Table_5_First comparative analysis of complete chloroplast genomes among six Hedysarum (Fabaceae) species.doc

Hedysarum is one of the largest genera in the Fabaceae family, mainly distributed in the Northern Hemisphere. Despite numerous molecular studies on the genus Hedysarum, there is still a lack of research aimed at defining the specific characteristics of the chloroplast genome (cp genome) of the genus. Furthermore, the interrelationships between sections in the genus based on the cp genome have not yet been studied. In this study, comprehensive analyses of the complete cp genomes of six Hedysarum species, corresponding to sections Multicaulia, Hedysarum, and Stracheya were conducted. The complete cp genomes of H. drobovii, H. flavescens, and H. lehmannianum were sequenced for this study. The cp genomes of six Hedysarum species showed high similarity with regard to genome size (except for H. taipeicum), gene sequences, and gene classes, as well as the lacking IR region. The whole cp genomes of the six species were found to contain 110 genes ranging from 121,176 bp to 126,738 bp in length, including 76 protein-coding genes, 4 rRNA genes, and 30 tRNA genes. In addition, chloroplast SSRs and repetitive sequence regions were reported for each species. The six Hedysarum species shared 7 common SSRs and exhibited 14 unique SSRs. As well, three highly variable genes (clpP, accD, and atpF) with high Pi values were detected among protein-coding genes. Furthermore, we conducted phylogenetic analyses using the complete cp genomes and 76 protein-coding genes of 14 legume species, including the seven Hedysarum species. The results showed that the Hedysarum species form a monophyletic clade closely related to the genera Onobrychis and Alhagi. Furthermore, both of our phylogenetic reconstructions showed that section Stracheya is more closely related to section Hedysarum than to section Multicaulia. This study is the first comprehensive work to investigate the genome characteristics of the genus Hedysarum, which provides useful genetic information for further research on the genus, including evolutionary studies, phylogenetic relationships, population genetics, and species identification.

Hedysarum属为豆科中最大的属之一，主要分布于北半球。尽管关于Hedysarum属的分子研究已颇丰，但对于该属叶绿体基因组（cp基因组）的特定特征研究仍显不足。此外，基于cp基因组对属内各节之间的关系研究亦未深入开展。在本研究中，对六种Hedysarum属植物的全叶绿体基因组进行了全面分析，这些植物分别对应Multicaulia、Hedysarum和Stracheya三个节。本研究中测序了H. drobovii、H. flavescens和H. lehmannianum的全叶绿体基因组。六种Hedysarum属植物的全叶绿体基因组在基因组大小（除H. taipeicum外）、基因序列和基因类别，以及缺失的IR区域上显示出高度相似性。这六种植物的全叶绿体基因组包含110个基因，长度介于121,176 bp至126,738 bp之间，包括76个编码蛋白基因、4个rRNA基因和30个tRNA基因。此外，每种植物的叶绿体简单序列重复（SSR）和重复序列区域也被报道。这六种Hedysarum属植物共享7个共同的SSR，并展现出14个独特的SSR。同时，在编码蛋白基因中检测到了三个高度变异的基因（clpP、accD和atpF），它们具有较高的Pi值。进一步地，我们利用14种豆科植物的全叶绿体基因组及76个编码蛋白基因，包括七个Hedysarum属植物，进行了系统发育分析。结果表明，Hedysarum属植物形成一个单系群，与Onobrychis属和Alhagi属紧密相关。此外，我们的系统发育重建亦显示，Stracheya节比Multicaulia节更接近Hedysarum节。本研究首次全面探讨了Hedysarum属的基因组特征，为该属的进一步研究，包括进化研究、系统发育关系、群体遗传学和物种鉴定等，提供了宝贵的遗传信息。