Data from: Unmapped sequencing reads identify additional candidate genes linked to magnetoreception in rainbow trout

A recent study identified candidate genes linked to magnetoreception in rainbow trout (Oncorhynchus mykiss) by sequencing transcriptomes from the brains of fish exposed to a magnetic pulse. However, the discovery of these candidate genes was limited to sequences that aligned to the reference genome. The unaligned, or unmapped, sequences may yet contain valuable information resulting from regions missing, misassembled, or divergent from the reference. Using the available sequencing data from the trout brain transcriptomes, we assembled >27 million unmapped sequences (5.8% of total sequences) into 45,142 contigs and identified 12 differentially expressed contigs as a result of exposure to a pulsed magnetic field. These contigs encoded a putative superoxide dismutase – a protein necessary to prevent oxidative damage – and collagen alpha-1 type II – a structural protein important for the development and integrity of the retina. These genes were consistent with the previous study suggesting an effect of the magnetic pulse on oxidative consequences of free iron and on non-visual encephalic photoreceptors. Our results demonstrate the utility of assembling unmapped sequencing reads in studies of gene expression and identify additional candidate genes associated with a magnetic sense in trout.

近期一项研究通过对受脉冲磁场刺激的虹鳟（Oncorhynchus mykiss）脑部转录组（transcriptome）进行测序，鉴定出了与磁感应相关的候选基因。然而，该研究仅针对与参考基因组（reference genome）比对成功的序列开展候选基因挖掘，未比对序列可能蕴藏着宝贵的研究信息，这些序列或来自参考基因组缺失、组装错误或序列分化的区域。本研究利用已公开的虹鳟脑转录组测序数据，将超过2700万条未比对序列（占总序列数的5.8%）组装为45142条重叠群（contig），并鉴定出12条在脉冲磁场刺激下呈现差异表达的重叠群。这些重叠群分别编码推定的超氧化物歧化酶——一种可抵御氧化损伤的必需蛋白质——以及Ⅱ型胶原蛋白α1链——一种对视网膜发育与结构完整性至关重要的结构蛋白。上述基因与此前研究的结论相符，即脉冲磁场可影响游离铁引发的氧化效应，以及非视觉性脑感光受体的功能。本研究结果证实了组装未比对测序读段在基因表达研究中的应用价值，并鉴定出虹鳟磁感应相关的额外候选基因。