Comparative Analysis of the Chloroplast Genome of the Genus Citrus

In this work, we report the comparative analyses of the chloroplast genomes of 34 citrus genotypes. The data indicated that the genus Citrus was composed of three superior clades, the citron/Australian species, the pummelo/micrantha and the papeda/mandarins that underwent three different radiation periods. Chloroplast genomes of citrus contained a remarkable level of heteroplasmy predominatly due to biparental inheritance, a phenomenon that allowed the identification of the parental parent of several citrus hybrids. There were also chloroplastic DNA regions of a few kb with slightly higher SNV and indel variability and intergenic stretches prone to generate deletions. On a finer scale, we identified 6 specific genes that in the coding region accumulated simultaneously high number of SNVs and indels that the average, suggesting that they may function as general hotspots of natural genetic variation in citrus. Positive selection was unambiguously detected in 4 of these genes, matK and ndhF, affecting the Australian species and ycf1 and ccsA, involved in the mandarin group. In here, we present the most comprehensive and detailed study to date upon the evolution and variability of the genus Citrus. Based on a set of high quality non redundant plastid SNVs we present a phylogenetic tree showing a well-supported topology reinforced with additional analyses on indels, heteroplasmic positions and structural variants, providing in this way independent support to this proposal. We then used the SNV set to estimate divergent times between the major citrus groups and to identify faster evolving chloroplastic genes.