Wang Chengkun, Li Yonglong, Yang Guangyao, Zhang Wengen, Guo Chunce
Jiangxi Provincial Key Laboratory of Improved Variety Breeding and Efficient Utilization of Native Tree Species, Forestry College, Jiangxi Agricultural University, Nanchang, China.
Front Plant Sci. 2024 Nov 11;15:1470311. doi: 10.3389/fpls.2024.1470311. eCollection 2024.
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.
The complete chloroplast genomes covering all 16 species and one variant of 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 were estimated to reveal their evolutionary history.
The plastomes of 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 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.
Comparative analysis of chloroplast genomes indicated that 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.
温竹是青篱竹族中一个分类颇具挑战性的小属。近期的分子研究表明它可能不是单系的。然而，物种取样有限以及分子标记信息不足，导致该属内的系统发育关系解析不佳。
对涵盖该属所有16个物种和1个变种的完整叶绿体基因组进行测序，并进行比较分析。使用不同的分子标记进行系统发育分析，包括叶绿体数据、核糖体DNA（nrDNA）重复区域和29个线粒体蛋白质编码基因。此外，估计了该属的分歧时间以揭示其进化历史。
该属的叶绿体基因组大小在139,500 bp至139,801 bp之间，共鉴定出137个基因，包括90个蛋白质编码基因、39个tRNA基因和8个rRNA基因。nrDNA重复序列的大小在5,802 bp至5,804 bp之间。基于叶绿体数据的系统发育分析表明该属是多系的，不同的亚分支分布在IV和V分支内。然而，基于nrDNA和线粒体基因的系统发育分析未能有效解析该属内的关系。
叶绿体基因组的比较分析表明，该属在叶绿体基因组共线性、密码子使用偏好和重复序列方面与近缘属具有高度相似性。分歧时间估计表明它是一个相对年轻的类群，所有成员在过去四百万年中相继出现。复杂的系统发育模式可能源于青篱竹族的快速辐射。本研究为进一步深入研究该属的系统发育、基因组结构特征和分歧时间提供了初步基础。
