Complete chloroplast genome sequence of pineapple (Ananas comosus)

Since chloroplasts are maternally inherited and have unique features in evolution, their genome sequences have been broadly used in phylogenetic studies of plants. Here, we assembled the chloroplast genome sequence of cultivated pineapple (Ananas comosus (L.) Merr.) that is the most economically significant plant in the Bromeliaceae using next-generation sequencers. The genome length was 159,636 bp and included a pair of inverted repeats of 26,774 bp separated by a small single-copy region of 18,622 bp and a large single-copy region of 87,466 bp. The genome contained 113 unique genes (79 protein-coding, 4 rRNA, and 30 tRNA genes), 19 of which were duplicated in the inverted repeats, giving a total of 132 genes. We identified a total of 65 simple sequence repeats of >10 bp in length. Phylogenetic tree identified Ananas as a basal member of the Poales, closer to Musa (Musaceae, Zingiberales) than to species of the Poaceae. The genes, indels, and simple sequence repeats identified in this study will provide tools for use in evolutionary studies at both intra- and interspecific levels.