Data from: Complete plastome sequence of Thalictrum coreanum (Ranunculaceae) and transfer of the rpl32 gene to the nucleus in the ancestor of the subfamily Thalictroideae

Background: Plastids originated from cyanobacteria and the majority of the ancestral genes were lost or functionally transferred to the nucleus after endosymbiosis. Comparative genomic investigations have shown that gene transfer from plastids to the nucleus is an ongoing evolutionary process but molecular evidence for recent functional gene transfers among seed plants have only been documented for the four genes accD, infA, rpl22, and rpl32. Results: The complete plastid genome of Thalictrum coreaum, the first from the subfamily Thalictroideae (Ranunculaceae), was sequenced and revealed the losses of two genes, infA and rpl32. The functional transfer of these two genes to the nucleus in Thalictrum was verified by examination of nuclear transcriptomes. A survey of the phylogenetic distribution of the rpl32 loss was performed using 17 species of Thalictrum and representatives of related genera in the subfamily Thalictroideae. The plastid-encoded rpl32 gene is likely nonfunctional in members of the subfamily Thalictroideae (Aquilegia, Enemion, Isopyrum, Leptopyrum, Paraquilegia, and Semiaquilegia) including 17 Thalictrum species due to the presence of indels that disrupt the reading frame. A nuclear-encoded rpl32 with high sequence identity was identified in both Thalictrum and Aquilegia. The phylogenetic distribution of this gene loss/transfer and the high level of sequence similarity in transit peptides suggest a single transfer of the plastid-encoded rpl32 to the nucleus in the ancestor of the subfamily Thalictroideae approximately 20-32 Mya. Conclusions: The genome sequence of Thalictrum coreanum provides valuable information for improving the understanding of the evolution of plastid genomes within Ranunculaceae and across angiosperms. Thalictrum is unusual among the three sequenced Ranunculaceae plastid genomes in the loss of two genes infA and rpl32, which have been functionally transferred to the nucleus. In the case of rpl32 this represents the third documented independent transfer from the plastid to the nucleus with the other two transfers occurring in the unrelated angiosperm families Rhizophoraceae and Salicaceae. Furthermore, the transfer of rpl32 provides additional molecular evidence for the monophyly of the subfamily Thalictroideae.

背景：质体（plastids）起源于蓝细菌，在内共生（endosymbiosis）事件发生后，绝大多数祖先基因发生了丢失或功能性转移至细胞核。比较基因组学研究显示，质体向细胞核的基因转移是一个持续进行的演化过程，但目前仅有accD、infA、rpl22和rpl32这4个基因有种子植物中近期功能性基因转移的分子证据。

结果：本研究首次对唐松草亚科（Thalictroideae，毛茛科Ranunculaceae）物种朝鲜唐松草（Thalictrum coreaum）的完整质体基因组进行了测序，发现其丢失了infA和rpl32两个基因。通过对细胞核转录组的分析，验证了这两个基因在唐松草属中已发生功能性转移至细胞核。本研究针对唐松草属的17个物种以及唐松草亚科相关类群的代表物种，开展了rpl32基因丢失的系统发育分布调查。由于存在破坏阅读框的插入缺失（indels），唐松草亚科的多个类群（含17个唐松草属物种，以及耧斗菜属（Aquilegia）、扁果草属（Enemion）、类叶升麻属（Isopyrum）、细果草属（Leptopyrum）、拟耧斗菜属（Paraquilegia）与假耧斗菜属（Semiaquilegia））中，质体编码的rpl32基因大概率已丧失功能。本研究在唐松草属和耧斗菜属中均鉴定出了序列相似度极高的核编码rpl32基因。结合该基因丢失与转移的系统发育分布，以及转运肽（transit peptides）序列的高度相似性，推测在约2000万至3200万年前，唐松草亚科的共同祖先中发生了一次质体编码的rpl32基因向细胞核的转移事件。

结论：朝鲜唐松草的质体基因组序列，为增进我们对毛茛科（Ranunculaceae）内以及被子植物整体质体基因组演化的认识提供了宝贵的研究资料。在已完成测序的3个毛茛科质体基因组中，唐松草属较为特殊，其丢失了infA与rpl32两个基因，且这两个基因已发生功能性转移至细胞核。就rpl32基因而言，本次转移是目前已报道的第三次独立的质体向细胞核的基因转移事件，另外两次独立转移分别发生在亲缘关系较远的被子植物科——红树科（Rhizophoraceae）和杨柳科（Salicaceae）中。此外，rpl32基因的转移为唐松草亚科的单系群（monophyly）属性提供了额外的分子生物学证据。