A deep transcriptomic resource for the copepod crustacean Labidocera madurae: A potential indicator species for assessing near shore ecosystem health.
A deep transcriptomic resource for the copepod crustacean Labidocera madurae: A potential indicator species for assessing near shore ecosystem health.
复制标题
DOI：
10.1371/journal.pone.0186794
复制
发表时间：
2017
期刊：
影响因子：
3.7
通讯作者：
Lenz PH
中科院分区：
文献类型：
--
作者：
Roncalli V;Christie AE;Sommer SA;Cieslak MC;Hartline DK;Lenz PH
许多亚热带和热带海洋沿海环境的珊瑚礁生态系统因人为活动而严重退化。为减轻压力和促进健康生态系统的管理战略提供信息的研究重点是珊瑚礁和相关生物的生态和生理。很少有研究集中在周围的远洋社区，这是同样重要的生态系统功能。浮游动物通常以桡足类等小型甲壳类动物为主，是无脊椎动物和鱼类，尤其是仔鱼的重要食物来源。与珊瑚礁有关的浮游动物包括一个亚浮游桡足类家庭，可以作为一个指示物种的社会。在这里，我们描述了这样的桡足类，Labidocera madurae，一个pontellid从一个深入研究的珊瑚礁生态系统，Kāne'ohe湾，夏威夷，Oakland从头转录组的一代。使用从整个生物体获得的高通量序列数据组装转录组。它包含211，002个独特的转录本，其中包括72，391个编码区。使用多个工作流程评估其质量和完整性。基准通用单拷贝直系同源物（BUSCO）分析确定了88%的预期真核核心蛋白的转录本。有针对性的基因发现分析包括搜索编码全长“巨型”蛋白（> 4，000个氨基酸）的转录本、电压门控钠通道的蛋白质和剪接变体以及参与昼夜信号传导途径的蛋白质。产生了四种不同的参考转录组，并比较了桡足类和成年雌性之间差异基因表达的检测; 6，229个基因被一致地鉴定为两者之间的差异表达，而不管参考。自动生物信息学分析和靶向人工基因治疗表明，从头组装的L。Madurae转录组具有高质量和完整性。该转录组为评估栖息在珊瑚礁生态系统中的水生物种的全球生理状态提供了新的资源，该生态系统受到多种人为压力。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。
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.
登录
查看更多内容
影响因子：
2.7
作者：
Christie, Andrew E.
通讯作者：
Christie, Andrew E.
影响因子：
1
作者：
Hartline, DK;Lenz, PH;Herren, CM
通讯作者：
Herren, CM
影响因子：
2.6
作者：
Havird, Justin C.;Santos, Scott R.
通讯作者：
Santos, Scott R.
DOI：
10.1126/science.1197761
发表时间：
2011-02-04
期刊：
Science (New York, N.Y.)
影响因子：
--
作者：
Colbourne JK;Pfrender ME;Gilbert D;Thomas WK;Tucker A;Oakley TH;Tokishita S;Aerts A;Arnold GJ;Basu MK;Bauer DJ;Cáceres CE;Carmel L;Casola C;Choi JH;Detter JC;Dong Q;Dusheyko S;Eads BD;Fröhlich T;Geiler-Samerotte KA;Gerlach D;Hatcher P;Jogdeo S;Krijgsveld J;Kriventseva EV;Kültz D;Laforsch C;Lindquist E;Lopez J;Manak JR;Muller J;Pangilinan J;Patwardhan RP;Pitluck S;Pritham EJ;Rechtsteiner A;Rho M;Rogozin IB;Sakarya O;Salamov A;Schaack S;Shapiro H;Shiga Y;Skalitzky C;Smith Z;Souvorov A;Sung W;Tang Z;Tsuchiya D;Tu H;Vos H;Wang M;Wolf YI;Yamagata H;Yamada T;Ye Y;Shaw JR;Andrews J;Crease TJ;Tang H;Lucas SM;Robertson HM;Bork P;Koonin EV;Zdobnov EM;Grigoriev IV;Lynch M;Boore JL
通讯作者：
Boore JL
影响因子：
18.2
作者：
Allada R;Chung BY
通讯作者：
Chung BY