Chloroplast Genomic Resources and Genetic Divergence of Endangered Species Bretschneidera sinensis (Bretschneideraceae)
Bretschneidera sinensis is an endangered woody species found in East and South China. Comprehensive intraspecies chloroplast genome studies have demonstrated novel genetic resources to assess the genetic variation and diversity of this species. Using genome skimming method, we assembled the whole ch...
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Frontiers Media S.A.
2022-06-01
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| Series: | Frontiers in Ecology and Evolution |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fevo.2022.873100/full |
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| author | Ce Shang Enze Li Zhucheng Yu Mengjia Lian Zhuo Chen Kangjia Liu Linli Xu Zhe Tong Meifang Wang Wenpan Dong |
| author_facet | Ce Shang Enze Li Zhucheng Yu Mengjia Lian Zhuo Chen Kangjia Liu Linli Xu Zhe Tong Meifang Wang Wenpan Dong |
| author_sort | Ce Shang |
| collection | DOAJ |
| description | Bretschneidera sinensis is an endangered woody species found in East and South China. Comprehensive intraspecies chloroplast genome studies have demonstrated novel genetic resources to assess the genetic variation and diversity of this species. Using genome skimming method, we assembled the whole chloroplast genome of 12 genotypes of B. sinensis from different geographical locations, covering most wild populations. The B. sinensis chloroplast genome size ranged from 158,959 to 159,045 base pairs (bp) and displayed a typical circular quadripartite structure. Comparative analyses of 12 B. sinensis chloroplast genome revealed 33 polymorphic simple sequence repeats (SSRs), 105 polymorphic single nucleotide polymorphisms (SNPs), and 55 indels. Phylogenetic analysis showed that the 12 genotypes were grouped into 2 branches, which is consistent with the geographical distribution (Eastern clade and Western clade). Divergence time estimates showed that the two clades were divergent from 0.6 Ma in the late Pleistocene. Ex situ conservation is essential for this species. In this study, we identified SNPs, indels, and microsatellites of B. sinensis by comparative analyses of chloroplast genomes and determined genetic variation between populations using these genomic markers. Chloroplast genomic resources are also important for further domestication, population genetic, and phylogenetic analysis, possibly in combination with molecular markers of mitochondrial and/or nuclear genomes. |
| first_indexed | 2024-04-13T22:16:59Z |
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| issn | 2296-701X |
| language | English |
| last_indexed | 2024-04-13T22:16:59Z |
| publishDate | 2022-06-01 |
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| series | Frontiers in Ecology and Evolution |
| spelling | doaj.art-f6c2c9c2dcc14c2faf4a25a653a8a2872022-12-22T02:27:30ZengFrontiers Media S.A.Frontiers in Ecology and Evolution2296-701X2022-06-011010.3389/fevo.2022.873100873100Chloroplast Genomic Resources and Genetic Divergence of Endangered Species Bretschneidera sinensis (Bretschneideraceae)Ce Shang0Enze Li1Zhucheng Yu2Mengjia Lian3Zhuo Chen4Kangjia Liu5Linli Xu6Zhe Tong7Meifang Wang8Wenpan Dong9Laboratory of Systematic Evolution and Biogeography of Woody Plants, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, ChinaLaboratory of Systematic Evolution and Biogeography of Woody Plants, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, ChinaXianxialing Provincial Nature Reserve Management Center, Jiangshan, ChinaLaboratory of Systematic Evolution and Biogeography of Woody Plants, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, ChinaXianxialing Provincial Nature Reserve Management Center, Jiangshan, ChinaLaboratory of Systematic Evolution and Biogeography of Woody Plants, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, ChinaXianxialing Provincial Nature Reserve Management Center, Jiangshan, ChinaXianxialing Provincial Nature Reserve Management Center, Jiangshan, ChinaXianxialing Provincial Nature Reserve Management Center, Jiangshan, ChinaLaboratory of Systematic Evolution and Biogeography of Woody Plants, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, ChinaBretschneidera sinensis is an endangered woody species found in East and South China. Comprehensive intraspecies chloroplast genome studies have demonstrated novel genetic resources to assess the genetic variation and diversity of this species. Using genome skimming method, we assembled the whole chloroplast genome of 12 genotypes of B. sinensis from different geographical locations, covering most wild populations. The B. sinensis chloroplast genome size ranged from 158,959 to 159,045 base pairs (bp) and displayed a typical circular quadripartite structure. Comparative analyses of 12 B. sinensis chloroplast genome revealed 33 polymorphic simple sequence repeats (SSRs), 105 polymorphic single nucleotide polymorphisms (SNPs), and 55 indels. Phylogenetic analysis showed that the 12 genotypes were grouped into 2 branches, which is consistent with the geographical distribution (Eastern clade and Western clade). Divergence time estimates showed that the two clades were divergent from 0.6 Ma in the late Pleistocene. Ex situ conservation is essential for this species. In this study, we identified SNPs, indels, and microsatellites of B. sinensis by comparative analyses of chloroplast genomes and determined genetic variation between populations using these genomic markers. Chloroplast genomic resources are also important for further domestication, population genetic, and phylogenetic analysis, possibly in combination with molecular markers of mitochondrial and/or nuclear genomes.https://www.frontiersin.org/articles/10.3389/fevo.2022.873100/fullchloroplast genomeBretschneidera sinensisex situ conservationgenetic resourcesgenetic variation |
| spellingShingle | Ce Shang Enze Li Zhucheng Yu Mengjia Lian Zhuo Chen Kangjia Liu Linli Xu Zhe Tong Meifang Wang Wenpan Dong Chloroplast Genomic Resources and Genetic Divergence of Endangered Species Bretschneidera sinensis (Bretschneideraceae) Frontiers in Ecology and Evolution chloroplast genome Bretschneidera sinensis ex situ conservation genetic resources genetic variation |
| title | Chloroplast Genomic Resources and Genetic Divergence of Endangered Species Bretschneidera sinensis (Bretschneideraceae) |
| title_full | Chloroplast Genomic Resources and Genetic Divergence of Endangered Species Bretschneidera sinensis (Bretschneideraceae) |
| title_fullStr | Chloroplast Genomic Resources and Genetic Divergence of Endangered Species Bretschneidera sinensis (Bretschneideraceae) |
| title_full_unstemmed | Chloroplast Genomic Resources and Genetic Divergence of Endangered Species Bretschneidera sinensis (Bretschneideraceae) |
| title_short | Chloroplast Genomic Resources and Genetic Divergence of Endangered Species Bretschneidera sinensis (Bretschneideraceae) |
| title_sort | chloroplast genomic resources and genetic divergence of endangered species bretschneidera sinensis bretschneideraceae |
| topic | chloroplast genome Bretschneidera sinensis ex situ conservation genetic resources genetic variation |
| url | https://www.frontiersin.org/articles/10.3389/fevo.2022.873100/full |
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