Data from: Comparative transcriptome resources of two Dysosma species (Berberidaceae) and molecular evolution of the CYP719A gene in Podophylloideae

Dysosma species (Berberidaceae, Podophylloideae) are of great medicinal pharmacogenetic importance and used as model systems to study the drivers and mechanisms of species diversification of temperate plants in East Asia. Recently, we have sequenced the transcriptome of the low-elevation D. versipellis. In this study, we sequenced the transcriptome of the high-elevation D. aurantiocaulis and used comparative genomic approaches to investigate the transcriptome evolution of the two species. We retrieved 53 929 unigenes from D. aurantiocaulis by de novo transcriptome assemblies using the Illumina HiSeq 2000 platform. Comparing the transcriptomes of both species, we identified 4593 orthologs. Estimation of Ka/Ks ratios for 3126 orthologs revealed that none had a Ka/Ks significantly greater than 1, whereas 1273 (Ka/Ks < 0.5, P < 0.05) were inferred to be under purifying selection. A total of 51 primer pairs were successfully designed from 461 EST-SSRs contained in 4593 orthologs. Marker validation assay revealed that 26 (51%) and 41 (80.4%) produced clear fragments with the expected sizes in all Podophylloideae species. Specifically, 19 different sequences of CYP719A were identified from PCR-amplified genomic DNA of all 12 species of Podophylloideae using primers designed from the assembled transcripts. The data further indicated that CYP719A was likely subject to strong selective constraints maintaining only one copy per genome. In Dysosma, there was relaxed purifying selection or more positive selection for high-elevation species. Overall, this study has generated a wealth of molecular resources potentially useful for pharmacogenetic and evolutionary studies in Dysosma and allied taxa.

八角莲属（Dysosma）植物隶属于小檗科（Berberidaceae）鬼臼亚科（Podophylloideae），具有重要的药用药理学遗传学研究价值，同时也是探究东亚温带植物物种分化驱动因素与演化机制的理想模式系统。此前，本团队已完成低海拔物种八角莲（D. versipellis）的转录组测序。本研究针对高海拔物种橙柄八角莲（D. aurantiocaulis）开展转录组测序，并通过比较基因组学方法解析两个物种的转录组演化特征。依托Illumina HiSeq 2000测序平台，通过从头转录组组装，本研究从橙柄八角莲中获得了53929条单基因簇（unigenes）。通过比对两个物种的转录组数据，共鉴定得到4593个直系同源基因（orthologs）。对3126个直系同源基因的Ka/Ks（同义替换速率与非同义替换速率的比值）比值进行估算，结果显示无任何基因的Ka/Ks值显著大于1；其中1273个基因（Ka/Ks < 0.5，P < 0.05）被推断处于纯化选择（purifying selection）之下。从4593个直系同源基因所包含的461个表达序列标签-简单序列重复（EST-SSRs）位点中，共成功设计出51对引物。引物标记验证实验结果显示，26对（51%）与41对（80.4%）引物可在所有鬼臼亚科物种中扩增出符合预期片段大小的清晰条带。具体而言，本研究基于组装得到的转录本设计引物，从鬼臼亚科全部12个物种的PCR扩增基因组DNA中，鉴定得到19条CYP719A基因的不同序列。数据进一步表明，CYP719A大概率受到强烈的选择约束，即每个基因组仅保留单拷贝。在八角莲属中，高海拔物种的CYP719A基因呈现出弱化的纯化选择或更强的正向选择（positive selection）信号。综上，本研究生成了丰富的分子资源，可为八角莲属及其近缘类群的药理学遗传学与演化生物学研究提供重要支撑。