Plastome evolution and phylogenomics of Trichosporeae (Gesneriaceae) with its morphological characters appraisal

Yan-Fang Cui; Peng Zhou; Kun-Li Xiang; Qiang Zhang; Hua Yan; Li-Guo Zhang; Bo Pan; Yu-Song Huang; Zhi-You Guo; Zhen-Yu Li; Xiao-Guo Xiang

doi:10.3389/fpls.2023.1160535

Plastome evolution and phylogenomics of Trichosporeae (Gesneriaceae) with its morphological characters appraisal

Front Plant Sci. 2023 May 9:14:1160535. doi: 10.3389/fpls.2023.1160535. eCollection 2023.

Authors

Yan-Fang Cui¹, Peng Zhou¹, Kun-Li Xiang², Qiang Zhang³, Hua Yan¹, Li-Guo Zhang¹, Bo Pan³, Yu-Song Huang³, Zhi-You Guo⁴, Zhen-Yu Li², Xiao-Guo Xiang¹

Affiliations

¹ Jiangxi Province Key Laboratory of Watershed Ecosystem Change and Biodiversity, Institute of Life Science and School of Life Sciences, Nanchang University, Nanchang, Jiangxi, China.
² State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China.
³ Guangxi Key Laboratory of Plant Conservation and Restoration Ecology in Karst Terrain, Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences, Guilin, China.
⁴ Qiannan Normal College for Nationalities, College of Biological Sciences and Agriculture, Duyun, Guizhou, China.

Abstract

Trichosporeae is the largest and most taxonomically difficult tribe of Gesneriaceae due to its diverse morphology. Previous studies have not clarified the phylogenetic relationships within this tribe on several DNA markers, including the generic relationships within subtribes. Recently, plastid phylogenomics have been successfully employed to resolve the phylogenetic relationships at different taxonomic levels. In this study, plastid phylogenomics were used to explore the relationships within Trichosporeae. Eleven plastomes of Hemiboea were newly reported. Comparative analyses, phylogeny and morphological character evolution within Trichosporeae were conducted on 79 species representing seven subtribes. The Hemiboea plastomes range from 152,742 bp to 153,695 bp in length. Within Trichosporeae, the sampled plastomes range from 152,196 bp to 156,614 bp and GC content from 37.2% to 37.8%. A total of 121-133 genes were annotated in each species, including 80-91 protein-coding genes, 34-37 tRNA genes, and 8 rRNA genes. The contraction and expansion of IR borders were not detected, and gene rearrangements and inversions did not occur. The 13 hypervariable regions were proposed as the potential molecular markers for species identification. A total of 24,299 SNPs and 3,378 indels were inferred, and most of the SNPs were functionally missense and silent variations. There were 1968 SSRs, 2055 tandem repeats and 2802 dispersed repeats. The RSCU and ENC values indicated that the codon usage pattern was conserved in Trichosporeae. Both the phylogenetic frameworks based on the whole plastome and 80 CDSs were basically concordant. The sister relationships between Loxocarpinae and Didymocarpinae were confirmed, and Oreocharis was a sister group of Hemiboea with high support. The morphological characters showed a complex evolutionary pattern of Trichosporeae. Our findings may contribute to future research on genetic diversity, morphological evolutionary patterns, and conservation of the tribe Trichosporeae.

Keywords: Gesneriaceae; Hemiboea; Trichosporeae; molecular markers; phylogenomics; plastome evolution.

Grants and funding

This research was supported by the National Natural Science Foundation of China (32060056, 31670212, 31370227 and 31300181), and the Thousand Talents Program of Jiangxi Province (jxsq2018106032).