Sequencing, de novo assembly and comparative analysis of Raphanus sativus transcriptome.
Sequencing, de novo assembly and comparative analysis of Raphanus sativus transcriptome.
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raphanus sativus转录组的测序，从头组装和比较分析。
DOI：
10.3389/fpls.2015.00198
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发表时间：
2015
影响因子：
5.6
通讯作者：
Li M
中科院分区：
文献类型：
--
作者：
Wu G;Zhang L;Yin Y;Wu J;Yu L;Zhou Y;Li M
萝卜是十字花科重要植物，也是一种具有重要经济价值的食用蔬菜。然而，目前关于大蒜组织的转录组信息还不够充分，这阻碍了大蒜功能基因组学的进一步研究。本研究利用RNA-seq技术对叶片组织的转录组进行了研究。获得了大约7000万个干净的双端读数，并通过三一程序进行从头组装，产生了68,086个单基因，平均长度为576个碱基。根据GO和KEGG数据库对所有的uniges进行了注释。同时，我们将叶片测序数据与已有的根测序数据进行了合并，利用OASS程序获得了更好的萝卜的从头组装。据此，在萝卜中鉴定了潜在的简单序列重复序列(SSR)、转录因子(TF)和酶的编码。此外，我们还检测到3563个显著差异表达的基因(degs，P=0.05)以及叶和根组织之间的组织特异性生物学过程。在此基础上，利用Cytoscape软件构建了基于TFS的调控网络。综上所述，这些结果不仅为大蒜提供了全面的基因组资源，而且为今后大蒜的功能基因组和蛋白质组学研究奠定了基础。
Raphanus sativus is an important Brassicaceae plant and also an edible vegetable with great economic value. However, currently there is not enough transcriptome information of R. sativus tissues, which impedes further functional genomics research on R. sativus. In this study, RNA-seq technology was employed to characterize the transcriptome of leaf tissues. Approximately 70 million clean pair-end reads were obtained and used for de novo assembly by Trinity program, which generated 68,086 unigenes with an average length of 576 bp. All the unigenes were annotated against GO and KEGG databases. In the meanwhile, we merged leaf sequencing data with existing root sequencing data and obtained better de novo assembly of R. sativus using Oases program. Accordingly, potential simple sequence repeats (SSRs), transcription factors (TFs) and enzyme codes were identified in R. sativus. Additionally, we detected a total of 3563 significantly differentially expressed genes (DEGs, P = 0.05) and tissue-specific biological processes between leaf and root tissues. Furthermore, a TFs-based regulation network was constructed using Cytoscape software. Taken together, these results not only provide a comprehensive genomic resource of R. sativus but also shed light on functional genomic and proteomic research on R. sativus in the future.
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使用 Illumina 测序对橡胶树 (Hevea brasiliensis Muell. Arg.) 中的树皮转录组进行从头组装和表征以及 EST-SSR 标记的开发
影响因子：
4.4
作者：
Li D;Deng Z;Qin B;Liu X;Men Z
通讯作者：
Men Z
影响因子：
2.4
作者：
Ohsako, Takanori;Hirai, Masashi;Yamabuki, Makoto
通讯作者：
Yamabuki, Makoto
影响因子：
7
作者：
Knowles, David G.;McLysaght, Aoife
通讯作者：
McLysaght, Aoife
影响因子：
6.7
作者：
HERRIG, VANESSA;FERRARESE, MARIA DE LOURDES L.;FERRARESE-FILHO, OSVALDO
通讯作者：
FERRARESE-FILHO, OSVALDO
影响因子：
5.4
作者：
Kamei, Akito;Tsuro, Masato;Hirai, Masashi
通讯作者：
Hirai, Masashi