Molecular relationships of Campomanesia xanthocarpa within Myrtaceae based on the complete plastome sequence and on the plastid ycf2 gene

Abstract Plastomes are very informative structures for comparative phylogenetic and evolutionary analyses. We sequenced and analyzed the complete plastome of Campomanesia xanthocarpa and compared its gene order, structure, and evolutionary characteristics within Myrtaceae. Analyzing 48 species of Myrtaceae, we identified six genes representing ‘hotspots’ of variability within the plastomes (ycf2, atpA, rpoC2, pcbE, ndhH and rps16), and performed phylogenetic analyses based on: (i) the ycf2 gene, (ii) all the six genes identified as ‘hotspots’ of variability, and (iii) the genes identified as ‘hotspots’ of variability, except the ycf2 gene. The structure, gene order, and gene content of the C. xanthocarpa plastome are similar to other Myrtaceae species. Phylogenetic analyses revealed the ycf2 gene as a promissing region for barcoding within this family, having also a robust phylogenetic signal. The synonymous and nonsynonymous substitution rates and the Ka/Ks ratio revealed low values for the ycf2 gene among C. xanthocarpa and the other 47 analyzed species of Myrtaceae, with moderate purifying selection acting on this gene. The average nucleotide identity (ANI) analysis of the whole plastomes produced phylogenetic trees supporting the monophyly of three Myrtaceae tribes. The findings of this study provide support for planning conservation, breeding, and biotechnological programs for this species.

摘要 质体基因组（plastome）是开展比较系统发育与进化分析的极具信息价值的结构。本研究对Campomanesia xanthocarpa的完整质体基因组完成测序与分析，并将其基因排列顺序、结构及进化特征与桃金娘科（Myrtaceae）类群进行对比。通过分析48种桃金娘科物种，本研究鉴定出6个质体基因组内的变异"热点"基因（ycf2、atpA、rpoC2、pcbE、ndhH及rps16），并基于三类数据集开展系统发育分析：(i) ycf2基因；(ii) 全部6个变异热点基因；(iii) 除ycf2基因外的其余变异热点基因。该物种的质体基因组结构、基因排列顺序及基因组成与其他桃金娘科物种高度相似。系统发育分析结果显示，ycf2基因可作为桃金娘科物种DNA条形码的候选区域，同时具备较强的系统发育信号。对该物种与其余47个分析的桃金娘科物种的ycf2基因进行同义替换率、非同义替换率及Ka/Ks比值分析后发现，该基因的相关参数值较低，且受到中等强度的纯化选择作用。全质体基因组的平均核苷酸一致性（average nucleotide identity, ANI）分析构建的系统发育树，支持桃金娘科3个族的单系性。本研究结果可为该物种的保护、育种及生物技术相关项目的规划提供理论支撑。