从头组装褐鳟（Salmo trutta m. fario）脑和肌肉转录组：转录本注释、组织差异表达谱和 SNP 发现。
De novo assembly of the Brown trout (Salmo trutta m. fario) brain and muscle transcriptome: transcript annotation, tissue differential expression profile and SNP discovery.
机构信息
Institute of Biomedical Research of Lleida (IRBLleida), University of Lleida, Lleida, Spain.
Complex Diseases Genetics, Departament de Ciències Mèdiques Bàsiques, Universitat de Lleida-IRBLLEIDA, Campus de Ciències de la Salut, Edifici Biomedicina I despatx b2.17, Av. Rovira Roure, 80, 25198, Lleida, Spain.
出版信息
BMC Res Notes. 2020 Nov 2;13(1):503. doi: 10.1186/s13104-020-05351-4.
OBJECTIVES
The Brown trout is a salmonid species with a high commercial value in Europe. Life history and spawning behaviour include resident (Salmo trutta m. fario) and migratory (Salmo trutta m. trutta) ecotypes. The main objective is to apply RNA-seq technology in order to obtain a reference transcriptome of two key tissues, brain and muscle, of the riverine trout Salmo trutta m. fario. Having a reference transcriptome of the resident form will complement genomic resources of salmonid species.
DATA DESCRIPTION
We generate two cDNA libraries from pooled RNA samples, isolated from muscle and brain tissues of adult individuals of Salmo trutta m. fario, which were sequenced by Illumina technology. Raw reads were subjected to de-novo transcriptome assembly using Trinity, and coding regions were predicted by TransDecoder. A final set of 35,049 non-redundant ORF unigenes were annotated. Tissue differential expression analysis was evaluated by Cuffdiff. A False Discovery Rate (FDR) ≤ 0.01 was considered for significant differential expression, allowing to identify key differentially expressed unigenes. Finally, we have identified SNP variants that will be useful tools for population genomic studies.
目的
褐鳟是一种具有高商业价值的鲑鱼，其生活史和繁殖行为包括居留型（Salmo trutta m. fario）和洄游型（Salmo trutta m. trutta）生态型。本研究的主要目的是应用 RNA-seq 技术，获得河流型褐鳟（Salmo trutta m. fario）两个关键组织（脑和肌肉）的参考转录组。获得居留型的参考转录组将补充鲑鱼物种的基因组资源。
数据描述
我们从成年个体的肌肉和脑组织的混合 RNA 样本中生成了两个 cDNA 文库，这些样本来自于居留型褐鳟，使用 Illumina 技术进行测序。使用 Trinity 对原始读取进行从头转录组组装，并使用 TransDecoder 预测编码区。最终注释了 35049 个非冗余的 ORF 基因。通过 Cuffdiff 评估组织差异表达分析。将 False Discovery Rate (FDR)≤0.01 作为显著差异表达的标准，以鉴定关键差异表达的基因。最后，我们已经确定了 SNP 变体，这些变体将是群体基因组研究的有用工具。
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