Enhalus acoroides is the largest tropic seagrass, occurring in the shallow coastal areas. In this study, we characterized the complete chloroplast genome sequence of this species. The whole chloroplast genome was 176,211 bp in length with a typical quadripartite structure, including one large single-copy (LSC) region (89,851 bp), one small single-copy (SSC) region (2150 bp), and a pair of inverted repeats (IRs) (42,105 bp). The guanine-cytosine (GC) content of this genome was 38.4%. A total of 142 genes were found in this genome, including 95 protein-coding genes, 39 tRNA genes, and 8 rRNA genes. The phylogenetic analysis indicated that E. acoroides and Thalassia hemprichii formed a distinct clade.
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