Comparative chloroplast genome analysis of six millet species along with related Poaceae family members

Millets considered as storehouse of nutrients, are C4 plants that offer a more reliable yield than other crops in low-rainfall regions. Within the millet species, comparative and reconstructed phylogenetic analysis were performed. We compared the two major millet, four minor millet and one cereal crop chloroplast genomes and obtained a complete map of the variability across the genomes. Despite variations in genome size, SSR, and the SC/IR boundary, we observed the high consistency patterns of codon bias, genome structure, and gene content. For comparison across the genome, a whole genome alignment was performed. The chloroplast genomes locally collinear blocks revealed that their gene organization and order had been well preserved. Based on the examination of the entire chloroplast genomes, phylogenetic relationships for the millet species were discovered with Oryza sativa as an outgroup using Maximum Likelihood analysis. Future breeding programmes for valuable millet and cereal crops in the Poaceae family would benefit greatly from this information. Graphical abstract