Department of Physiology, University of Toronto, 3308 MSB, 1 King's College Circle, Toronto, ON, M5S 1A8, Canada.
Donnelly Centre for Cellular and Biomolecular Research and Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 3E1, Canada.
BMC Genomics. 2021 Jan 6;22(1):18. doi: 10.1186/s12864-020-07287-2.
The pond snail Lymnaea stagnalis (L. stagnalis) has been widely used as a model organism in neurobiology, ecotoxicology, and parasitology due to the relative simplicity of its central nervous system (CNS). However, its usefulness is restricted by a limited availability of transcriptome data. While sequence information for the L. stagnalis CNS transcripts has been obtained from EST libraries and a de novo RNA-seq assembly, the quality of these assemblies is limited by a combination of low coverage of EST libraries, the fragmented nature of de novo assemblies, and lack of reference genome.
In this study, taking advantage of the recent availability of a preliminary L. stagnalis genome, we generated an RNA-seq library from the adult L. stagnalis CNS, using a combination of genome-guided and de novo assembly programs to identify 17,832 protein-coding L. stagnalis transcripts. We combined our library with existing resources to produce a transcript set with greater sequence length, completeness, and diversity than previously available ones. Using our assembly and functional domain analysis, we profiled L. stagnalis CNS transcripts encoding ion channels and ionotropic receptors, which are key proteins for CNS function, and compared their sequences to other vertebrate and invertebrate model organisms. Interestingly, L. stagnalis transcripts encoding numerous putative Ca channels showed the most sequence similarity to those of Mus musculus, Danio rerio, Xenopus tropicalis, Drosophila melanogaster, and Caenorhabditis elegans, suggesting that many calcium channel-related signaling pathways may be evolutionarily conserved.
Our study provides the most thorough characterization to date of the L. stagnalis transcriptome and provides insights into differences between vertebrates and invertebrates in CNS transcript diversity, according to function and protein class. Furthermore, this study provides a complete characterization of the ion channels of Lymnaea stagnalis, opening new avenues for future research on fundamental neurobiological processes in this model system.
由于其中枢神经系统（CNS）相对简单，圆田螺（Lymnaea stagnalis）已被广泛用作神经生物学、生态毒理学和寄生虫学的模式生物。然而，由于其转录组数据的可用性有限，其用途受到限制。虽然已经从 EST 文库和从头 RNA-seq 组装中获得了 L. stagnalis CNS 转录本的序列信息，但这些组装的质量受到 EST 文库覆盖度低、从头组装的碎片化以及缺乏参考基因组的限制。
在这项研究中，我们利用最近获得的初步 L. stagnalis 基因组，从成年 L. stagnalis CNS 生成了一个 RNA-seq 文库，结合使用基因组指导和从头组装程序来鉴定 17832 个编码 L. stagnalis 的蛋白质编码转录本。我们将我们的文库与现有资源相结合，生成了一个转录本集，其序列长度、完整性和多样性都比以前可用的转录本集更大。使用我们的组装和功能结构域分析，我们对编码离子通道和离子型受体的 L. stagnalis CNS 转录本进行了分析，这些转录本是 CNS 功能的关键蛋白，并将它们的序列与其他脊椎动物和无脊椎动物模型生物进行了比较。有趣的是，L. stagnalis 编码许多假定的 Ca 通道的转录本与 Mus musculus、Danio rerio、Xenopus tropicalis、Drosophila melanogaster 和 Caenorhabditis elegans 的序列最相似，这表明许多钙通道相关的信号通路可能在进化上是保守的。
我们的研究提供了迄今为止对 L. stagnalis 转录组最全面的描述，并根据功能和蛋白质类别深入了解了中枢神经系统转录本多样性在脊椎动物和无脊椎动物之间的差异。此外，这项研究还提供了对 Lymnaea stagnalis 离子通道的完整描述，为在这个模型系统中研究基本神经生物学过程开辟了新的途径。
