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

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

JOURNAL=Frontiers in Plant Science

VOLUME=14

YEAR=2023

URL=https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2023.1170004

DOI=10.3389/fpls.2023.1170004

ISSN=1664-462X

ABSTRACT=<p><italic>Hordeum</italic> L. is widely distributed in mountain or plateau of subtropical and warm temperate regions around the world. Three wild perennial <italic>Hordeum</italic> species, including <italic>H. bogdanii</italic>, <italic>H. brevisubulatum</italic>, and <italic>H. violaceum</italic>, 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 <italic>Hordeum</italic> 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 <italic>H. bogdanii</italic> showed certain sequence variations compared with the cp genomes of the other two species (<italic>H. brevisubulatum</italic> and <italic>H. violaceum</italic>), and the latter two were characterized by a higher relative affinity. Parity rule 2 plot (PR2) analysis illuminated that most genes of all ten <italic>Hordeum</italic> species were concentrated in nucleotide T and G. Numerous single nucleotide polymorphism (SNP) and insertion/deletion (In/Del) events were detected in the three <italic>Hordeum</italic> species. A series of hotspots regions (<italic>tRNA</italic>-<italic>GGU</italic> ~ <italic>tRNA</italic>-<italic>GCA</italic>, <italic>tRNA</italic>-<italic>UGU</italic> ~ <italic>ndhJ</italic>, <italic>psbE</italic> ~ <italic>rps18</italic>, <italic>ndhF</italic> ~ <italic>tRNA-UAG</italic>, etc.) were identified by mVISTA procedures, and the five highly polymorphic genes (<italic>tRNA-UGC</italic>, <italic>tRNA-UAA</italic>, <italic>tRNA-UUU</italic>, <italic>tRNA-UAC</italic>, and <italic>ndhA</italic>) were proved by the nucleotide diversity (Pi). Although the distribution and existence of cp simple sequence repeats (cpSSRs) were predicted in the three <italic>Hordeum</italic> cp genomes, no rearrangement was found between them. A similar phenomenon has been found in the cp genome of the other seven <italic>Hordeum</italic> species, which has been published so far. In addition, evolutionary relationships were reappraised based on the currently reported cp genome of <italic>Hordeum</italic> L. This study offers a framework for gaining a better understanding of the evolutionary history of <italic>Hordeum</italic> 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.</p>