个假基因缺失，中国芍药（Penthorum chinense）的rps16基因中有1个内含子缺失。通过对72个共同蛋白编码基因的比较，证实了白芍和白芍叶绿体基因组的序列进化速度加快。此外，在基因组进化速率和基因组大小之间观察到很强的相关性。检测到的基因组大小变化主要是由基因间间隔的长度引起的，而不是由基因和内含子的损失、基因假原化或IR扩张或收缩引起的。这些物种的基因组大小与核苷酸取代率呈负相关。生命周期较短的物种往往比生命周期较长的物种表现出更短的叶绿体基因组。
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 of Sedum sarmentosum and take advantage of several available (or elucidated) chloroplast genomes to examine the evolution of chloroplast genomes in Saxifragales. The chloroplast genome of S. sarmentosum is 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 in Paeonia obovata, and the loss of an intron was detected in the rps16 gene of Penthorum chinense. Comparisons among the 72 common protein-coding genes confirmed that the chloroplast genomes of S. sarmentosum and Paeonia obovata exhibit 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.
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影响因子：
1.9
作者：
Goremykin, V;Hirsch-Ernst, KI;Hellwig, FH
通讯作者：
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