De Novo Assembly and Characterization of Early Embryonic Transcriptome of the Horseshoe Crab Tachypleus tridentatus.
De Novo Assembly and Characterization of Early Embryonic Transcriptome of the Horseshoe Crab Tachypleus tridentatus.
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马蹄蟹 Tachypleus tridentatus 早期胚胎转录组的从头组装和表征。
DOI：
10.1371/journal.pone.0145825
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发表时间：
2016
期刊：
影响因子：
3.7
通讯作者：
Chen J
中科院分区：
文献类型：
--
作者：
Chen M;Wang C;Wang W;Ji G;Hu B;Du M;Liu G;Li Z;Wang W;Lin X;Zheng W;Chen J
中国鲎（Tachypleus tridentatus）是一种独特的海洋物种，也是一种潜在的海洋无脊椎动物模式动物。有限的基因组和转录数据目前可用于了解T.三叉戟在此，我们首次报道了T.使用Illumina RNA-seq平台，在胚胎发育阶段对tridentatus进行测序。获得了大约3800万个读段，并进一步组装成133，212个单基因。与公共数据库的序列同源性分析显示，33，796个unigenes可以用基因描述进行注释。在注释的unigenes中，我们确定了一些保守的后生动物信号通路（Hedgehog，Wnt，TGF-β和Notch通路）的关键组分和其他参与胚胎发育的重要调控基因。通过对Pax家族基因的定向搜索，发现了一套完整的Pax家族基因，这些基因在胚胎发育过程中的组织和器官的形成中起着关键作用。此外，全长T.根据转录组序列测定了中国三叉戟Pax 1/9a（TtPax 1/9a）和Pax 1/9 b（TtPax 1/9 b）的cDNA序列，证明了我们的数据库的即时应用。采用真实的实时定量PCR技术，分析了TtPax 1/9 a和TtPax 1/9 b在鲎不同组织中的表达模式。利用果蝇模型，我们进一步发现TtPax 1/9 b，而不是TtPax 1/9a，可以部分挽救果蝇同源物Poxm功能障碍引起的幼虫期死亡。我们的研究提供了T. tridentatus的功能基因组学研究，可以立即用于基因发现和表征，在T。三叉戟该转录组数据库的建立也将有助于T. tridentatus和其他海洋节肢动物。
The horseshoe crab Tachypleus tridentatus is a unique marine species and a potential model for marine invertebrate. Limited genomic and transcriptional data are currently available to understand the molecular mechanisms underlying the embryonic development of T. tridentatus. Here, we reported for the first time the de novo transcriptome assembly for T. tridentatus at embryonic developmental stage using Illumina RNA-seq platform. Approximate 38 million reads were obtained and further assembled into 133,212 unigenes. Sequence homology analysis against public databases revealed that 33,796 unigenes could be annotated with gene descriptions. Of the annotated unigenes, we identified a number of key components of several conserved metazoan signaling pathways (Hedgehog, Wnt, TGF-beta and Notch pathways) and other important regulatory genes involved in embryonic development. Targeted searching of Pax family genes which play critical roles in the formation of tissue and organ during embryonic development identified a complete set of Pax family genes. Moreover, the full length T. tridentatus Pax1/9a (TtPax1/9a) and Pax1/9b (TtPax1/9b) cDNA sequences were determined based on the transcriptome, demonstrating the immediate application of our database. Using quantitative real time PCR, we analyzed the expression patterns of TtPax1/9a and TtPax1/9b in different tissues of horseshoe crab. Taking advantage of Drosophila model, we further found that TtPax1/9b, but not TtPax1/9a, can partly rescue the Drosophila homolog Poxm dysfunction-caused lethality at the larval stage. Our study provides the embryonic transcriptome of T. tridentatus which could be immediately used for gene discovery and characterization, functional genomics studies in T. tridentatus. This transcriptome database will also facilitate the investigations of molecular mechanisms underlying embryonic development of T. tridentatus and other marine arthropods as well.