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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.

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