Genome Comparison Reveals Mutation Hotspots in the Chloroplast Genome and Phylogenetic Relationships of<i> Ormosia</i> Species

Abstract

The papilionoid legume genus <i>Ormosia</i> comprises approximately 130 species, which are distributed mostly in the Neotropics, with some species in eastern Asia and northeastern Australia. The taxonomy and evolutionary history remain unclear due to the lack of a robust species-level phylogeny. Chloroplast genomes can provide important information for phylogenetic and population genetic studies. In this study, we determined the complete chloroplast genome sequences of five <i>Ormosia</i> species by Illumina sequencing. The <i>Ormosia</i> chloroplast genomes displayed the typical quadripartite structure of angiosperms, which consisted of a pair of inverted regions separated by a large single-copy region and a small single-copy region. The location and distribution of repeat sequences and microsatellites were determined. Comparative analyses highlighted a wide spectrum of variation, with <i>trnK-rbcL</i>, <i>atpE-trnS-rps4</i>, <i>trnC-petN</i>, <i>trnS-psbZ-trnG</i>, <i>trnP-psaJ-rpl33,</i> and <i>clpP</i> intron being the most variable regions. Phylogenetic analysis revealed that <i>Ormosia</i> is in the Papilionoideae clade and is sister to the <i>Lupinus</i> clade. Overall, this study, which provides <i>Ormosia</i> chloroplast genomic resources and a comparative analysis of <i>Ormosia</i> chloroplast genomes, will be beneficial for the evolutionary study and phylogenetic reconstruction of the genus <i>Ormosia</i> and molecular barcoding in population genetics and will provide insight into the chloroplast genome evolution of legumes.