Complete chloroplast genomes of three wild perennial Hordeum species from Central Asia: genome structure, mutation hotspot, phylogenetic relationships, and comparative analysis
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 are...
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Frontiers Media S.A.
2023-07-01
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| Series: | Frontiers in Plant Science |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fpls.2023.1170004/full |
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| author | Shuai Yuan 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 |
| author_facet | Shuai Yuan 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 |
| author_sort | Shuai Yuan |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-03-12T22:05:46Z |
| format | Article |
| id | doaj.art-11f2664560ae4bff971d9cb58c3999a9 |
| institution | Directory Open Access Journal |
| issn | 1664-462X |
| language | English |
| last_indexed | 2024-03-12T22:05:46Z |
| publishDate | 2023-07-01 |
| publisher | Frontiers Media S.A. |
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| series | Frontiers in Plant Science |
| spelling | doaj.art-11f2664560ae4bff971d9cb58c3999a92023-07-24T13:33:52ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2023-07-011410.3389/fpls.2023.11700041170004Complete chloroplast genomes of three wild perennial Hordeum species from Central Asia: genome structure, mutation hotspot, phylogenetic relationships, and comparative analysisShuai Yuan0Shuai Yuan1Cong Nie2Shangang Jia3Tianqi Liu4Junming Zhao5Jinghan Peng6Weixia Kong7Wei Liu8Wenlong Gou9Xiong Lei10Yi Xiong11Yanli Xiong12Qingqing Yu13Yao Ling14Xiao Ma15College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, ChinaSichuan Academy of Grassland Sciences, Chengdu, ChinaCollege of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, ChinaCollege of Grassland Science and Technology, China Agricultural University, Beijing, ChinaCollege of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, ChinaCollege of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, ChinaCollege of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, ChinaCollege of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, ChinaCollege of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, ChinaSichuan Academy of Grassland Sciences, Chengdu, ChinaSichuan Academy of Grassland Sciences, Chengdu, ChinaCollege of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, ChinaCollege of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, ChinaCollege of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, ChinaCollege of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, ChinaCollege of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, ChinaHordeum 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.https://www.frontiersin.org/articles/10.3389/fpls.2023.1170004/fullHordeumchloroplast genomeparity rule 2repeated sequenceshotpotphylogenic tree |
| spellingShingle | Shuai Yuan 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 Complete chloroplast genomes of three wild perennial Hordeum species from Central Asia: genome structure, mutation hotspot, phylogenetic relationships, and comparative analysis Frontiers in Plant Science Hordeum chloroplast genome parity rule 2 repeated sequences hotpot phylogenic tree |
| title | Complete chloroplast genomes of three wild perennial Hordeum species from Central Asia: genome structure, mutation hotspot, phylogenetic relationships, and comparative analysis |
| title_full | Complete chloroplast genomes of three wild perennial Hordeum species from Central Asia: genome structure, mutation hotspot, phylogenetic relationships, and comparative analysis |
| title_fullStr | Complete chloroplast genomes of three wild perennial Hordeum species from Central Asia: genome structure, mutation hotspot, phylogenetic relationships, and comparative analysis |
| title_full_unstemmed | Complete chloroplast genomes of three wild perennial Hordeum species from Central Asia: genome structure, mutation hotspot, phylogenetic relationships, and comparative analysis |
| title_short | Complete chloroplast genomes of three wild perennial Hordeum species from Central Asia: genome structure, mutation hotspot, phylogenetic relationships, and comparative analysis |
| title_sort | complete chloroplast genomes of three wild perennial hordeum species from central asia genome structure mutation hotspot phylogenetic relationships and comparative analysis |
| topic | Hordeum chloroplast genome parity rule 2 repeated sequences hotpot phylogenic tree |
| url | https://www.frontiersin.org/articles/10.3389/fpls.2023.1170004/full |
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