背景:鲑鱼虱子(Lepeophtheirussalmonis)是一种专性外寄生co足类动物,生活在海洋环境中的大西洋鲑鱼和其他鲑鱼上。鲑鱼虱每年都会引起许多环境问题,并在水产养殖中造成巨大的经济损失。为了开发新的寄生虫控制策略,需要在转录水平上更好地了解鲑鱼虱的蜕皮和发育机制。
方法:基于不同生命阶段鲑鱼虱基因表达谱的成对相关性,构建了三个加权基因共表达网络。基于网络的方法和基因注释信息用于鉴定可能对鲑鱼虱的蜕皮和发育很重要的基因。进行RNA干扰用于验证。通过检查转录因子基因与中间阶段和蜕皮阶段的优先表达基因之间的共表达模式的变化,计算了所有转录因子基因的调控影响因子。
结果:八个基因模块被预测为重要的,在RNA干扰实验中,八个模块中的六个模块中的10个基因被发现显示出可观察到的表型。我们从三个模块中击倒了五个hub基因,并在所有实验中观察到了表型后果。在感染试验中,在鱼上没有发现RAB1A样基因敲低的co足类,而对照样品发展为chalimus-1幼虫。此外,FOXO样转录因子在调节影响因子计算中获得最高分.
结论:我们提出了一种基于基因共表达网络的方法来鉴定在鲑鱼虱蜕皮和发育中起重要作用的基因。RNA干扰实验证实了我们方法的有效性,并证明了RAB1A样基因在鲑鱼虱子发育中不可或缺的作用。我们建议我们的方法可以推广到鉴定与其他生物体中感兴趣的表型相关的重要基因。
BACKGROUND: The salmon louse (Lepeophtheirus salmonis) is an obligate ectoparasitic copepod living on Atlantic salmon and other salmonids in the marine environment. Salmon lice cause a number of environmental problems and lead to large economical losses in aquaculture every year. In order to develop novel parasite control strategies, a better understanding of the mechanisms of moulting and development of the salmon louse at the transcriptional level is required.
METHODS: Three weighted gene co-expression networks were constructed based on the pairwise correlations of salmon louse gene expression profiles at different life stages. Network-based approaches and gene annotation information were applied to identify genes that might be important for the moulting and development of the salmon louse. RNA interference was performed for validation. Regulatory impact factors were calculated for all the transcription factor genes by examining the changes in co-expression patterns between transcription factor genes and deferentially expressed genes in middle stages and moulting stages.
RESULTS: Eight gene modules were predicted as important, and 10 genes from six of the eight modules have been found to show observable phenotypes in RNA interference experiments. We knocked down five hub genes from three modules and observed phenotypic consequences in all experiments. In the infection trial, no copepodids with a RAB1A-like gene knocked down were found on fish, while control samples developed to chalimus-1 larvae. Also, a FOXO-like transcription factor obtained highest scores in the regulatory impact factor calculation.
CONCLUSIONS: We propose a gene co-expression network-based approach to identify genes playing an important role in the moulting and development of salmon louse. The RNA interference experiments confirm the effectiveness of our approach and demonstrated the indispensable role of a RAB1A-like gene in the development of the salmon louse. We propose that our approach could be generalized to identify important genes associated with a phenotype of interest in other organisms.