Comparative transcriptome resources of two Dysosma species (Berberidaceae) and molecular evolution of the CYP719A gene in Podophylloideae
Comparative transcriptome resources of two Dysosma species (Berberidaceae) and molecular evolution of the CYP719A gene in Podophylloideae
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小檗科两种八角莲的转录组资源比较及鬼臼科CYP719A基因的分子进化
DOI：
10.1111/1755-0998.12415
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发表时间：
2016-01
影响因子：
7.7
通讯作者：
Qiu Yingxiong
中科院分区：
文献类型：
--
作者：
Mao Yunrui;Zhang Yonghua;Xu Chuan;Qiu Yingxiong
八角莲属植物(小檗科、鬼臼亚科)具有重要的药用遗传学意义，是研究东亚温带植物物种多样性的驱动因素和机制的模式系统。最近，我们已经对低海拔地区的金龟子的转录组进行了测序。在这项研究中，我们对高海拔地区的金龟子的转录组进行了测序，并使用比较基因组学方法研究了这两个物种的转录组进化。我们利用Illumina HiSeq 2000平台，通过重新组装转录组，从橙色假单胞菌中检索到53 929个单基因。比较两个物种的转录本，我们鉴定出4593个同源基因。对3126个同源基因的Ka/Ks比值的估计表明，没有一个同源基因的Ka/Ks显著大于1，而1273个(Ka/Ks<；0.5，P<；0.05)被推断为处于净化选择之下。从4593个同源序列中的461个EST-SSR序列中成功设计出51对引物。标记验证分析表明，26个(51%)和41个(80.4%)在所有蜈蚣亚科物种中分别产生了预期大小的清晰片段。根据转录产物设计的引物，从所有12种蜈蚣亚科植物的基因组DNA中扩增出19个不同的序列。数据进一步表明，CYP719A可能受到很强的选择性限制，每个基因组只保持一个拷贝。在八角莲中，对高海拔物种有宽松的净化选择或较多的正向选择。总体而言，这项研究产生了丰富的分子资源，可能对八角莲及其近缘类群的药用遗传学和进化研究有用。
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.
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影响因子：
5.8
作者：
Tong, Mark Y.;Cassa, Christopher A.;Kohane, Isaac S.
通讯作者：
Kohane, Isaac S.
影响因子：
16.8
作者：
Yang Z;Bielawski JP
通讯作者：
Bielawski JP
影响因子：
3
作者：
Guan, Bi-Cai;Fu, Cheng-Xing;Comes, Hans Peter
通讯作者：
Comes, Hans Peter
DOI：
--
发表时间：
2006
期刊：
Journal of Tropical and Subtropical Botany
影响因子：
--
作者：
Wang Wu-yuan
通讯作者：
Wang Wu-yuan
转录组分析揭示了两种入侵粉虱物种肠道的适应性特征和生物学差异
影响因子：
4.4
作者：
Ye XD;Su YL;Zhao QY;Xia WQ;Liu SS;Wang XW
通讯作者：
Wang XW