Comparative analyses of Linderniaceae plastomes, with implications for its phylogeny and evolution

Rongrong Yan; Yanfei Geng; Yuhuan Jia; Chunlei Xiang; Xinxin Zhou; Guoxiong Hu

doi:10.3389/fpls.2023.1265641

Comparative analyses of Linderniaceae plastomes, with implications for its phylogeny and evolution

Front Plant Sci. 2023 Sep 26:14:1265641. doi: 10.3389/fpls.2023.1265641. eCollection 2023.

Authors

Rongrong Yan^{1

2}, Yanfei Geng³, Yuhuan Jia^{1

2}, Chunlei Xiang⁴, Xinxin Zhou⁵, Guoxiong Hu^{1

2}

Affiliations

¹ Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Guizhou University, Guiyang, Guizhou, China.
² College of Life Sciences, Guizhou University, Guiyang, Guizhou, China.
³ College of Tea Science, Guizhou University, Guiyang, Guizhou, China.
⁴ Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China.
⁵ South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, Guangdong, China.

Abstract

Introduction: The recently established Linderniaceae, separated from the traditionally defined Scrophulariaceae, is a taxonomically complicated family. Although previous phylogenetic studies based on a few short DNA markers have made great contributions to the taxonomy of Linderniaceae, limited sampling and low resolution of the phylogenetic tree have failed to resolve controversies between some generic circumscriptions. The plastid genome exhibits a powerful ability to solve phylogenetic relationships ranging from shallow to deep taxonomic levels. To date, no plastid phylogenomic studies have been carried out in Linderniaceae.

Methods: In this study, we newly sequenced 26 plastid genomes of Linderniaceae, including eight genera and 25 species, to explore the phylogenetic relationships and genome evolution of the family through plastid phylogenomic and comparative genomic analyses.

Results: The plastid genome size of Linderniaceae ranged from 152,386 bp to 154,402 bp, exhibiting a typical quartile structure. All plastomes encoded 114 unique genes, comprising 80 protein-coding genes, 30 tRNA genes, and four rRNA genes. The inverted repeat regions were more conserved compared with the single-copy regions. A total of 1803 microsatellites and 1909 long sequence repeats were identified, and five hypervariable regions (petN-psbM, rps16-trnQ, rpl32-trnL, rpl32, and ycf1) were screened out. Most protein-coding genes were relatively conserved, with only the ycf2 gene found under positive selection in a few species. Phylogenomic analyses confirmed that Linderniaceae was a distinctive lineage and revealed that the presently circumscribed Vandellia and Torenia were non-monophyletic.

Discussion: Comparative analyses showed the Linderniaceae plastomes were highly conservative in terms of structure, gene order, and gene content. Combining morphological and molecular evidence, we supported the newly established Yamazakia separating from Vandellia and the monotypic Picria as a separate genus. These findings provide further evidence to recognize the phylogenetic relationships among Linderniaceae and new insights into the evolution of the plastid genomes.

Keywords: Lindernia; Lindernieae; Picria; Scrophulariaceae; Torenia; chloroplast genome; phylogenomics.

Grants and funding

The authors declare financial support was received for the research, authorship, and/or publication of this article. This research was funded by the National Natural Science Foundation of China (32060048, 32260099), the Natural Science Foundation of Guizhou Province (Qiankehejichu-ZK [2021] 091, Qiankehezhongyindi [2023] 029).