AUTHOR=Juramurodov Inom , Makhmudjanov Dilmurod , Yusupov Ziyoviddin , Tojibaev Komiljon 

TITLE=First comparative analysis of complete chloroplast genomes among six Hedysarum (Fabaceae) species

JOURNAL=Frontiers in Plant Science

VOLUME=14

YEAR=2023

URL=https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2023.1211247

DOI=10.3389/fpls.2023.1211247

ISSN=1664-462X

ABSTRACT=<p><italic>Hedysarum</italic> is one of the largest genera in the Fabaceae family, mainly distributed in the Northern Hemisphere. Despite numerous molecular studies on the genus <italic>Hedysarum</italic>, 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 <italic>Hedysarum</italic> species, corresponding to sections <italic>Multicaulia</italic>, <italic>Hedysarum</italic>, and <italic>Stracheya</italic> were conducted. The complete cp genomes of <italic>H. drobovii</italic>, <italic>H. flavescens</italic>, and <italic>H. lehmannianum</italic> were sequenced for this study. The cp genomes of six <italic>Hedysarum</italic> species showed high similarity with regard to genome size (except for <italic>H. taipeicum</italic>), 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 <italic>Hedysarum</italic> species shared 7 common SSRs and exhibited 14 unique SSRs. As well, three highly variable genes (<italic>clpP, accD</italic>, and <italic>atpF</italic>) 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 <italic>Hedysarum</italic> species. The results showed that the <italic>Hedysarum</italic> species form a monophyletic clade closely related to the genera <italic>Onobrychis</italic> and <italic>Alhagi</italic>. Furthermore, both of our phylogenetic reconstructions showed that section <italic>Stracheya</italic> is more closely related to section <italic>Hedysarum</italic> than to section <italic>Multicaulia</italic>. This study is the first comprehensive work to investigate the genome characteristics of the genus <italic>Hedysarum</italic>, which provides useful genetic information for further research on the genus, including evolutionary studies, phylogenetic relationships, population genetics, and species identification.</p>