College of Life Science, Zhejiang University, Hangzhou 310058, China.
BMC Genomics. 2010 Aug 13;11:472. doi: 10.1186/1471-2164-11-472.
Systematic research on fish immunogenetics is indispensable in understanding the origin and evolution of immune systems. This has long been a challenging task because of the limited number of deep sequencing technologies and genome backgrounds of non-model fish available. The newly developed Solexa/Illumina RNA-seq and Digital gene expression (DGE) are high-throughput sequencing approaches and are powerful tools for genomic studies at the transcriptome level. This study reports the transcriptome profiling analysis of bacteria-challenged Lateolabrax japonicus using RNA-seq and DGE in an attempt to gain insights into the immunogenetics of marine fish.
RNA-seq analysis generated 169,950 non-redundant consensus sequences, among which 48,987 functional transcripts with complete or various length encoding regions were identified. More than 52% of these transcripts are possibly involved in approximately 219 known metabolic or signalling pathways, while 2,673 transcripts were associated with immune-relevant genes. In addition, approximately 8% of the transcripts appeared to be fish-specific genes that have never been described before. DGE analysis revealed that the host transcriptome profile of Vibrio harveyi-challenged L. japonicus is considerably altered, as indicated by the significant up- or down-regulation of 1,224 strong infection-responsive transcripts. Results indicated an overall conservation of the components and transcriptome alterations underlying innate and adaptive immunity in fish and other vertebrate models. Analysis suggested the acquisition of numerous fish-specific immune system components during early vertebrate evolution.
This study provided a global survey of host defence gene activities against bacterial challenge in a non-model marine fish. Results can contribute to the in-depth study of candidate genes in marine fish immunity, and help improve current understanding of host-pathogen interactions and evolutionary history of immunogenetics from fish to mammals.
系统性的鱼类免疫遗传学研究对于理解免疫系统的起源和进化是不可或缺的。由于缺乏非模式鱼类的深度测序技术和基因组背景，这一直是一个具有挑战性的任务。新开发的 Solexa/Illumina RNA-seq 和 Digital gene expression (DGE) 是高通量测序方法，是转录组水平基因组研究的有力工具。本研究采用 RNA-seq 和 DGE 对细菌攻毒的鲈（Lateolabrax japonicus）进行了转录组谱分析，试图深入了解海洋鱼类的免疫遗传学。
RNA-seq 分析生成了 169950 个非冗余的一致序列，其中鉴定出 48987 个具有完整或各种长度编码区的功能转录本。这些转录本中超过 52%的可能涉及大约 219 个已知的代谢或信号通路，而 2673 个转录本与免疫相关基因有关。此外，大约 8%的转录本似乎是以前从未描述过的鱼类特异性基因。DGE 分析表明，哈维氏弧菌攻毒鲈的宿主转录组谱发生了显著改变，1224 个强感染反应转录本的显著上调或下调表明了这一点。结果表明，鱼类和其他脊椎动物模型中的先天和适应性免疫的组成成分和转录组改变总体上是保守的。分析表明，在早期脊椎动物进化过程中获得了许多鱼类特异性的免疫系统成分。
本研究对非模式海洋鱼类对细菌挑战的宿主防御基因活性进行了全面调查。研究结果有助于深入研究海洋鱼类免疫候选基因，有助于提高对宿主-病原体相互作用和免疫遗传学进化历史的认识，从鱼类到哺乳动物。
