The Genome and Transcriptome Analysis of the Chloroplast.

is cultivated in approximately 5 million hectares worldwide. The chloroplast genome of this species has not been previously reported. In this study, we sequenced the genome and transcriptome of the chloroplast. We identified many positively selected genes in the photosynthetic pathway (e.g., , , and ) and RNA polymerase genes (e.g., ) from the comparison of the chloroplast genome of , temperate legume species, and tropical legume species. Our transcriptome data from PacBio isoform sequencing showed that the 51-kb DNA inversion could affect the transcriptional regulation of polycistronic. Using Illumina deep RNA sequencing, we found RNA editing of in the leaf, shoot, flower, fruit, and root tissues of . We also found three G-to-A RNA editing events that change guanine to adenine in the transcripts transcribed from the adenine-rich regions of the gene. The edited guanine bases were found particularly in the chloroplast genome of the species. These G-to-A RNA editing events were likely to provide a mechanism for correcting DNA base mutations. The chloroplast genome sequence and the analysis results obtained in this study can apply to phylogenetic studies and chloroplast genome engineering.