Comparative chloroplast genome analysis of Citrus (Rutaceae) species: Insights into genomic characterization, phylogenetic relationships, and discrimination of subgenera

Abstract

Citrus species are fruit trees with great economic value worldwide and have been domesticated and cultivated for several years. Although numerous phylogenetic taxonomy studies have been conducted since the establishment of the genus Citrus, the determination of phylogenetic relationships of Citrus species and the discrimination of Citrus subgenera face some challenges due to species hybridization, polyembryony, and asexual reproduction. In this study, the complete chloroplast genomes of 16 Citrus species were de novo assembled, then several unique characters were identified. For example, infA and rpl22 gene losses occurred in Citrus species; the trnQ-UUG gene may have played a significant role in the evolution of Citrus species; the rpoC1 gene in chloroplast genomes of Citrus species was under positive selection; and several highly variable loci (trnK-UUU–trnQ-UUG, atpF–atpH, trnG-GCC–trnfM-CAU, accD–psaI, petD–rpoA, and rpl32–trnL-UAG) were found in the chloroplast genomes of the Citrus species. These variable loci could serve as potential markers for phylogenetic studies. The genus Citrus was subdivided into seven subgenera based on phylogenetic analyses of the complete chloroplast genomes of Citrus species: Poncirus, Fortunella, Papeda, Citron, Cephalocitrus, Aurantium, and Sinocitrus. This study may help with the identification, taxonomy, use, and evolution of Citrus species.