4.7 Article

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

Journal

FRONTIERS IN PLANT SCIENCE
Volume 13, Issue -, Pages -

Publisher

FRONTIERS MEDIA SA
DOI: 10.3389/fpls.2022.1019831

Keywords

Paraboea; phylogenetic; positive selection; chloroplast; genome

Categories

Funding

  1. Key Sci. & Tech. Research and Development Project of Guangxi [Guike AD20159091, ZY21195050]
  2. Guangxi Natural Science Foundation [2020GXNSFBA297049]
  3. capacity-building project of SBR of CAS [KFJ-BRP-017-68]
  4. Anhui Provincial Natural Science Foundation [1908085QC1]
  5. Fund of Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations [PSESP2021F07]

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In this study, the complete chloroplast genomes of twelve Paraboea species were sequenced and analyzed, revealing the genomic structure and composition, as well as potential molecular markers. In the phylogenetic tree, all Paraboea species formed a distinct clade, confirming their monophyly. Additionally, genes related to photosynthesis and protein synthesis were found to play crucial roles in the adaptability of Paraboea to diverse karst environments.
Paraboea (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 Paraboea 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 Paraboea chloroplast genomes. We found ten divergent regions (trnH-GUG-psbA, trnM-CAU, trnC-GCA, atpF-atpH, ycf1, trnK-UUU-rps16, rps15, petL, trnS-GCU-trnR-UCU and psaJ-rpl33) among the 12 Paraboea species to be potential molecular markers. In the phylogenetic tree of 31 Gesneriaceae plants including twelve Paraboea species, all Paraboea species clustered in a clade and confirmed the monophyly of Paraboea. 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 Paraboea to diverse karst environments. These findings are valuable for further study of the phylogeny and karst adaptability of Gesneriaceae plants.

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