Chana-Munoz Andres, Jendroszek Agnieszka, Sønnichsen Malene, Kristiansen Rune, Jensen Jan K, Andreasen Peter A, Bendixen Christian, Panitz Frank
Department of Molecular Biology and Genetics, Aarhus University, Tjele, Denmark.
Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark.
PLoS One. 2017 Aug 23;12(8):e0182756. doi: 10.1371/journal.pone.0182756. eCollection 2017.
The spiny dogfish shark (Squalus acanthias) is one of the most commonly used cartilaginous fishes in biological research, especially in the fields of nitrogen metabolism, ion transporters and osmoregulation. Nonetheless, transcriptomic data for this organism is scarce. In the present study, a multi-tissue RNA-seq experiment and de novo transcriptome assembly was performed in four different spiny dogfish tissues (brain, liver, kidney and ovary), providing an annotated sequence resource. The characterization of the transcriptome greatly increases the scarce sequence information for shark species. Reads were assembled with the Trinity de novo assembler both within each tissue and across all tissues combined resulting in 362,690 transcripts in the combined assembly which represent 289,515 Trinity genes. BUSCO analysis determined a level of 87% completeness for the combined transcriptome. In total, 123,110 proteins were predicted of which 78,679 and 83,164 had significant hits against the SwissProt and Uniref90 protein databases, respectively. Additionally, 61,215 proteins aligned to known protein domains, 7,208 carried a signal peptide and 15,971 possessed at least one transmembrane region. Based on the annotation, 81,582 transcripts were assigned to gene ontology terms and 42,078 belong to known clusters of orthologous groups (eggNOG). To demonstrate the value of our molecular resource, we show that the improved transcriptome data enhances the current possibilities of osmoregulation research in spiny dogfish by utilizing the novel gene and protein annotations to investigate a set of genes involved in urea synthesis and urea, ammonia and water transport, all of them crucial in osmoregulation. We describe the presence of different gene copies and isoforms of key enzymes involved in this process, including arginases and transporters of urea and ammonia, for which sequence information is currently absent in the databases for this model species. The transcriptome assemblies and the derived annotations generated in this study will support the ongoing research for this particular animal model and provides a new molecular tool to assist biological research in cartilaginous fishes.
棘鲨（Squalus acanthias）是生物学研究中最常用的软骨鱼类之一，尤其在氮代谢、离子转运体和渗透压调节等领域。尽管如此，该生物的转录组数据却很匮乏。在本研究中，我们对四种不同的棘鲨组织（脑、肝、肾和卵巢）进行了多组织RNA测序实验和从头转录组组装，提供了一个带注释的序列资源。转录组的特征极大地增加了鲨鱼物种稀缺的序列信息。使用Trinity从头组装器在每个组织内以及所有组织组合中进行reads组装，在组合组装中产生了362,690个转录本，代表289,515个Trinity基因。BUSCO分析确定组合转录组的完整性水平为87%。总共预测了123,110种蛋白质，其中分别有78,679种和83,164种与SwissProt和Uniref90蛋白质数据库有显著匹配。此外，61,215种蛋白质与已知蛋白质结构域对齐，7,208种带有信号肽，15,971种至少拥有一个跨膜区域。基于注释，81,582个转录本被分配到基因本体术语，42,078个属于已知的直系同源群簇（eggNOG）。为了证明我们分子资源的价值，我们表明改进的转录组数据通过利用新的基因和蛋白质注释来研究一组参与尿素合成以及尿素、氨和水运输的基因，增强了当前棘鲨渗透压调节研究的可能性，所有这些基因在渗透压调节中都至关重要。我们描述了参与此过程的关键酶的不同基因拷贝和异构体的存在，包括精氨酸酶以及尿素和氨的转运体，而该模式物种的数据库中目前缺少这些酶的序列信息。本研究中生成的转录组组装和衍生注释将支持对这种特定动物模型的 ongoing研究，并提供一种新的分子工具来辅助软骨鱼类的生物学研究。
