Insights into comparative genomics, structural features, and phylogenetic relationship of species from Eurasian Aster and its related genera (Asteraceae: Astereae) based on complete chloroplast genome

Hui Chen; Tingyu Li; Xinyu Chen; Tianmeng Qu; Xinyi Zheng; Junjia Luo; Bo Li; Guojin Zhang; Zhixi Fu

doi:10.3389/fpls.2024.1367132

Insights into comparative genomics, structural features, and phylogenetic relationship of species from Eurasian Aster and its related genera (Asteraceae: Astereae) based on complete chloroplast genome

Front Plant Sci. 2024 Apr 26:15:1367132. doi: 10.3389/fpls.2024.1367132. eCollection 2024.

Authors

Hui Chen^{1

2}, Tingyu Li¹, Xinyu Chen¹, Tianmeng Qu¹, Xinyi Zheng¹, Junjia Luo¹, Bo Li³, Guojin Zhang⁴, Zhixi Fu^{1

2

5}

Affiliations

¹ Key Laboratory of Land Resources Evaluation and Monitoring in Southwest, Sichuan Normal University, Ministry of Education, Chengdu, China.
² College of Life Sciences, Sichuan Normal University, Chengdu, China.
³ Sichuan Environmental Monitoring Center, Chengdu, China.
⁴ College of Life Sciences, Hunan Normal University, Changsha, China.
⁵ Sustainable Development Research Center of Resources and Environment of Western Sichuan, Sichuan Normal University, Chengdu, China.

Abstract

Aster L. is an economically and phylogenetically important genus in the tribe Astereae. Here, the complete plastomes of the eight Aster species were assembled and characterized using next-generation sequencing datasets. The results indicated the complete plastomes of Aster had a quadripartite structure. These genomes were 152,045-152,729 bp in length and contained 132-133 genes, including 87 protein-coding genes, 37-38 tRNA genes, and eight rRNA genes. Expansion or contraction of inverted repeat regions and forward, palindromic, complement, and reverse repeats were detected in the eight Aster species. Additionally, our analyses showed the richest type of simple sequence repeats was A/T mononucleotides, and 14 highly variable regions were discovered by analyzing the border regions, sequence divergence, and hotspots. Phylogenetic analyses indicated that 27 species in Astereae were clustered into six clades, i.e., A to D, North American, and outgroup clades, and supported that the genera Heteropappus, Kalimeris, and Heteroplexis are nested within Aster. The results indicated the clades B to D might be considered as genera. Divergence time estimate showed the clades A, B, C, and D diverged at 23.15 Mya, 15.13 Mya, 24.29 Mya, and 21.66 Mya, respectively. These results shed light on the phylogenetic relationships of Aster and provided new information on species identification of Aster and its related genera.

Keywords: Aster; Astereae; chloroplast genome; comparative analysis; divergence time; phylogenetic relationship.

Grants and funding

The author(s) declare financial support was received for the research, authorship, and/or publication of this article. This study was financially supported by the National Natural Science Foundation of China (No. 32000158); the National Science and Technology Fundamental Resources Investigation Program of China (No. 2021XJKK0702); the Foundation of Sustainable Development Research Center of Resources and Environment of Western Sichuan, Sichuan Normal University (No. 2020CXZYHJZX03); Key Laboratory of Chemistry in Ethnic Medicinal Resources (Yunnan Minzu University); State Ethnic Affairs Commission and Ministry of Education (No. MZY2301); and Laboratory equipment research projects, Sichuan Normal University (No. SYJS2022014).