Key Laboratory of Ecological Protection of Agro-Pastoral Ecotones in the Yellow River Basin, College of Biological Science & Engineering, National Ethnic Affairs Commission of the People's Republic of China, North Minzu University, Yinchuan, 750021, China.
Key Laboratory of the Ministry of Education for Protection and Utilization of Special Biological Resources in the Western, School of Life Science, Ningxia University, Yinchuan, Ningxia, 750021, China.
BMC Genomics. 2024 Jun 6;25(1):569. doi: 10.1186/s12864-024-10487-9.
Lycium is an economically and ecologically important genus of shrubs, consisting of approximately 70 species distributed worldwide, 15 of which are located in China. Despite the economic and ecological importance of Lycium, its phylogeny, interspecific relationships, and evolutionary history remain relatively unknown. In this study, we constructed a phylogeny and estimated divergence time based on the chloroplast genomes (CPGs) of 15 species, including subspecies, of the genus Lycium from China.
We sequenced and annotated 15 CPGs in this study. Comparative analysis of these genomes from these Lycium species revealed a typical quadripartite structure, with a total sequence length ranging from 154,890 to 155,677 base pairs (bp). The CPGs was highly conserved and moderately differentiated. Through annotation, we identified a total of 128-132 genes. Analysis of the boundaries of inverted repeat (IR) regions showed consistent positioning: the junctions of the IRb/LSC region were located in rps19 in all Lycium species, IRb/SSC between the ycf1 and ndhF genes, and SSC/IRa within the ycf1 gene. Sequence variation in the SSC region exceeded that in the IR region. We did not detect major expansions or contractions in the IR region or rearrangements or insertions in the CPGs of the 15 Lycium species. Comparative analyses revealed five hotspot regions in the CPG: trnR(UCU), atpF-atpH, ycf3-trnS(GGA), trnS(GGA), and trnL-UAG, which could potentially serve as molecular markers. In addition, phylogenetic tree construction based on the CPG indicated that the 15 Lycium species formed a monophyletic group and were divided into two typical subbranches and three minor branches. Molecular dating suggested that Lycium diverged from its sister genus approximately 17.7 million years ago (Mya) and species diversification within the Lycium species of China primarily occurred during the recent Pliocene epoch.
The divergence time estimation presented in this study will facilitate future research on Lycium, aid in species differentiation, and facilitate diverse investigations into this economically and ecologically important genus.
枸杞是一种经济和生态上都很重要的灌木属，由分布在全球的约 70 个种组成，其中 15 种在中国。尽管枸杞具有经济和生态重要性，但它的系统发育、种间关系和进化历史仍然相对未知。在这项研究中，我们构建了一个基于来自中国的 15 种枸杞属种（包括亚种）的叶绿体基因组（CPGs）的系统发育树并估计了分歧时间。
我们在这项研究中测序并注释了 15 个 CPG。对这些枸杞属物种的基因组进行比较分析表明，它们具有典型的四分体结构，总序列长度在 154890 到 155677 碱基对（bp）之间。CPGs 高度保守且适度分化。通过注释，我们总共鉴定了 128-132 个基因。分析反向重复（IR）区的边界表明，IRb/LSC 区的交界处都位于所有枸杞属物种的 rps19 中，IRb/SSC 位于 ycf1 和 ndhF 基因之间，而 SSC/IRa 位于 ycf1 基因内。SSC 区的序列变异超过了 IR 区。我们没有在 15 种枸杞属物种的 CPG 中检测到 IR 区的主要扩张或收缩、CPG 的重排或插入。比较分析揭示了 CPG 中的五个热点区域：trnR(UCU)、atpF-atpH、ycf3-trnS(GGA)、trnS(GGA)和 trnL-UAG，它们可能作为分子标记。此外，基于 CPG 的系统发育树构建表明，15 种枸杞属物种形成了一个单系群，并分为两个典型的分支和三个小分支。分子定年表明，枸杞属与它的姊妹属大约在 1770 万年前分化，而中国枸杞属物种的多样性主要发生在最近的上新世时期。
本研究中的分歧时间估计将有助于未来对枸杞属的研究，有助于物种分化，并促进对这个经济和生态上都很重要的属的各种研究。
