Complete chloroplast genomes of four Atalantia (Rutaceae) species: insights into comparative analysis, phylogenetic relationships, and divergence time estimation.

Atalantia plants are small trees in the family Rutaceae that have great potential for use in agriculture, medicine, and carving. However, the phylogenetic relationships of Atalantia species have not been systematically studied due to the lack of available molecular resources and highly variable molecular markers. In this study, the complete chloroplast genomes of four Atalantia species were newly sequenced and characterized. The length of the chloroplast genomes in Atalantia species ranged from 159,557 to 160,341 bp, which was more similar to Fortunella and Citrus species in the Rutaceae. The rpl22 genes were pseudogenized at the SSC/IRa boundary. Certain mechanisms have been evolved to compensate for the pseudogenization of the accD and infA genes in Atalantia chloroplast genomes. Some highly divergent intergenic regions (trnH-GUG–psbA, rps16–trnQ-UUG, trnS-GCU–trnG-UCC, atpF–atpI, petN–psbM, psbM–trnD-GUC, ndhC–trnV-UAC, atpB–rbcL, accD–psaI, and ycf4–cemA) and genes (psbM, trnD-GUC, rpl32, ndhF, and ycf1) were detected, which serve as potential phylogenetic markers. The phylogenetic relationships and divergence times of Atalantia species were explored based on the complete chloroplast genome. Based on the phylogenetic trees, Atalantia species were grouped into two sub-branches. Atalantia monophylla and A. buxifolia were found to be more closely related, whereas A. ceylanica and A. roxburghiana exhibited a closer relationship. The divergence time estimation indicated that the common ancestor of the Atalantia species diverged approximately 14.26 million years ago. These findings will help with the identification, categorization, and utilization of Atalantia species. [ABSTRACT FROM AUTHOR]