Journal
INTEGRATIVE AND COMPARATIVE BIOLOGY
Volume 56, Issue 6, Pages 1067-1079Publisher
OXFORD UNIV PRESS INC
DOI: 10.1093/icb/icw117
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Funding
- National Science Foundation [IOS-1551003]
- Society for Integrative and Comparative Biology
- SICB Division of Comparative Physiology and Biochemistry
- Crustacean Society
- Direct For Biological Sciences
- Division Of Integrative Organismal Systems [1551003] Funding Source: National Science Foundation
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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.
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