DataSheet1_Comparative genomics and phylogenomics of the genus Glycyrrhiza (Fabaceae) based on chloroplast genomes.PDF

Glycyrrhiza (Fabaceae) species are rich in metabolites and widely used in medicine. Research on the chloroplast genome of Glycyrrhiza is important for understanding its phylogenetics, biogeography, genetic diversity, species identification, and medicinal properties. In this study, comparative genomics and phylogenomics of Glycyrrhiza were analyzed based on the chloroplast genome. The chloroplast genomes of six Glycyrrhiza species were obtained using various assembly and annotation tools. The final assembled chloroplast genome sizes for the six Glycyrrhiza species ranged from 126,380 bp to 129,115 bp, with a total of 109–110 genes annotated. Comparative genomics results showed that the chloroplast genomes of Glycyrrhiza showed typically lacking inverted repeat regions, and the genome length, structure, GC content, codon usage, and gene distribution were highly similar. Bioinformatics analysis revealed the presence of 69–96 simple sequence repeats and 61–138 long repeats in the chloroplast genomes. Combining the results of mVISTA and nucleotide diversity, four highly variable regions were screened for species identification and relationship studies. Selection pressure analysis indicated overall purifying selection in the chloroplast genomes of Glycyrrhiza, with a few positively selected genes potentially linked to environmental adaptation. Phylogenetic analyses involving all tribes of Fabaceae with published chloroplast genomes elucidated the evolutionary relationships, and divergence time estimation estimated the chronological order of species differentiations within the Fabaceae family. The results of phylogenetic analysis indicated that species from the six subfamilies formed distinct clusters, consistent with the classification scheme of the six subfamilies. In addition, the inverted repeat-lacking clade in the subfamily Papilionoideae clustered together, and it was the last to differentiate. Co-linear analysis confirmed the conserved nature of Glycyrrhiza chloroplast genomes, and instances of gene rearrangements and inversions were observed in the subfamily Papilionoideae.

甘草属（Glycyrrhiza）隶属于豆科（Fabaceae），其富含代谢产物，在医药领域应用广泛。针对甘草属叶绿体基因组（chloroplast genome）的研究，对于阐明其系统发育、生物地理学特征、遗传多样性、物种鉴定及药用特性均具有重要意义。本研究基于叶绿体基因组数据，对甘草属开展比较基因组学与系统基因组学分析。研究通过多种组装与注释工具，成功获取了6种甘草属植物的叶绿体基因组序列。6种受试甘草属植物的叶绿体基因组组装长度介于126,380 bp至129,115 bp之间，共注释得到109至110个功能基因。比较基因组学分析结果显示，甘草属叶绿体基因组普遍缺失反向重复序列（inverted repeat）区域，且基因组长度、结构、GC含量、密码子使用偏好及基因分布均高度相似。生物信息学分析表明，这些叶绿体基因组中包含69至96个简单序列重复（Simple Sequence Repeats, SSR）以及61至138个长重复序列。结合mVISTA分析与核苷酸多样性（nucleotide diversity）结果，本研究筛选得到4个高变区域，可用于物种鉴定及类群亲缘关系研究。选择压力分析显示，甘草属叶绿体基因组整体呈现净化选择（purifying selection）模式，少数正选择基因可能与物种的环境适应过程相关。本研究纳入所有已发布叶绿体基因组的豆科族级类群开展系统发育分析，阐明了豆科的演化关系，并通过分化时间估计（divergence time estimation）推测了豆科内各物种的分化时序。系统发育分析结果表明，6个亚科（subfamilies）的物种各自形成单系聚类簇，与当前6亚科的分类框架相一致。此外，蝶形花亚科（Papilionoideae）中缺失反向重复序列的演化分支聚为一支，且为最晚分化的类群。共线性分析（co-linear analysis）证实了甘草属叶绿体基因组的整体保守性，同时在蝶形花亚科中观察到基因重排与染色体倒位现象。