Complete chloroplast genome sequence of the mangrove species Kandelia obovata and comparative analyses with related species
As one of the most cold and salt-tolerant mangrove species, Kandelia obovata is widely distributed in China. Here, we report the complete chloroplast genome sequence K. obovata (Rhizophoraceae) obtained via next-generation sequencing, compare the general features of the sampled plastomes of this spe...
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PeerJ Inc.
2019-09-01
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| author | Yong Yang Ying Zhang Yukai Chen Juma Gul Jingwen Zhang Qiang Liu Qing Chen |
| author_facet | Yong Yang Ying Zhang Yukai Chen Juma Gul Jingwen Zhang Qiang Liu Qing Chen |
| author_sort | Yong Yang |
| collection | DOAJ |
| description | As one of the most cold and salt-tolerant mangrove species, Kandelia obovata is widely distributed in China. Here, we report the complete chloroplast genome sequence K. obovata (Rhizophoraceae) obtained via next-generation sequencing, compare the general features of the sampled plastomes of this species to those of other sequenced mangrove species, and perform a phylogenetic analysis based on the protein-coding genes of these plastomes. The complete chloroplast genome of K. obovata is 160,325 bp in size and has a 35.22% GC content. The genome has a typical circular quadripartite structure, with a pair of inverted repeat (IR) regions 26,670 bp in length separating a large single-copy (LSC) region (91,156 bp) and a small single-cope (SSC) region (15,829 bp). The chloroplast genome of K. obovata contains 128 unique genes, including 80 protein-coding genes, 38 tRNA genes, 8 rRNA genes and 2 pseudogenes (ycf1 in the IRA region and rpl22 in the IRB region). In addition, a simple sequence repeat (SSR) analysis found 108 SSR loci in the chloroplast genome of K. obovata, most of which are A/T rich. IR expansion and contraction regions were compared between K. obovata and five related species: two from Malpighiales and three mangrove species from different orders. The mVISTA results indicated that the genome structure, gene order and gene content are highly conserved among the analyzed species. The phylogenetic analysis using 54 common protein-coding genes from the chloroplast genome showed that the plant most closely related to K. obovata is Ceriops tagal of Rhizophoraceae. The results of this study provide useful molecular information about the evolution and molecular biology of these mangrove trees. |
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| spelling | doaj.art-ca762eddd63d4d8aac09c0a69eb06cd42023-12-03T10:34:09ZengPeerJ Inc.PeerJ2167-83592019-09-017e771310.7717/peerj.7713Complete chloroplast genome sequence of the mangrove species Kandelia obovata and comparative analyses with related speciesYong Yang0Ying Zhang1Yukai Chen2Juma Gul3Jingwen Zhang4Qiang Liu5Qing Chen6Ministry of Education Key Laboratory for Ecology of Tropical Islands, College of Life Sciences, Hainan Normal University, Haikou, ChinaLife Sciences and Technology School, Lingnan Normal University, Zhanjiang, ChinaMinistry of Education Key Laboratory for Ecology of Tropical Islands, College of Life Sciences, Hainan Normal University, Haikou, ChinaMinistry of Education Key Laboratory for Ecology of Tropical Islands, College of Life Sciences, Hainan Normal University, Haikou, ChinaMinistry of Education Key Laboratory for Ecology of Tropical Islands, College of Life Sciences, Hainan Normal University, Haikou, ChinaMinistry of Education Key Laboratory for Ecology of Tropical Islands, College of Life Sciences, Hainan Normal University, Haikou, ChinaBawangling National Nature Reserve, Changjiang, Hainan Province, ChinaAs one of the most cold and salt-tolerant mangrove species, Kandelia obovata is widely distributed in China. Here, we report the complete chloroplast genome sequence K. obovata (Rhizophoraceae) obtained via next-generation sequencing, compare the general features of the sampled plastomes of this species to those of other sequenced mangrove species, and perform a phylogenetic analysis based on the protein-coding genes of these plastomes. The complete chloroplast genome of K. obovata is 160,325 bp in size and has a 35.22% GC content. The genome has a typical circular quadripartite structure, with a pair of inverted repeat (IR) regions 26,670 bp in length separating a large single-copy (LSC) region (91,156 bp) and a small single-cope (SSC) region (15,829 bp). The chloroplast genome of K. obovata contains 128 unique genes, including 80 protein-coding genes, 38 tRNA genes, 8 rRNA genes and 2 pseudogenes (ycf1 in the IRA region and rpl22 in the IRB region). In addition, a simple sequence repeat (SSR) analysis found 108 SSR loci in the chloroplast genome of K. obovata, most of which are A/T rich. IR expansion and contraction regions were compared between K. obovata and five related species: two from Malpighiales and three mangrove species from different orders. The mVISTA results indicated that the genome structure, gene order and gene content are highly conserved among the analyzed species. The phylogenetic analysis using 54 common protein-coding genes from the chloroplast genome showed that the plant most closely related to K. obovata is Ceriops tagal of Rhizophoraceae. The results of this study provide useful molecular information about the evolution and molecular biology of these mangrove trees.https://peerj.com/articles/7713.pdfChloroplast genomeKandelia obovataMangrove speciesPhylogeny comparative analysis |
| spellingShingle | Yong Yang Ying Zhang Yukai Chen Juma Gul Jingwen Zhang Qiang Liu Qing Chen Complete chloroplast genome sequence of the mangrove species Kandelia obovata and comparative analyses with related species PeerJ Chloroplast genome Kandelia obovata Mangrove species Phylogeny comparative analysis |
| title | Complete chloroplast genome sequence of the mangrove species Kandelia obovata and comparative analyses with related species |
| title_full | Complete chloroplast genome sequence of the mangrove species Kandelia obovata and comparative analyses with related species |
| title_fullStr | Complete chloroplast genome sequence of the mangrove species Kandelia obovata and comparative analyses with related species |
| title_full_unstemmed | Complete chloroplast genome sequence of the mangrove species Kandelia obovata and comparative analyses with related species |
| title_short | Complete chloroplast genome sequence of the mangrove species Kandelia obovata and comparative analyses with related species |
| title_sort | complete chloroplast genome sequence of the mangrove species kandelia obovata and comparative analyses with related species |
| topic | Chloroplast genome Kandelia obovata Mangrove species Phylogeny comparative analysis |
| url | https://peerj.com/articles/7713.pdf |
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