Analysis of Annotation and Differential Expression Methods used in RNA-seq Studies in Crustacean Systems
Analysis of Annotation and Differential Expression Methods used in RNA-seq Studies in Crustacean Systems
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DOI：
10.1093/icb/icw117
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发表时间：
2016-12-01
影响因子：
2.6
通讯作者：
Durica, David S.
中科院分区：
文献类型：
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作者：
Das, Sunetra;Shyamal, Sharmishtha;Durica, David S.
在甲壳类生物学领域，利用 RNA-seq 研究基因表达的情况正在迅速增长。测序技术的重大进步有助于检查多种生物体中基因组活动的复杂模式，这些生物体广泛用于比较生理学、生态学和进化、环境监测和商业水产养殖。然而，相对于昆虫和脊椎动物模型生物，甲壳类动物基因组的组织信息实际上不存在，这使得从头转录组组装、注释和量化成为问题和挑战。我们在此总结了最近 23 篇出版物中采用的方法和软件分析，这些出版物描述了各种甲壳动物实验系统中的从头转录组组装、注释和差异基因表达。我们专注于建立一系列最佳实践，使研究人员能够生成可理解、可重复且对相关分析和交叉研究比较具有通用性的数据集。
In the field of crustacean biology, usage of RNA-seq to study gene expression is rapidly growing. Major advances in sequencing technology have contributed to the ability to examine complex patterns of genome activity in a wide range of organisms that are extensively used for comparative physiology, ecology and evolution, environmental monitoring, and commercial aquaculture. Relative to insect and vertebrate model organisms, however, information on the organization of crustacean genomes is virtually nonexistent, making de novo transcriptome assembly, annotation and quantification problematic and challenging. We present here a summary of the methodologies and software analyses employed in 23 recent publications, which describe de novo transcriptome assembly, annotation, and differential gene expression in a variety of crustacean experimental systems. We focus on establishing a series of best practices that will allow for investigators to produce datasets that are understandable, reproducible, and of general utility for related analyses and cross-study comparisons.