Phylotranscriptomics of Theaceae: generic-level relationships,
reticulation and whole-genome duplication
Background and Aims
Theaceae, with three tribes, nine genera and more than 200 species, are of great economic and ecological importance. Recent phylogenetic analyses based on plastomic data resolved the relationships among the three tribes and the intergeneric relationships within two of those tribes. However, generic-level relationships within the largest tribe, Theeae, were not fully resolved. The role of putative whole-genome duplication (WGD) events in the family and possible hybridization events among genera within Theeae also remain to be tested further.
Methods
Transcriptomes or low-depth whole-genome sequencing of 57 species of Theaceae, as well as additional plastome sequence data, were generated. Using a dataset of low-copy nuclear genes, we reconstructed phylogenetic relationships using concatenated, species tree and phylogenetic network approaches. We further conducted molecular dating analyses and inferred possible WGD events by examining the distribution of the number of synonymous substitutions per synonymous site (Ks) for paralogues in each species. For plastid protein-coding sequences , phylogenies were reconstructed for comparison with the results obtained from analysis of the nuclear dataset.
Results
Based on the 610 low-copy nuclear genes (858 606 bp in length) investigated, Stewartieae was resolved as sister to the other two tribes. Within Theeae, the Apterosperma–Laplacea clade grouped with Pyrenaria, leaving Camellia and Polyspora as sister. The estimated ages within Theaceae were largely consistent with previous studies based mainly on plastome data. Two reticulation events within Camellia and one between the common ancestor of Gordonia and Schima were found. All members of the tea family shared two WGD events, an older At-γ and a recent Ad-β; both events were also shared with the outgroups (Diapensiaceae, Pentaphylacaceae, Styracaceae and Symplocaceae).
Conclusions
Our analyses using low-copy nuclear genes improved understanding of phylogenetic relationships at the tribal and generic levels previously proposed based on plastome data, but the phylogenetic position of the Apterosperma–Laplacea clade needs more attention. There is no evidence for extensive intergeneric hybridization within Theeae or for a Theaceae-specific WGD event. Land bridges (e.g. the Bering land bridge) during the Late Oligocene may have permitted the intercontinental plant movements that facilitated the putative ancient introgression between the common ancestor of Gordonia and Schima.
⼭茶科隶属于被子植物菊分支杜鹃花目,共包含3族9属约300余种,该科植物多为灌⽊及乔⽊树种,具有重要的生态和经济价值。其中,⽊荷属(Schima)为亚洲特有属,约含20种,该属植物多为森林建群种及乔⽊层优势种,以⽊荷为优势种且与其它典型常绿阔叶树种共同组成的“⽊荷林”,是我国中亚热带地区常见的常绿阔叶林类型。山茶属(Camellia)含约120种,以我国长江以南的亚热带地区为其现代分布中⼼,该属含有众多重要的林木种质资源,如茶(C. sinensis)是世界著名天然保健饮料之一;油茶(C. oleifera)堪称世界四大木本油料植物之一;山茶(C. japonica)及滇山茶(C. reticulata)是享誉国际的观赏花卉。针对山茶科开展植物分类、分子系统学等研究将为有效保护及合理开发利用该科优质种质资源提供科学理论依据。
中国科学院昆明植物研究所“植物分类与演化”专题攻关组围绕唇形科、山茶科、禾本科等东亚特征性成分开展植物分类学、生物地理学及进化基因组学等方面的研究。前期,攻关组成员余香琴副研究员利用叶绿体基因组数据构建了该科的系统发育框架,并在此基础上探讨了东亚亚热带常绿阔叶林的演化历史(Yu et al., 2017, New Phytologist),同时基于野外调查发现并报导了部分新分类群(Yu et al., 2021, Phytotaxa)。在此基础上,通过与美国、哥斯达黎加及国内多位学者合作,收集到覆盖山茶科所有3族9属的57种植物,通过转录组测序(RNA-seq)和基因组浅层测序(low-depth whole-genome sequencing),获得了57个物种的核基因转录本的数据,以GenBank中已发表数据,即来自安息香科、山矾科、五列木科等6个物种为外类群。通过分析,最终利用610个直系同源的低拷贝核基因(858606 bp)构建了山茶科的系统发育框架,同时对科内类群分化时间、网状进化及全基因组加倍事件(WGD)进行了探讨。
研究结果表明,与前期基于叶绿体基因组数据得到的族间演化关系一致,紫茎族为山茶科的基部分支,大头茶族与山茶族构成姐妹类群。紫茎族与大头茶族内部属间关系与基于叶绿体基因组得到的关系一致。对于山茶族内部,同时结合来自核基因及叶绿体基因组的证据,(((Apterosperma–Laplacea), Pyrenaria), (Camellia–Polyspora))是最可能的系统发育拓扑结构,但Apterosperma–Laplacea分支的位置需要今后的研究利用更多数据进一步探究。网状进化分析结果表明,山茶属内部存在2次杂交事件,有趣的是,北美分布的Franklinia alatamaha 可能是由现今仅分布于北美及中美洲的Gordonia 的祖先类群与现今仅分布于亚洲的木荷属的祖先类群杂交而来,分化时间分析将这次古杂交事件推向渐新世(Oligocene)晚期,这一时期存在的白令陆桥(Bering land bridge)可能为该洲际间的植物扩散和古杂交事件提供可能。值得一提的是,山茶族内部并没有检测到属间杂交事件,澄清了之前研究中存在的争议。通过Ks峰值的分析发现,山茶科在进化过程中与其它类群共享了两次WGD事件,即核心真双子叶植物共享的At-γ及核心杜鹃花目共享的Ad-β,与部分前人研究结果(e.g. Chen et al., 2020, Horticulture Research)不同,该科并没有发生自身独有的WGD事件。
研究成果以“Phylotranscriptomics of Theaceae: generic-level relationships, reticulation and whole-genome duplication”为题在线发表于植物学领域专业期刊Annals of Botany上。博士研究生张琼为论文第一作者,彭华研究员和余香琴副研究员为论文通讯作者。昆明植物所赵磊博士、杨世雄副研究员、高连明研究员,美国密西西比大学Ryan A. Folk博士,佛罗里达大学Douglas E. Soltis和Pamela S. Soltis教授,云南大学赵建立副研究员及哥斯达黎加生物多样性研究所Nelson A. Zamora博士等参与了该研究。
研究得到了国家自然科学基金(32070369, 31700182)、中国科学院重大科技基础设施开放研究项目(2017-LSFGBOWS-02)、中国科学院“青年创新促进会”会员(2021393)及西部之光人才引进计划等项目的支持。同时,工作受到中国西南野生生物种质资源库保藏中心、昆明植物所标本馆(KUN)及昆明植物园等部门的大力协助与支持,在此一并表示感谢!
文章链接:https://doi.org/10.1093/aob/mcac007
图1 基于610个直系同源低拷贝核基因数据串联分析得到的山茶科ML树(左)及物种树(右)
图2 基于610个直系同源低拷贝核基因数据的山茶科分化时间树及Ks峰值分布图