Biology Department, Woods Hole Oceanographic Institution, 45 Water Street, Woods Hole, MA 02544, USA.
Department of Science and Environment, Roskilde University, Universitetsvej 1, Roskilde, Denmark.
Comp Biochem Physiol Part D Genomics Proteomics. 2019 Jun;30:230-247. doi: 10.1016/j.cbd.2019.03.005. Epub 2019 Mar 19.
Planktonic copepods are a diverse and abundant group of small (~mm sized) aquatic animals that play a critical role in linking the base of the food chain with higher trophic levels. These invertebrates are a primary food source for marine fish larvae. Their ubiquitous presence is thus of vital importance for recruitment of fish stocks and also as promising live feed for finfish production in aquaculture. This paper reviews the application of molecular approaches to understanding copepod physiology, particularly in non-parasitic species. The review includes both targeted gene approaches and untargeted transcriptomic approaches, with suggestions for best practices in each case. Issues particularly relevant to studies of copepods include heterogeneity within species, morphologically cryptic species, experimental artifacts associated with sample handling, and limited annotation of copepod genes and transcripts. The emergence of high-throughput sequencing and associated increased availability of genomic and transcriptomic databases have presented a huge opportunity to advance knowledge of copepod physiology. The research community can leverage this opportunity through efforts to maintain or improve data accessibility, database annotation, and documentation of analytical pipelines.
浮游桡足类是一类多样且丰富的小型（~mm 大小）水生动物，在将食物链的基础与更高营养级联系起来方面发挥着关键作用。这些无脊椎动物是海洋鱼类幼体的主要食物来源。因此，它们的普遍存在对于鱼类种群的补充以及作为水产养殖中鱼类生产有前途的活饵料都至关重要。本文综述了分子方法在了解桡足类生理学中的应用，特别是在非寄生物种中。该综述包括有针对性的基因方法和无针对性的转录组学方法，并针对每种方法提出了最佳实践建议。与桡足类研究特别相关的问题包括种内异质性、形态上隐匿的物种、与样品处理相关的实验假象以及桡足类基因和转录本的有限注释。高通量测序的出现以及相关基因组和转录组数据库的可用性增加，为推进桡足类生理学知识提供了巨大的机会。研究界可以通过努力维护或提高数据可及性、数据库注释以及分析管道文档来利用这一机会。
