A Comprehensive Analysis of Chloroplast Genome Provides New Insights into the Evolution of the Genus <i>Chrysosplenium</i>
<i>Chrysosplenium</i>, a perennial herb in the family Saxifragaceae, prefers to grow in low light and moist environments and is divided into two sections of <i>Alternifolia</i> and <i>Oppositifolia</i> based on phyllotaxy. Although there has been some progress in...
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MDPI AG
2023-09-01
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| Series: | International Journal of Molecular Sciences |
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| Online Access: | https://www.mdpi.com/1422-0067/24/19/14735 |
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| author | Tiange Yang Zhihua Wu Jun Tie Rui Qin Jiangqing Wang Hong Liu |
| author_facet | Tiange Yang Zhihua Wu Jun Tie Rui Qin Jiangqing Wang Hong Liu |
| author_sort | Tiange Yang |
| collection | DOAJ |
| description | <i>Chrysosplenium</i>, a perennial herb in the family Saxifragaceae, prefers to grow in low light and moist environments and is divided into two sections of <i>Alternifolia</i> and <i>Oppositifolia</i> based on phyllotaxy. Although there has been some progress in the phylogeny of <i>Chrysosplenium</i> over the years, the phylogenetic position of some species is still controversial. In this study, we assembled chloroplast genomes (cp genomes) of 34 <i>Chrysosplenium</i> species and performed comparative genomic and phylogenetic analyses in combination with other cp genomes of previously known <i>Chrysosplenium</i> species, for a total of 44 <i>Chrysosplenium</i> species. The comparative analyses revealed that cp genomes of <i>Chrysosplenium</i> species were more conserved in terms of genome structure, gene content and arrangement, SSRs, and codon preference, but differ in genome size and SC/IR boundaries. Phylogenetic analysis showed that cp genomes effectively improved the phylogenetic support and resolution of <i>Chrysosplenium</i> species and strongly supported <i>Chrysosplenium</i> species as a monophyletic taxon and divided into three branches. The results also showed that the sections of <i>Alternifolia</i> and <i>Oppositifolia</i> were not monophyletic with each other, and that <i>C. microspermum</i> was not clustered with other <i>Chrysosplenium</i> species with alternate leaves, but with <i>C. sedakowii</i> into separate branches. In addition, we identified 10 mutational hotspot regions that could serve as potential DNA barcodes for <i>Chrysosplenium</i> species identification. In contrast to <i>Peltoboykinia</i>, the <i>clp</i>P and <i>ycf</i>2 genes of <i>Chrysosplenium</i> were subjected to positive selection and had multiple significant positive selection sites. We further detected a significant positive selection site on the <i>pet</i>G gene between the two sections of <i>Chrysosplenium</i>. These evolutionary characteristics may be related to the growth environment of <i>Chrysosplenium</i> species. This study enriches the cp genomes of <i>Chrysosplenium</i> species and provides a reference for future studies on its evolution and origin. |
| first_indexed | 2024-03-10T21:42:37Z |
| format | Article |
| id | doaj.art-48bbe107e91c47b1bd6321b274128fc8 |
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| issn | 1661-6596 1422-0067 |
| language | English |
| last_indexed | 2024-03-10T21:42:37Z |
| publishDate | 2023-09-01 |
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| spelling | doaj.art-48bbe107e91c47b1bd6321b274128fc82023-11-19T14:30:57ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672023-09-0124191473510.3390/ijms241914735A Comprehensive Analysis of Chloroplast Genome Provides New Insights into the Evolution of the Genus <i>Chrysosplenium</i>Tiange Yang0Zhihua Wu1Jun Tie2Rui Qin3Jiangqing Wang4Hong Liu5Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, College of Life Sciences, South-Central Minzu University, Wuhan 430074, ChinaCollege of Life Sciences, Zhejiang Normal University, Jinhua 321004, ChinaHubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, College of Life Sciences, South-Central Minzu University, Wuhan 430074, ChinaHubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, College of Life Sciences, South-Central Minzu University, Wuhan 430074, ChinaHubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, College of Life Sciences, South-Central Minzu University, Wuhan 430074, ChinaHubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, College of Life Sciences, South-Central Minzu University, Wuhan 430074, China<i>Chrysosplenium</i>, a perennial herb in the family Saxifragaceae, prefers to grow in low light and moist environments and is divided into two sections of <i>Alternifolia</i> and <i>Oppositifolia</i> based on phyllotaxy. Although there has been some progress in the phylogeny of <i>Chrysosplenium</i> over the years, the phylogenetic position of some species is still controversial. In this study, we assembled chloroplast genomes (cp genomes) of 34 <i>Chrysosplenium</i> species and performed comparative genomic and phylogenetic analyses in combination with other cp genomes of previously known <i>Chrysosplenium</i> species, for a total of 44 <i>Chrysosplenium</i> species. The comparative analyses revealed that cp genomes of <i>Chrysosplenium</i> species were more conserved in terms of genome structure, gene content and arrangement, SSRs, and codon preference, but differ in genome size and SC/IR boundaries. Phylogenetic analysis showed that cp genomes effectively improved the phylogenetic support and resolution of <i>Chrysosplenium</i> species and strongly supported <i>Chrysosplenium</i> species as a monophyletic taxon and divided into three branches. The results also showed that the sections of <i>Alternifolia</i> and <i>Oppositifolia</i> were not monophyletic with each other, and that <i>C. microspermum</i> was not clustered with other <i>Chrysosplenium</i> species with alternate leaves, but with <i>C. sedakowii</i> into separate branches. In addition, we identified 10 mutational hotspot regions that could serve as potential DNA barcodes for <i>Chrysosplenium</i> species identification. In contrast to <i>Peltoboykinia</i>, the <i>clp</i>P and <i>ycf</i>2 genes of <i>Chrysosplenium</i> were subjected to positive selection and had multiple significant positive selection sites. We further detected a significant positive selection site on the <i>pet</i>G gene between the two sections of <i>Chrysosplenium</i>. These evolutionary characteristics may be related to the growth environment of <i>Chrysosplenium</i> species. This study enriches the cp genomes of <i>Chrysosplenium</i> species and provides a reference for future studies on its evolution and origin.https://www.mdpi.com/1422-0067/24/19/14735<i>Chrysosplenium</i>chloroplastselection pressurephylogenycomparative genome |
| spellingShingle | Tiange Yang Zhihua Wu Jun Tie Rui Qin Jiangqing Wang Hong Liu A Comprehensive Analysis of Chloroplast Genome Provides New Insights into the Evolution of the Genus <i>Chrysosplenium</i> International Journal of Molecular Sciences <i>Chrysosplenium</i> chloroplast selection pressure phylogeny comparative genome |
| title | A Comprehensive Analysis of Chloroplast Genome Provides New Insights into the Evolution of the Genus <i>Chrysosplenium</i> |
| title_full | A Comprehensive Analysis of Chloroplast Genome Provides New Insights into the Evolution of the Genus <i>Chrysosplenium</i> |
| title_fullStr | A Comprehensive Analysis of Chloroplast Genome Provides New Insights into the Evolution of the Genus <i>Chrysosplenium</i> |
| title_full_unstemmed | A Comprehensive Analysis of Chloroplast Genome Provides New Insights into the Evolution of the Genus <i>Chrysosplenium</i> |
| title_short | A Comprehensive Analysis of Chloroplast Genome Provides New Insights into the Evolution of the Genus <i>Chrysosplenium</i> |
| title_sort | comprehensive analysis of chloroplast genome provides new insights into the evolution of the genus i chrysosplenium i |
| topic | <i>Chrysosplenium</i> chloroplast selection pressure phylogeny comparative genome |
| url | https://www.mdpi.com/1422-0067/24/19/14735 |
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