Data from: Whole plastome sequencing reveals deep plastid divergence and cytonuclear discordance between closely related balsam poplars, Populus balsamifera and P. trichocarpa (Salicaceae)

As molecular phylogenetic analyses incorporate ever-greater numbers of loci, cases of cytonuclear discordance – the phenomenon in which nuclear gene trees deviate significantly from organellar gene trees – are being reported more frequently. Plant examples of topological discordance, caused by recent hybridization between extant species, are well known. However, examples of branch-length discordance are less reported in plants relative to animals. We use a combination of de novo assembly and reference-based mapping using short-read shotgun sequences to construct a robust phylogeny of the plastome for multiple individuals of all the common Populus species in North America. We demonstrate a case of strikingly high plastome divergence, in contrast to little nuclear genome divergence, in two closely related balsam poplars, Populus balsamifera and Populus trichocarpa (Populus balsamifera ssp. trichocarpa). Previous studies with nuclear loci indicate that the two species (or subspecies) diverged since the late Pleistocene, whereas their plastomes indicate deep divergence, dating to at least the Pliocene (6–7 Myr ago). Our finding is in marked contrast to the estimated Pleistocene divergence of the nuclear genomes, previously calculated at 75 000 yr ago, suggesting plastid capture from a ‘ghost lineage’ of a now-extinct North American poplar.

随着分子系统发育分析纳入的基因座数量持续攀升，核质冲突（cytonuclear discordance）——即核基因树与细胞器基因树出现显著偏离的现象——的相关报道正愈发频繁。现存物种间近期杂交引发的拓扑结构冲突植物案例已广为人知。不过，相较于动物类群，植物中枝长冲突的相关报道相对较少。本研究结合从头组装（de novo assembly）与基于参考基因组的比对策略，利用短读长鸟枪测序序列，为北美所有常见杨属（Populus）物种的多个个体构建了稳健的质体基因组（plastome）系统发育树。本研究在两个亲缘关系密切的香脂杨类群——美洲杨（Populus balsamifera）与毛果杨（Populus trichocarpa，即Populus balsamifera ssp. trichocarpa）——中发现了质体基因组分化程度极高、而核基因组分化程度极低的案例。过往基于核基因座的研究表明，这两个物种（或亚种）的分化始于更新世晚期，而二者的质体基因组却显示出更深的分化时间，可追溯至至少上新世（600万至700万年前）。本研究结果与此前估算的核基因组更新世分化时间（7.5万年前）形成显著反差，表明其质体捕获自一个现已灭绝的北美杨属“幽灵支系（ghost lineage）”。