AUTHOR=Wang Yifei , Wen Fang , Hong Xin , Li Zhenglong , Mi Yaolei , Zhao Bo 

TITLE=Comparative chloroplast genome analyses of Paraboea (Gesneriaceae): Insights into adaptive evolution and phylogenetic analysis

JOURNAL=Frontiers in Plant Science

VOLUME=13

YEAR=2022

URL=https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2022.1019831

DOI=10.3389/fpls.2022.1019831

ISSN=1664-462X

ABSTRACT=<p><italic>Paraboea</italic> (Gesneriaceae) distributed in the karst areas of South and Southwest China and Southeast Asia, is an ideal genus to study the phylogeny and adaptive evolution of karst plants. In this study, the complete chloroplast genomes of twelve <italic>Paraboea</italic> species were sequenced and analyzed. Twelve chloroplast genomes ranged in size from 153166 to 154245 bp. Each chloroplast genome had a typical quartile structure, and relatively conserved type and number of gene components, including 131 genes which are composed of 87 protein coding genes, 36 transfer RNAs and 8 ribosomal RNAs. A total of 600 simple sequence repeats and 389 non-overlapped sequence repeats were obtained from the twelve <italic>Paraboea</italic> chloroplast genomes. We found ten divergent regions (<italic>trn</italic>H-GUG-<italic>psb</italic>A, <italic>trn</italic>M-CAU, <italic>trn</italic>C-GCA, <italic>atp</italic>F-<italic>atp</italic>H, <italic>ycf1</italic>, <italic>trn</italic>K-UUU-<italic>rps</italic>16, <italic>rps</italic>15, <italic>pet</italic>L, <italic>trn</italic>S-GCU-<italic>trn</italic>R-UCU and <italic>psa</italic>J-<italic>rpl</italic>33) among the 12 <italic>Paraboea</italic> species to be potential molecular markers. In the phylogenetic tree of 31 Gesneriaceae plants including twelve <italic>Paraboea</italic> species, all <italic>Paraboea</italic> species clustered in a clade and confirmed the monophyly of <italic>Paraboea</italic>. Nine genes with positive selection sites were detected, most of which were related to photosynthesis and protein synthesis, and might played crucial roles in the adaptability of <italic>Paraboea</italic> to diverse karst environments. These findings are valuable for further study of the phylogeny and karst adaptability of Gesneriaceae plants.</p>