Organelle genomes of Indigofera amblyantha and Indigofera pseudotinctoria: comparative genome analysis, and intracellular gene transfer

Organelles (chloroplast and mitochondria) are involved in some essential processes, including energy production and photosynthesis, while proteins coded by genes in organelle genomes regulate gene transcription. Research on Indigofera species has been limited by lack of organelle information on population genetics, species identification, and breeding researches. Here, we sequenced and assembled the organelle genomes of two ecologically and medicinally important Indigofera species, namely Indigofera amblyantha and I. pseudotinctoria. Comparative genome analysis among the chloroplast genomes of both species, and a further three Indigofera species revealed some intergenic ‘hotspot’ regions with potential as markers for species identification. mVISTA analysis revealed significant variations in two genes, ribosomal protein L32 (rpl32) and hypothetical chloroplast reading frame 1 (ycf1), evidenced by high nucleic acid diversity values (0.0222 for rpl32 and 0.0342 for ycf1). Furthermore, both genes exhibited nonsynonymous/synonymous substitution values greater than one between some pairwise chloroplast genomes, suggesting that they play an important role in evolution. We detected abundant repeated sequences in both mitogenomes. Notably, two large repeats with length of more than 1000 bp were identified in the I. amblyantha mitogenome, which might lead to the complex structure of I. amblyantha and I. pseudotinctoria mitogenomes. Our results further indicated that some homologous sequences in the mitogenomes migrated from chloroplast genes via intracellular gene transfer. Collectively, these findings provide valuable insights to guide future species identification and molecular evolution of Indigofera species.