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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...
Autores principales: | , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
PeerJ Inc.
2019
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6756139/ https://www.ncbi.nlm.nih.gov/pubmed/31579601 http://dx.doi.org/10.7717/peerj.7713 |
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author | Yang, Yong Zhang, Ying Chen, Yukai Gul, Juma Zhang, Jingwen Liu, Qiang Chen, Qing |
author_facet | Yang, Yong Zhang, Ying Chen, Yukai Gul, Juma Zhang, Jingwen Liu, Qiang Chen, Qing |
author_sort | Yang, Yong |
collection | PubMed |
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. |
format | Online Article Text |
id | pubmed-6756139 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2019 |
publisher | PeerJ Inc. |
record_format | MEDLINE/PubMed |
spelling | pubmed-67561392019-10-02 Complete chloroplast genome sequence of the mangrove species Kandelia obovata and comparative analyses with related species Yang, Yong Zhang, Ying Chen, Yukai Gul, Juma Zhang, Jingwen Liu, Qiang Chen, Qing PeerJ Bioinformatics 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. PeerJ Inc. 2019-09-20 /pmc/articles/PMC6756139/ /pubmed/31579601 http://dx.doi.org/10.7717/peerj.7713 Text en ©2019 Yang et al. https://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ) and either DOI or URL of the article must be cited. |
spellingShingle | Bioinformatics Yang, Yong Zhang, Ying Chen, Yukai Gul, Juma Zhang, Jingwen Liu, Qiang Chen, Qing Complete chloroplast genome sequence of the mangrove species Kandelia obovata and comparative analyses with related species |
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 | Bioinformatics |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6756139/ https://www.ncbi.nlm.nih.gov/pubmed/31579601 http://dx.doi.org/10.7717/peerj.7713 |
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