Department of Plant Biology, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran.
School of Life Science, Arizona State University, Tempe, Arizona, United States of America.
PLoS One. 2023 May 23;18(5):e0286083. doi: 10.1371/journal.pone.0286083. eCollection 2023.
Astragalus is the largest flowering plant genus. We assembled the plastid genomes of four Astragalus species (Astragalus iranicus, A. macropelmatus, A. mesoleios, A. odoratus) using next-generation sequencing and analyzed their plastomes including genome organization, codon usage, nucleotide diversity, prediction of RNA editing and etc. The total length of the newly sequenced Astragalus plastomes ranged from 121,050 bp to 123,622 bp, with 110 genes comprising 76 protein-coding genes, 30 transfer RNA (tRNA) genes and four ribosome RNA (rRNA) genes. Comparative analysis of the chloroplast genomes of Astragalus revealed several hypervariable regions comprising three non-coding sites (trnQ(UUG)-accD, rps7 -trnV(GAC) and trnR(ACG)-trnN(GUU)) and four protein-coding genes (ycf1, ycf2, accD and clpP), which have potential as molecular markers. Positive selection signatures were found in five genes in Astragalus species including rps11, rps15, accD, clpP and ycf1. The newly sequenced species, A. macropelmatus, has an approximately 13-kb inversion in IR region. Phylogenetic analysis based on 75 protein-coding gene sequences confirmed that Astragalus form a monophyletic clade within the tribe Galegeae and Oxytropis is sister group to the Coluteoid clade. The results of this study may helpful in elucidating the chloroplast genome structure, understanding the evolutionary dynamics at genus Astragalus and IRLC levels and investigating the phylogenetic relationships. Moreover, the newly plastid genomes sequenced have been increased the plastome data resources on Astragalus that can be useful in further phylogenomic studies.
黄芪是最大的开花植物属。我们使用下一代测序技术组装了四个黄芪物种（黄芪伊朗亚种、黄芪 macroschizus、黄芪 mesoleios、黄芪 odoratus）的质体基因组，并分析了它们的质体基因组，包括基因组组织、密码子使用、核苷酸多样性、RNA 编辑预测等。新测序的黄芪质体基因组的总长度范围为 121050bp 至 123622bp，包含 110 个基因，包括 76 个蛋白质编码基因、30 个转移 RNA（tRNA）基因和 4 个核糖体 RNA（rRNA）基因。对黄芪叶绿体基因组的比较分析揭示了几个高变区，包括三个非编码位点（trnQ(UUG)-accD、rps7-trnV(GAC)和 trnR(ACG)-trnN(GUU))和四个蛋白质编码基因（ycf1、ycf2、accD 和 clpP），它们可能作为分子标记。在黄芪属的五个基因中发现了正选择信号，包括 rps11、rps15、accD、clpP 和 ycf1。新测序的物种黄芪 macroschizus 在 IR 区有一个约 13kb 的倒位。基于 75 个蛋白质编码基因序列的系统发育分析证实，黄芪在 Galegeae 族内形成一个单系分支，而 Oxytropis 是 Coluteoid 分支的姊妹群。本研究的结果可能有助于阐明叶绿体基因组结构，了解黄芪属和 IRLC 水平的进化动态，以及研究系统发育关系。此外，新测序的质体基因组增加了黄芪的质体基因组数据资源，这对于进一步的系统基因组学研究可能是有用的。
