CrusTF: a comprehensive resource of transcriptomes for evolutionary and functional studies of crustacean transcription factors.
CrusTF: a comprehensive resource of transcriptomes for evolutionary and functional studies of crustacean transcription factors.
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CrusTF：用于甲壳类转录因子进化和功能研究的转录组综合资源
DOI：
10.1186/s12864-017-4305-2
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发表时间：
2017-11-25
期刊：
影响因子：
4.4
通讯作者：
Chu KH
中科院分区：
文献类型：
--
作者：
Qin J;Hu Y;Ma KY;Jiang X;Ho CH;Tsang LM;Yi L;Leung RWT;Chu KH
背景甲壳纲是节肢动物的第二大亚门，包括具有重要生态和经济重要性的物种，如螃蟹、龙虾、小龙虾、虾和藤壶。随着甲壳类水产养殖的快速发展和生物多样性的丧失，了解甲壳类动物生长、繁殖和发育的基因调控机制对于甲壳类水产养殖的发展和生物多样性保护至关重要。在这些生物过程中，转录因子（TF）在调节基因表达方面发挥着至关重要的作用。然而，甲壳类转录因子仍然很大程度上未知，因为大多数甲壳类物种缺乏完整的基因组序列，阻碍了在全系统范围内对其转录调控的研究。因此，目前基于基因组序列的转录因子数据库仅包含少数甲壳类动物物种的转录因子信息，不足以阐明如此大的动物群体的转录多样性。结果我们的数据库CrusTF（http://qinlab.sls.cuhk.edu.hk/CrusTF）为甲壳类转录调控系统的进化和功能研究提供了全面的信息。 CrusTF 通过探索 170 种甲壳类动物的公开可用和新测序的转录组并鉴定 63 个 TF 家族中的 131,941 个 TF，填补了甲壳类动物转录调控的知识空白。 CrusTF 具有三类信息：甲壳类 TF 的序列、功能和进化。该数据库可以搜索、浏览和下载甲壳类 TF 序列。 CrusTF 推断甲壳类 TF 的 DNA 结合基序，从而方便用户预测潜在的下游 TF 目标。该数据库还提供了甲壳类转录因子的进化分析，这提高了我们对甲壳类转录调控系统进化的理解。结论鉴于转录因子信息在甲壳类转录调控系统进化和功能研究中的重要性，该数据库将构成甲壳类生物学和进化生物学研究界的关键资源。此外，CrusTF 作为构建源自转录组数据的 TF 数据库的模型。类似的方法可以应用于其他生物体群体，对于这些生物体来说，转录组比基因组更容易获得。
BackgroundCrustacea, the second largest subphylum of Arthropoda, includes species of major ecological and economic importance, such as crabs, lobsters, crayfishes, shrimps, and barnacles. With the rapid development of crustacean aquaculture and biodiversity loss, understanding the gene regulatory mechanisms of growth, reproduction, and development of crustaceans is crucial to both aquaculture development and biodiversity conservation of this group of organisms. In these biological processes, transcription factors (TFs) play a vital role in regulating gene expression. However, crustacean transcription factors are still largely unknown, because the lack of complete genome sequences of most crustacean species hampers the studies on their transcriptional regulation on a system-wide scale. Thus, the current TF databases derived from genome sequences contain TF information for only a few crustacean species and are insufficient to elucidate the transcriptional diversity of such a large animal group.ResultsOur database CrusTF ( http://qinlab.sls.cuhk.edu.hk/CrusTF ) provides comprehensive information for evolutionary and functional studies on the crustacean transcriptional regulatory system. CrusTF fills the knowledge gap of transcriptional regulation in crustaceans by exploring publicly available and newly sequenced transcriptomes of 170 crustacean species and identifying 131,941 TFs within 63 TF families. CrusTF features three categories of information: sequence, function, and evolution of crustacean TFs. The database enables searching, browsing and downloading of crustacean TF sequences. CrusTF infers DNA binding motifs of crustacean TFs, thus facilitating the users to predict potential downstream TF targets. The database also presents evolutionary analyses of crustacean TFs, which improve our understanding of the evolution of transcriptional regulatory systems in crustaceans.ConclusionsGiven the importance of TF information in evolutionary and functional studies on transcriptional regulatory systems of crustaceans, this database will constitute a key resource for the research community of crustacean biology and evolutionary biology. Moreover, CrusTF serves as a model for the construction of TF database derived from transcriptome data. A similar approach could be applied to other groups of organisms, for which transcriptomes are more readily available than genomes.
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影响因子：
4.6
作者：
Gurkov A;Shchapova E;Bedulina D;Baduev B;Borvinskaya E;Meglinski I;Timofeyev M
通讯作者：
Timofeyev M
影响因子：
5.8
作者：
Castro, H;Ramalheira, F;Rodrigues, AM
通讯作者：
Rodrigues, AM
影响因子：
4.4
作者：
Toyota K;Kato Y;Sato M;Sugiura N;Miyagawa S;Miyakawa H;Watanabe H;Oda S;Ogino Y;Hiruta C;Mizutani T;Tatarazako N;Paland S;Jackson C;Colbourne JK;Iguchi T
通讯作者：
Iguchi T
AnimalTFDB 2.0：动物转录因子表达、预测和功能研究的资源
影响因子：
14.9
作者：
Zhang HM;Liu T;Liu CJ;Song S;Zhang X;Liu W;Jia H;Xue Y;Guo AY
通讯作者：
Guo AY
影响因子：
5.8
作者：
Xie, Zhi;Hu, Shaohui;Qian, Jiang
通讯作者：
Qian, Jiang