Bain Peter A, Papanicolaou Alexie, Kumar Anupama
Commonwealth Scientific and Industrial Research Organisation (CSIRO), Division of Land and Water, Urrbrae, South Australia, Australia.
Commonwealth Scientific and Industrial Research Organisation (CSIRO), Division of Land and Water, Black Mountain, Australian Capital Territory, Australia.
PLoS One. 2015 Nov 23;10(11):e0142636. doi: 10.1371/journal.pone.0142636. eCollection 2015.
Murray-Darling rainbowfish (Melanotaenia fluviatilis [Castelnau, 1878]; Atheriniformes: Melanotaeniidae) is a small-bodied teleost currently under development in Australasia as a test species for aquatic toxicological studies. To date, efforts towards the development of molecular biomarkers of contaminant exposure have been hindered by the lack of available sequence data. To address this, we sequenced messenger RNA from brain, liver and gonads of mature male and female fish and generated a high-quality draft transcriptome using a de novo assembly approach. 149,742 clusters of putative transcripts were obtained, encompassing 43,841 non-redundant protein-coding regions. Deduced amino acid sequences were annotated by functional inference based on similarity with sequences from manually curated protein sequence databases. The draft assembly contained protein-coding regions homologous to 95.7% of the complete cohort of predicted proteins from the taxonomically related species, Oryzias latipes (Japanese medaka). The mean length of rainbowfish protein-coding sequences relative to their medaka homologues was 92.1%, indicating that despite the limited number of tissues sampled a large proportion of the total expected number of protein-coding genes was captured in the study. Because of our interest in the effects of environmental contaminants on endocrine pathways, we manually curated subsets of coding regions for putative nuclear receptors and steroidogenic enzymes in the rainbowfish transcriptome, revealing 61 candidate nuclear receptors encompassing all known subfamilies, and 41 putative steroidogenic enzymes representing all major steroidogenic enzymes occurring in teleosts. The transcriptome presented here will be a valuable resource for researchers interested in biomarker development, protein structure and function, and contaminant-response genomics in Murray-Darling rainbowfish.
墨累-达令虹银汉鱼（Melanotaenia fluviatilis [卡斯泰尔诺，1878年]；银汉鱼目：虹银汉鱼科）是一种小型硬骨鱼，目前在澳大拉西亚地区正被开发用作水生毒理学研究的试验物种。迄今为止，由于缺乏可用的序列数据，污染物暴露分子生物标志物的开发工作受到了阻碍。为了解决这一问题，我们对成熟雄鱼和雌鱼的脑、肝和性腺中的信使核糖核酸进行了测序，并采用从头组装方法生成了高质量的转录组草图。获得了149,742个假定转录本簇，其中包括43,841个非冗余蛋白质编码区。通过与人工整理的蛋白质序列数据库中的序列进行相似性比较，基于功能推断对推导的氨基酸序列进行了注释。该草图组装包含与分类学相关物种日本青鳉（Oryzias latipes）预测蛋白质完整队列中95.7%的蛋白质编码区同源的区域。相对于其青鳉同源物，虹银汉鱼蛋白质编码序列的平均长度为92.1%，这表明尽管采样的组织数量有限，但研究中捕获了预期蛋白质编码基因总数的很大一部分。由于我们对环境污染物对内分泌途径的影响感兴趣，我们人工整理了虹银汉鱼转录组中假定核受体和类固醇生成酶的编码区子集，发现了61个候选核受体，涵盖所有已知亚家族，以及41个假定类固醇生成酶，代表硬骨鱼中出现的所有主要类固醇生成酶。本文呈现的转录组将为对墨累-达令虹银汉鱼生物标志物开发、蛋白质结构和功能以及污染物反应基因组学感兴趣的研究人员提供宝贵资源。
