Complete chloroplast genomes of three wild perennial Hordeum species from Central Asia: genome structure, mutation hotspot, phylogenetic relationships, and comparative analysis

Shuai Yuan; Cong Nie; Shangang Jia; Tianqi Liu; Junming Zhao; Jinghan Peng; Weixia Kong; Wei Liu; Wenlong Gou; Xiong Lei; Yi Xiong; Yanli Xiong; Qingqing Yu; Yao Ling; Xiao Ma

doi:10.3389/fpls.2023.1170004

Complete chloroplast genomes of three wild perennial Hordeum species from Central Asia: genome structure, mutation hotspot, phylogenetic relationships, and comparative analysis

Front Plant Sci. 2023 Jul 24:14:1170004. doi: 10.3389/fpls.2023.1170004. eCollection 2023.

Authors

Shuai Yuan^{1

2}, Cong Nie¹, Shangang Jia³, Tianqi Liu¹, Junming Zhao¹, Jinghan Peng¹, Weixia Kong¹, Wei Liu¹, Wenlong Gou², Xiong Lei², Yi Xiong¹, Yanli Xiong¹, Qingqing Yu¹, Yao Ling¹, Xiao Ma¹

Affiliations

¹ College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China.
² Sichuan Academy of Grassland Sciences, Chengdu, China.
³ College of Grassland Science and Technology, China Agricultural University, Beijing, China.

Abstract

Hordeum L. is widely distributed in mountain or plateau of subtropical and warm temperate regions around the world. Three wild perennial Hordeum species, including H. bogdanii, H. brevisubulatum, and H. violaceum, have been used as forage and for grassland ecological restoration in high-altitude areas in recent years. To date, the degree of interspecies sequence variation in the three Hordeum species within existing gene pools is still not well-defined. Herein, we sequenced and assembled chloroplast (cp) genomes of the three species. The results revealed that the cp genome of H. bogdanii showed certain sequence variations compared with the cp genomes of the other two species (H. brevisubulatum and H. violaceum), and the latter two were characterized by a higher relative affinity. Parity rule 2 plot (PR2) analysis illuminated that most genes of all ten Hordeum species were concentrated in nucleotide T and G. Numerous single nucleotide polymorphism (SNP) and insertion/deletion (In/Del) events were detected in the three Hordeum species. A series of hotspots regions (tRNA-GGU ~ tRNA-GCA, tRNA-UGU ~ ndhJ, psbE ~ rps18, ndhF ~ tRNA-UAG, etc.) were identified by mVISTA procedures, and the five highly polymorphic genes (tRNA-UGC, tRNA-UAA, tRNA-UUU, tRNA-UAC, and ndhA) were proved by the nucleotide diversity (Pi). Although the distribution and existence of cp simple sequence repeats (cpSSRs) were predicted in the three Hordeum cp genomes, no rearrangement was found between them. A similar phenomenon has been found in the cp genome of the other seven Hordeum species, which has been published so far. In addition, evolutionary relationships were reappraised based on the currently reported cp genome of Hordeum L. This study offers a framework for gaining a better understanding of the evolutionary history of Hordeum species through the re-examination of their cp genomes, and by identifying highly polymorphic genes and hotspot regions that could provide important insights into the genetic diversity and differentiation of these species.

Keywords: Hordeum; chloroplast genome; hotpot; parity rule 2; phylogenic tree; repeated sequences.

Grants and funding

This study was supported by the National Natural Science Foundation of China (grant numbers 31570654), the Regional Innovation Cooperation Project of Sichuan Province (2022YFQ0076), the Project of Cooperation between Provincial School and Provincial College (2023YFSY0012). The Forage Position Expert Project of Sichuan Beef Cattle Innovation Team (SCCXTD-2020-13).