Data from: Phylotranscriptomic analysis and genome evolution of the Cypripedioideae (Orchidaceae)

Premise of Study: The slipper orchids (Cypripedioideae) are a morphologically distinct subfamily of Orchidaceae. They also have some of the largest genomes in the orchids, which may be due to polyploidy or some other mechanism of genome evolution. We generated ten transcriptomes and incorporated existing RNA-seq data to infer a multi-locus nuclear phylogeny of the Cypripedioideae and to determine if a whole genome duplication event (WGD) correlated to the large genome size of this subfamily. Knowing more about timing of ancient polyploidy events can help us understand the evolution of one of the most species-rich plant families.
Methods: Transcriptome data was used to identify low-copy orthologous genes to infer a phylogeny of Orchidaceae and to identify paralogs to place any WGD events on the species tree.
Key results: Our transcriptome phylogeny confirmed relationships published in previous studies that used fewer markers but incorporated more taxa. We did not find a WGD event at the base of the slipper orchids; however, we did identify one on the Orchidaceae stem lineage. We also confirmed the presence of a previously identified WGD event deeper in the monocot phylogeny.
Conclusions: Although WGD has played a role in the evolution of Orchidaceae, polyploidy does not appear to be responsible for the large genome size of slipper orchids. The conserved set of 775 largely single-copy nuclear genes identified in this study should prove useful in future studies of orchid evolution.

研究背景：兜兰亚科（Cypripedioideae）是兰科（Orchidaceae）中形态特征独特的亚科类群，同时拥有兰科中最大的基因组之一，其基因组扩张可能源于多倍化（polyploidy）或其他基因组进化机制。本研究构建了10套转录组（transcriptome）数据，并整合已公开的RNA测序（RNA-seq）数据，旨在推断兜兰亚科的多位点核基因系统发育树，并探究全基因组复制（whole genome duplication, WGD）事件是否与该亚科的超大基因组规模存在关联。解析古多倍化事件的发生时间，有助于我们深入理解这个全球物种最丰富的植物类群之一的进化历程。
研究方法：本研究利用转录组数据鉴定低拷贝直系同源基因（orthologous genes），以推断兰科的系统发育关系；同时鉴定旁系同源基因（paralogs），以将全基因组复制事件精准定位到物种树之上。
主要结果：本研究基于转录组数据构建的系统发育树，验证了此前采用较少分子标记但涵盖更多类群的相关研究中所发表的类群亲缘关系。本研究未在兜兰亚科的基部分支处检测到全基因组复制事件，但在兰科的茎干谱系上鉴定到了一次全基因组复制事件。此外，本研究证实了单子叶植物（monocot）系统发育中更深演化分支处此前已被报道的全基因组复制事件的存在。
研究结论：尽管全基因组复制在兰科的进化历程中发挥了一定作用，但多倍化似乎并非导致兜兰亚科基因组规模庞大的原因。本研究中鉴定得到的775个高度保守的单拷贝核基因集合，将为未来兰科进化相关研究提供可靠的研究工具。