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

Inom Juramurodov; Dilmurod Makhmudjanov; Ziyoviddin Yusupov; Komiljon Tojibaev

doi:10.3389/fpls.2023.1211247

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

Front Plant Sci. 2023 Aug 18:14:1211247. doi: 10.3389/fpls.2023.1211247. eCollection 2023.

Authors

Inom Juramurodov^{1

2

3

4}, Dilmurod Makhmudjanov^{1

2

3

4}, Ziyoviddin Yusupov⁵, Komiljon Tojibaev^{2

3}

Affiliations

¹ Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China.
² Yunnan International Joint Laboratory for Biodiversity of Central Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China.
³ Flora of Uzbekistan Laboratory, Institute of Botany of the Academy of Sciences of the Republic of Uzbekistan, Tashkent, Uzbekistan.
⁴ University of Chinese Academy of Sciences, Beijing, China.
⁵ International Joint Lab for Molecular Phylogeny and Biogeography, Institute of Botany, Academy Sciences of Uzbekistan, Tashkent, Uzbekistan.

Abstract

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.

Keywords: Hedysarum; chloroplast genome; comparative analysis; phylogeny; protein-coding genes.

Grants and funding

This study was supported by grants from the state research project “Taxonomic revision of polymorphic plant families of the flora of Uzbekistan” (FZ-20200929321) and the State Programs for 2021–2025 years “Grid mapping of the flora of Uzbekistan” and the “Tree of life: monocots of Uzbekistan” of the Institute of Botany of the Academy of Sciences of the Republic of Uzbekistan, the National Natural Science Foundation of China (32170215), the International Partnership Program of Chinese Academy of Sciences (151853KYSB20180009), Yunnan Young and Elite Talents Project (YNWRQNBJ-2019-033), the Ten Thousand Talents Program of Yunnan Province (202005AB160005), and the Chinese Academy of Sciences “Light of West China” Program.