Complete chloroplast genome sequence of the mangrove species Kandelia obovata and comparative analyses with related species.

Yong Yang,Yukai Chen,Qiang Liu,Jingwen Zhang,Ying Zhang,Juma Gul,Qing Chen

doi:10.7717/peerj.7713

Yong Yang, Yukai Chen + Show 5 more

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https://doi.org/10.7717/peerj.7713

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Abstract

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.

Highlights

Kandelia obovata Sheue, Liu & Yong, 2003 is a viviparous mangrove species belonging to Rhizophoraceae in Malpighiales that inhabits the intertidal zones of tropical and subtropical coasts
As the rRNA genes rrn23, rrn16, rrn5 and rrn4.5 are located in the inverted repeat (IR) region, the IR region shows a higher GC content
The K. obovata chloroplast genome includes 128 unique genes encoding 80 proteins, 8 rRNAs, 38 tRNAs and two 2 pseudogenes. rps19 and cemA begin with GTG, and ndhD begin with ACG; these changes are most likely made at the RNA stage

Summary

Introduction

Kandelia obovata Sheue, Liu & Yong, 2003 is a viviparous mangrove species belonging to Rhizophoraceae in Malpighiales that inhabits the intertidal zones of tropical and subtropical coasts. It is distributed from northern Vietnam through southeast China to south Japan in. East Asia (Sheue, Liu & Yong, 2003; Tomlinson, 1986). This species is naturally distributed in the Hainan, Guangdong (including Hong Kong and Macau), Guangxi, Fujian and Taiwan Provinces of China (Li & Lee, 1997). There has been no report of the chloroplast genome of K. obovata, which may be important for illuminating the evolution of mangrove species

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