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Abstract：
BACKGROUND: 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.
RESULTS: 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.
CONCLUSIONS: 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.
RESULTS: 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.
CONCLUSIONS: 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.
摘要：
背景：枸杞是经济和生态上重要的灌木属，由分布在世界各地的大约70个物种组成，其中15个位于中国。尽管枸杞的经济和生态重要性，它的系统发育，种间关系，和进化史仍然相对未知。在这项研究中,我们根据15个物种的叶绿体基因组（CPG）构建了系统发育和估计的发散时间，包括亚种，来自中国的枸杞属。
结果：我们在这项研究中对15个CPG进行了测序和注释。这些枸杞物种基因组的比较分析揭示了典型的四方结构，总序列长度范围为154,890至155,677个碱基对(bp)。CPG高度保守且中等分化。通过注释，我们总共鉴定了128-132个基因。对反向重复（IR）区域边界的分析显示出一致的定位：IRb/LSC区域的连接处位于所有枸杞物种的rps19中，ycf1和ndhF基因之间的IRb/SSC，和Ycf1基因内的SSC/IRa。SSC区的序列变异超过了IR区。我们没有检测到15种枸杞物种的IR区域的主要扩张或收缩或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,可能作为分子标记。此外,基于CPG的系统发育树构建表明，15个枸杞物种形成了一个单系群，并分为两个典型的子分支和三个次要分支。分子年代测定表明，枸杞与大约1770万年前（Mya）的姊妹属不同，中国枸杞物种的物种多样化主要发生在最近的上新世时期。
结论：本研究中提出的发散时间估计将促进对枸杞的未来研究，有助于物种分化，并促进对这一经济和生态重要属的多样化研究。
结果：我们在这项研究中对15个CPG进行了测序和注释。这些枸杞物种基因组的比较分析揭示了典型的四方结构，总序列长度范围为154,890至155,677个碱基对(bp)。CPG高度保守且中等分化。通过注释，我们总共鉴定了128-132个基因。对反向重复（IR）区域边界的分析显示出一致的定位：IRb/LSC区域的连接处位于所有枸杞物种的rps19中，ycf1和ndhF基因之间的IRb/SSC，和Ycf1基因内的SSC/IRa。SSC区的序列变异超过了IR区。我们没有检测到15种枸杞物种的IR区域的主要扩张或收缩或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,可能作为分子标记。此外,基于CPG的系统发育树构建表明，15个枸杞物种形成了一个单系群，并分为两个典型的子分支和三个次要分支。分子年代测定表明，枸杞与大约1770万年前（Mya）的姊妹属不同，中国枸杞物种的物种多样化主要发生在最近的上新世时期。
结论：本研究中提出的发散时间估计将促进对枸杞的未来研究，有助于物种分化，并促进对这一经济和生态重要属的多样化研究。
