Comparative chloroplast genome analyses of potentilleae: insights into genome characteristics, mutational hotspots, and adaptive evolution.

Abstract

Potentilleae Sweet is a large tribe within Rosaceae Juss., with over 1700 species across 13 genera worldwide. Some achievements have been obtained in the study of phylogenetic relationships among Potentilleae genera and its origin and diversification, while its chloroplast (cp.) genome characteristics, mutational hotspots and adaptive evolution are still open questions. In this study, we conducted comparative genomic study on 79 complete cp. genomes of Potentilleae. The Potentilleae cp. genome has a typical quadripartite structure, with a total length of 150,586 - 156,798 bp and Guanine and cytosine (GC) content of 36.7-37.3%. Although some slight differences were present in cp. genome size, GC content, and inverted repeat (IR)/single-copy (SC) boundary regions, gene structure, gene content and gene order of the Potentilleae cp. genome were conserved. Thirteen regions (psaJ-rpl33, rpl16-rps3, petA-psbJ, rpl16 intron, rpl32-trnL^-UAG, trnH^-GUG-psbA, trnR^-UCU-atpA, ndhG-ndhI, accD-psaI, trnL^-UAA-trnF^-GAA, trnP^-UGG-psaJ, ycf4-cemA, ndhC-trnV^-UAC) were identified as excellent molecular markers for phylogenetic application. Twenty-three genes (rps16, rpl20, rpl22, rpl23, rpoA, rpoC2, psaA, psbB, psbC, psbH, psbF, psbJ, rbcL, ndhA, ndhB, ndhD, ndhF, ndhI, accD, ccsA, matK, ycf1, ycf2) were positively selected. The adaptive evolution of these genes might play essential roles in the long evolutionary history of Potentilleae. This study will lay a foundation for the future research on identification, phylogeny and adaptive evolution of Potentilleae species.