Comparative analysis of chloroplast genomes and phylogenetic relationships in the endemic Chinese bamboo Gelidocalamus (Bambusoideae)

Chengkun Wang; Yonglong Li; Guangyao Yang; Wengen Zhang; Chunce Guo

doi:10.3389/fpls.2024.1470311

Comparative analysis of chloroplast genomes and phylogenetic relationships in the endemic Chinese bamboo Gelidocalamus (Bambusoideae)

Front Plant Sci. 2024 Nov 11:15:1470311. doi: 10.3389/fpls.2024.1470311. eCollection 2024.

Authors

Chengkun Wang¹, Yonglong Li¹, Guangyao Yang¹, Wengen Zhang¹, Chunce Guo¹

Affiliation

¹ Jiangxi Provincial Key Laboratory of Improved Variety Breeding and Efficient Utilization of Native Tree Species, Forestry College, Jiangxi Agricultural University, Nanchang, China.

Abstract

Introduction: Gelidocalamus Wen is a small yet taxonomically challenging genus within the Arundinarieae tribe. Recent molecular studies have suggested it may not be monophyletic. However, limited species sampling and insufficient molecular marker information have resulted in poorly resolved phylogenetic relationships within this genus.

Methods: The complete chloroplast genomes covering all 16 species and one variant of Gelidocalamus were sequenced, and comparative analyses were conducted. Phylogenetic analyses were performed using different molecular markers, including chloroplast data, the nuclear ribosomal DNA (nrDNA) repeats region, and 29 mitochondrial protein-coding genes. Additionally, the divergence times of Gelidocalamus were estimated to reveal their evolutionary history.

Results: The plastomes of Gelidocalamus ranged in size from 139,500 bp to 139,801 bp, with a total of 137 identified genes, including 90 protein-coding genes, 39 tRNA genes, and 8 rRNA genes. The size of the nrDNA repeats ranged from 5,802 bp to 5,804 bp. Phylogenetic analysis based on chloroplast data revealed that Gelidocalamus is polyphyletic, with different subclades distributed within the IV and V clades. However, phylogenetic analysis based on nrDNA and mitochondrial genes did not effectively resolve the relationships within the genus.

Discussion: Comparative analysis of chloroplast genomes indicated that Gelidocalamus shares a high degree of similarity with closely related genera in terms of chloroplast genome collinearity, codon usage bias, and repetitive sequences. Divergence time estimation suggests that it is a relatively young group, with all members appearing successively over the past four million years. The complex phylogenetic patterns may arise from the rapid radiation of Arundinarieae. This study provides a preliminary foundation for further in-depth research on the phylogeny, genomic structural features, and divergence times of this genus.

Keywords: Gelidocalamus Wen; divergence times; molecular markers; phylogenetic relationships; plastome evolution.

Grants and funding

The author(s) declare financial support was received for the research, authorship, and/or publication of this article. This work was supported by the National Natural Science Foundation of China (No. 31960051) and the Natural Science Foundation for Young Scientists of Jiangxi Province (No. 20192ACB21005).