Roncalli Vittoria, Christie Andrew E, Sommer Stephanie A, Cieslak Matthew C, Hartline Daniel K, Lenz Petra H
Békésy Laboratory of Neurobiology, University of Hawai'i at Mānoa, Honolulu, HI, United States of America.
PLoS One. 2017 Oct 24;12(10):e0186794. doi: 10.1371/journal.pone.0186794. eCollection 2017.
Coral reef ecosystems of many sub-tropical and tropical marine coastal environments have suffered significant degradation from anthropogenic sources. Research to inform management strategies that mitigate stressors and promote a healthy ecosystem has focused on the ecology and physiology of coral reefs and associated organisms. Few studies focus on the surrounding pelagic communities, which are equally important to ecosystem function. Zooplankton, often dominated by small crustaceans such as copepods, is an important food source for invertebrates and fishes, especially larval fishes. The reef-associated zooplankton includes a sub-neustonic copepod family that could serve as an indicator species for the community. Here, we describe the generation of a de novo transcriptome for one such copepod, Labidocera madurae, a pontellid from an intensively-studied coral reef ecosystem, Kāne'ohe Bay, Oahu, Hawai'i. The transcriptome was assembled using high-throughput sequence data obtained from whole organisms. It comprised 211,002 unique transcripts, including 72,391 with coding regions. It was assessed for quality and completeness using multiple workflows. Bench-marking-universal-single-copy-orthologs (BUSCO) analysis identified transcripts for 88% of expected eukaryotic core proteins. Targeted gene-discovery analyses included searches for transcripts coding full-length "giant" proteins (>4,000 amino acids), proteins and splice variants of voltage-gated sodium channels, and proteins involved in the circadian signaling pathway. Four different reference transcriptomes were generated and compared for the detection of differential gene expression between copepodites and adult females; 6,229 genes were consistently identified as differentially expressed between the two regardless of reference. Automated bioinformatics analyses and targeted manual gene curation suggest that the de novo assembled L. madurae transcriptome is of high quality and completeness. This transcriptome provides a new resource for assessing the global physiological status of a planktonic species inhabiting a coral reef ecosystem that is subjected to multiple anthropogenic stressors. The workflows provide a template for generating and assessing transcriptomes in other non-model species.
许多亚热带和热带海洋沿岸环境的珊瑚礁生态系统因人为因素而遭受了严重退化。旨在为减轻压力源并促进生态系统健康的管理策略提供依据的研究，主要集中在珊瑚礁及相关生物的生态学和生理学方面。很少有研究关注周围的浮游生物群落，而它们对生态系统功能同样重要。浮游动物通常以小型甲壳类动物（如桡足类）为主，是无脊椎动物和鱼类（尤其是幼鱼）的重要食物来源。与珊瑚礁相关的浮游动物包括一个亚表层桡足类家族，它可以作为该群落的指示物种。在此，我们描述了一种这样的桡足类动物——马都拉角水蚤（Labidocera madurae）的从头转录组的生成，它是一种来自夏威夷瓦胡岛卡内奥赫湾一个经过深入研究的珊瑚礁生态系统的尖头水蚤科动物。该转录组是使用从整个生物体获得的高通量序列数据组装而成的。它包含211,002个独特转录本，其中72,391个具有编码区。使用多种工作流程对其质量和完整性进行了评估。基准通用单拷贝直系同源物（BUSCO）分析确定了88%预期真核核心蛋白的转录本。靶向基因发现分析包括搜索编码全长“巨型”蛋白（>4000个氨基酸）的转录本、电压门控钠通道的蛋白和剪接变体，以及参与昼夜节律信号通路的蛋白。生成并比较了四种不同的参考转录组，以检测桡足幼体和成体雌性之间的差异基因表达；无论使用何种参考，始终有6229个基因被鉴定为在两者之间差异表达。自动化生物信息学分析和靶向手动基因整理表明，从头组装的马都拉角水蚤转录组具有高质量和完整性。这个转录组为评估栖息在受多种人为压力源影响的珊瑚礁生态系统中的浮游物种的全球生理状态提供了新资源。这些工作流程为在其他非模式物种中生成和评估转录组提供了模板。
