School of Landscape and Architecture, Zhejiang A & F University, Hangzhou, 311300, China.
Zhejiang Provincial Key Laboratory of Germplasm Innovation and Utilization for Garden Plants, Zhejiang A & F University, Hangzhou, 311300, China.
Plant Mol Biol. 2020 Apr;102(6):659-676. doi: 10.1007/s11103-020-00972-6. Epub 2020 Jan 29.
Seven divergence hotspots as plastid markers for DNA barcoding was selected, and the phylogeny of 13 Lagerstroemia species based on the cp genome data was reconstructed within Myrtales. The Lagerstroemia species used in this study originated in China and have high economic and ecological value. The shared interspecific morphological characteristics and intraspecific morphological variation resulting from hybridization among Lagerstroemia taxa have made resolving their classification problems and phylogenetic relationships difficult. Systematic comparative genomic analysis has been shown to resolve phylogenetic relationships. We sequenced and annotated 6 Lagerstroemia cp genomes (Lagerstroemia excelsa, Lagerstroemia limii, Lagerstroemia siamica, Lagerstroemia tomentosa, Lagerstroemia venusta, and Lagerstroemia calyculata) for the first time and combined them with previously published genomes for Lagerstroemia species. Bioinformatics was used to analyse the 13 cp genomes in terms of gene structure and organization, codon usage, contraction and expansion of inverted repeat regions, repeat structure, divergence hotspots, species pairwise Ka/Ks ratios and phylogenetic relationships. The length varied between 152,049 bp in Lagerstroemia subcostata and 152,521 bp in L. venusta. We selected seven divergence hotspots in the cp genomes that had the potential to act as plastid markers to distinguish Lagerstroemia species. The phylogenetic relationships within Myrtales inferred from the cp genomes of 13 Lagerstroemia species and 27 other Myrtales species were highly supported, which illustrated several novel relationships within Myrtales. Taken together, our results provide comprehensive chloroplast genomic resources, which can be used further for species identification and molecular breeding of Lagerstroemia species.
选取了七个叶绿体基因组分歧热点作为 DNA 条形码的标记，基于 Myrtales 中的 cp 基因组数据重建了 13 种紫薇属物种的系统发育关系。本研究中使用的紫薇属物种原产于中国，具有很高的经济和生态价值。由于紫薇类群之间的杂交导致种间具有共享的形态特征和种内形态变异，使得解决其分类问题和系统发育关系变得困难。系统比较基因组分析已被证明可以解决系统发育关系问题。我们首次对 6 个紫薇属叶绿体基因组（紫薇、细叶紫薇、暹罗紫薇、紫薇、紫薇和紫薇）进行了测序和注释，并与之前发表的紫薇属物种基因组进行了组合。通过生物信息学分析，从基因结构和组织、密码子使用、反向重复区的收缩和扩张、重复结构、分歧热点、物种间 Ka/Ks 比值和系统发育关系等方面对 13 个 cp 基因组进行了分析。紫薇属物种 cp 基因组的长度在紫薇亚属的 152,049 bp 和紫薇的 152,521 bp 之间变化。我们在 cp 基因组中选择了七个具有潜在潜力的分歧热点作为叶绿体标记，以区分紫薇属物种。从 13 个紫薇属物种和 27 个其他桃金娘目物种的 cp 基因组推断出的桃金娘目内的系统发育关系得到了高度支持，这说明了桃金娘目内的几个新关系。总之，我们的研究结果提供了全面的叶绿体基因组资源，可进一步用于紫薇属物种的物种鉴定和分子育种。
