The chloroplast genome of the Iris japonica Thunberg (Butterfly flower) reveals the genomic and evolutionary characteristics of Iris species

Iris japonica Thunberg is one of the horticultural species belonging to the Iris genus and Iridaceae family. Previous studies have revealed its hepatoprotective activity and ornamental values. However, little genetic and genomic information about this species is available. Here, to decipher the chloroplast genome and reveal its evolutionary characteristics, we sequenced, de novo assembled, and comprehensively analyzed the chloroplast genome of I. japonica. The genome was 152,453 bp in length and displayed a circular structure with a large single-copy region, a small single-copy region, and two inverted repeat regions. It contained 131 genes, including 85 protein-coding genes, eight ribosomal RNA genes, and 38 transfer RNA genes. We also identified 23 microsatellite repeat sequences, 34 tandem repeat sequences, and 60 dispersed repeat sequences in the chloroplast genome of I. japonica. Sequence divergence analyses of the chloroplast genomes of 20 Iris species revealed that the top four most highly variable regions were ndhC-trnV-UAC, rpl22-rps19, rps16-trnQ-UUG, and trnG-UCC-trnR-UCU. Phylogenetic analysis showed that I. japonica was most closely related to I. tectorum. This study reported a new chloroplast genome of I. japonica and performed comparative analyses of 20 Iris chloroplast genomes. The results would facilitate the evolutionary research and development of molecular markers for Iris species.