RNA-seq analysis of Macrobrachium rosenbergii hepatopancreas in response to Vibrio parahaemolyticus infection.
RNA-seq analysis of Macrobrachium rosenbergii hepatopancreas in response to Vibrio parahaemolyticus infection.
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DOI：
10.1186/s13099-015-0052-6
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发表时间：
2015
期刊：
影响因子：
4.2
通讯作者：
Bhassu S
中科院分区：
文献类型：
--
作者：
Rao R;Bing Zhu Y;Alinejad T;Tiruvayipati S;Lin Thong K;Wang J;Bhassu S
罗氏沼虾（Macrobrachium rosenbergium）是一种重要的经济甲壳动物。然而，这种对虾的生产正面临着由副溶血性弧菌等弧菌引起的弧菌病的严重威胁。不幸的是，该物种对细菌感染的免疫反应所涉及的机制尚未完全了解。因此，我们使用高通量深度测序技术来研究感染副溶血性弧菌的淡水对虾肝胰腺的转录组和比较表达谱，以增加对该物种对这种病原性细菌免疫反应的分子机制的理解。从对照组获得总共59，122，940个原始读数，从弧菌感染组获得58，385，094个读数。通过Trinity组装程序进行从头组装，获得59，050个对照组单基因和73，946个弧菌感染组单基因。通过对来自两个文库的unigenes进行聚类，总共产生了64，411个标准unigenes。针对NCBI非冗余、Swiss-Prot、京都基因和基因组途径百科全书（KEGG）和蛋白质正交组（COG）数据库注释标准单基因，具有19，799个（30.73%）、16，832（26.13%）、14，706（22.83%）和7，856（12.19%）的命中，最终总共得到22，455个显著命中（占所有unigenes的34.86%）。使用Blast 2GO程序的基因本体（GO）分析搜索导致6，007个单一基因（9.32%）被分类为55个功能组。差异基因表达分析共产生14，569个异常表达的unigenes，其中11，446个unigenes显著上调，3，103个unigenes显著下调。差异表达的免疫基因属于动物免疫系统的各种过程。本研究为深入了解M. rosenbertyline和差异表达的免疫基因在响应副溶血性弧菌感染中的作用。此外，本研究还获得了丰富的罗氏沼虾转录本序列，为该领域的基因组学研究奠定了基础。本文的在线版本（doi：10.1186/s13099-015-0052-6）包含补充材料，可供授权用户使用。
The Malaysian giant freshwater prawn, Macrobrachium rosenbergii, is an economically important crustacean worldwide. However, production of this prawn is facing a serious threat from Vibriosis disease caused by Vibrio species such as Vibrio parahaemolyticus. Unfortunately, the mechanisms involved in the immune response of this species to bacterial infection are not fully understood. We therefore used a high-throughput deep sequencing technology to investigate the transcriptome and comparative expression profiles of the hepatopancreas from this freshwater prawn infected with V. parahaemolyticus to gain an increased understanding of the molecular mechanisms underlying the species’ immune response to this pathogenic bacteria. A total of 59,122,940 raw reads were obtained from the control group, and 58,385,094 reads from the Vibrio-infected group. Via de novo assembly by Trinity assembler, 59,050 control unigenes and 73,946 Vibrio-infected group unigenes were obtained. By clustering unigenes from both libraries, a total of 64,411 standard unigenes were produced. The standard unigenes were annotated against the NCBI non-redundant, Swiss-Prot, Kyoto Encyclopaedia of Genes and Genome pathway (KEGG) and Orthologous Groups of Proteins (COG) databases, with 19,799 (30.73%), 16,832 (26.13%), 14,706 (22.83%) and 7,856 (12.19%) hits respectively, giving a final total of 22,455 significant hits (34.86% of all unigenes). A Gene Ontology (GO) analysis search using the Blast2GO program resulted in 6,007 unigenes (9.32%) being categorized into 55 functional groups. A differential gene expression analysis produced a total of 14,569 unigenes aberrantly expressed, with 11,446 unigenes significantly up-regulated and 3,103 unigenes significantly down-regulated. The differentially expressed immune genes fall under various processes of the animal immune system. This study provided an insight into the antibacterial mechanism in M. rosenbergii and the role of differentially expressed immune genes in response to V. parahaemolyticus infection. Furthermore, this study has generated an abundant list of transcript from M.rosenbergii which will provide a fundamental basis for future genomics research in this field. The online version of this article (doi:10.1186/s13099-015-0052-6) contains supplementary material, which is available to authorized users.
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