Evolutionary Analysis of Plastid Genomes of Seven L. Species: Implications for Sequence Divergence and Phylogenetic Relationships.

Plant plastomes play crucial roles in species evolution and phylogenetic reconstruction studies due to being maternally inherited and due to the moderate evolutionary rate of genomes. However, patterns of sequence divergence and molecular evolution of the plastid genomes in the horticulturally- and economically-important L. species are poorly understood. In this study, we collected the complete plastomes of seven species and determined the various repeat sequence variations and protein sequence evolution by comparative genomic analysis. A total of 498 repeats were identified in plastid genomes, which included tandem (130), dispersed (277), and palindromic (91) types of repeat variations. Simple sequence repeat (SSR) elements analysis indicated the enriched SSRs in seven genomes to be mononucleotides, followed by tetra-nucleotides, dinucleotides, tri-nucleotides, hex-nucleotides, and penta-nucleotides. We identified 18 divergence hotspot regions (, , , , , , , , , , , , , , , , intron, and ) that could be used as the potential molecular genetic markers for the further study of population genetics and phylogenetic evolution of species. We found that a large number of repeat sequences were distributed in the divergence hotspots of plastid genomes. Interestingly, 16 genes were determined under positive selection, which included four genes for the subunits of ribosome proteins ( , and ), three genes for the subunits of photosystem proteins (, and ), three NADH oxidoreductase genes (, , and ), two subunits of ATP genes ( and ), and four other genes (, , , and ). Phylogenetic analysis based on the whole plastome demonstrated that the seven species form a highly-supported monophyletic clade. The availability of these plastid genomes provides important genetic information for further species identification and biological research on .