The complete chloroplast genome of a mangrove Kandelia obovata Sheue, Liu & Yong.
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ABSTRACT:
SUBMITTER: Du Z
PROVIDER: S-EPMC7707256 | biostudies-literature | 2019 Oct
REPOSITORIES: biostudies-literature
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The complete chloroplast genome of a mangrove <i>Kandelia obovata</i> Sheue, Liu & Yong.
Du Zhaokui Z Li Junmin J Yang Dang D
Mitochondrial DNA. Part B, Resources 20191007 2
<i>Kandelia obovata</i> is a widely distributed species of mangrove in Eastern Asia. In this study, the complete chloroplast genome sequence of <i>K. obovata</i> was assembled and characterised from high-throughput sequencing data. The chloroplast genome was 168,244 bp in length, consisting of large single-copy (LSC) and small single-copy (SSC) regions of 94,869 bp and 20,088 bp, respectively, which were separated by a pair of 26,618 bp inverted repeat (IR) regions. The genome is predicted to co ...[more]
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Project 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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