三脉水丝梨叶绿体基因组特征及系统发育分析

Chloroplast genomic characteristics and phylogeneticanalysis of Sycopsis triplinervia

关键词:  三脉水丝梨, 叶绿体基因组, 水丝梨属, 金缕梅科, 基因组系统学

Key words:  Sycopsis triplinervia, chloroplast genome, Sycopsis, Hamamelidaceae, phylogenomic phylogenetics

摘要:

三脉水丝梨(Sycopsis triplinervia)是金缕梅科(Hamamelidaceae)水丝梨属(Sycopsis)的一种常绿灌木。水丝梨属的系统发育地位仍存在争议且与假蚊母属(Distyliopsis)、蚊母树属(Distylium)等近缘属之间的亲缘关系尚不明确。该研究对三脉水丝梨的叶绿体基因组进行测序与组装,结合公共数据库中金缕梅科其他物种的叶绿体基因组数据,开展比较基因组分析和叶绿体基因组系统发育分析。结果表明:(1)三脉水丝梨基因组大小为159 375 bp,共编码133个基因,包括8个rRNA基因、37个tRNA基因、87个蛋白编码基因和1个假基因。(2)共检测到33个散在重复序列、39个串联重复序列和82个简单重复序列(SSRs)。(3)密码子偏好以A/U结尾,共包含9个最优密码子且密码子偏好主要受自然选择的影响。(4)与近缘种相比,三脉水丝梨的叶绿体基因组整体较为保守,从水丝梨属中筛选到的15个高变异区域具有潜在用于分子鉴定的价值。(5)系统发育分析显示,金缕梅科为单系类群,金缕梅属(Hamamelis)、白缕梅属(Parrotiopsis)、水丝梨属、假蚊母属、波斯铁木属(Parrotia)和蚊母树属形成了一个强力支持的单系分支,6个属之间具有较近的亲缘关系,其中三脉水丝梨与该分支中的其他类群互为姐妹群,而水丝梨属、波斯铁木属、假蚊母属和蚊母树属均非单系。该研究结果为金缕梅科的系统发育研究提供了重要的基础数据和参考。

Abstract:

Sycopsis triplinervia is an evergreen shrub in the genus Sycopsis (Hamamelidaceae). The phylogenetic position of Sycopsis has been a subject of debate, and its evolutionary relationships with closely related genera such as Distyliopsis and Distylium remain unclear. Here we sequenced and assembled its chloroplast genome and conducted comparative genomic and phylogenomic analyses together with publicly available Hamamelidaceae chloroplast genomes. The results were as follows:(1)The chloroplast genome of S. triplinervia was 159 375 bp in length and encoded 133 genes, including 8 rRNA genes, 37 tRNA genes, 87 protein-coding genes and 1 pseudogene.(2)A total of 33 interpersed repeats, 39 tandem repeats and 82 simple sequence repeats(SSRs)were identified.(3)Codon usage was biased toward A/U endings. Nine optimal codons were detected, and natural selection was determined to be the main driver of codon usage bias.(4)Overall, the chloroplast genome of S. triplinervia was highly conserved relative to its close relatives. Fifteen highly variable regions were identified as potential markers for molecular identification in Sycopsis.(5)Phylogenetic analyses indicated that Hamamelidaceae was monophyletic, and Hamamelis, Parrotiopsis, Sycopsis, Distyliopsis, Parrotia, and Distylium formed a strongly supported monophyletic clade. Within this clade, several genera were closely related to each other, and S. triplinervia was sister to the remaining taxa. However, Sycopsis, Parrotia, Distyliopsis, and Distylium were each non-monophyletic. This study provides fundamental data and a valuable reference for further phylogenetic research on Hamamelidaceae.