Data from: "De novo assembly transcriptome for the rostrum dace (Leuciscus burdigalensis, Cyprinidae: fish) naturally infected by a copepod ectoparasite" in Genomic Resources Notes accepted 1 December 2014 to 31 January 2015

The emergence of pathogens represents substantial threats to public health, livestock, domesticated animals, and biodiversity. How wild populations respond to emerging pathogens has generated a lot of interest in the last two decades. With the recent advent of high-throughput sequencing technologies it is now possible to develop large transcriptomic resources for non-model organisms, hence allowing new research avenues on the immune responses of hosts from a large taxonomic spectra. We here focused on a wild population of the rostrum dace (Leuciscus burgiladensis) that is infected by Tracheliastes polycolpus, an emerging freshwater ectoparasite copepod. We used next generation Illumina sequencing technology to sequence the transcriptome of eight L. burdigalensis adult individuals collected in natura from the same sampling site. Four individuals were non-infected and four individuals were infected by T. polycolpus. We specifically focused on the spleen, the head kidney and epithelial cells and mucus from the fins, three tissues known to be involved in the immune response of fish. We used the Trinity methodology to reconstruct a de novo full-length transcriptome for L. burdigalensis. The resulting transcriptome will serve as an important broad-scale genomic resource for further studying the response of local population of L. burdigalensis to T. polycolpus pressures.

病原体的出现对公共卫生、家畜与家养动物以及生物多样性均构成严重威胁。近二十年来，野生种群对新兴病原体的响应机制已成为学界广泛关注的研究热点。近年来，随着高通量测序技术（high-throughput sequencing technologies）的兴起，如今已可针对非模式生物（non-model organisms）构建大规模转录组资源（transcriptomic resources），从而为探索广泛分类学谱系（taxonomic spectra）内宿主的免疫应答（immune responses）开辟了全新的研究路径。
本研究聚焦于被多突管巢蚤（Tracheliastes polycolpus）——一种新兴淡水外寄生桡足类（freshwater ectoparasite copepod）——侵染的波尔多雅罗鱼（Leuciscus burdigalensis）野生种群。我们采用下一代Illumina测序技术（Illumina sequencing technology），对从同一采样点野外自然采集的8尾成体波尔多雅罗鱼进行转录组（transcriptome）测序：其中4尾为未侵染个体，4尾为被多突管巢蚤侵染的个体。本研究重点关注与鱼类免疫应答密切相关的三类组织：脾脏、头肾（head kidney），以及鳍部上皮细胞（epithelial cells）与黏液。我们借助Trinity分析方法（Trinity methodology），为波尔多雅罗鱼从头组装得到全长转录组（de novo full-length transcriptome）。该转录组将作为重要的规模化基因组资源（genomic resource），用于后续研究波尔多雅罗鱼本地种群对多突管巢蚤侵染压力的响应机制。