Resources and Recommendations for Using Transcriptomics to Address Grand Challenges in Comparative Biology

Area of Science:

• Comparative genomics
• Transcriptomics
• Crustacean biology

Background:

• High-throughput RNA sequencing (RNA-seq) is crucial for studying organismal responses to environmental changes.
• De novo assembly of RNA-seq data allows gene cataloging and expression quantification, even without a complete genome sequence.
• Symposium contributions highlight successes and limitations of RNA-seq in crustacean research.

Purpose of the Study:

• To identify challenges and opportunities in crustacean transcriptomics research.
• To gather community input on best practices and resource needs.
• To propose recommendations for advancing the field of crustacean functional genomics.

Main Methods:

• Collation of participant comments from the "Tapping the Power of Crustacean Transcriptomics" symposium.
• Analysis of community feedback from novices and experts on transcriptomics challenges.
• Review of available bioinformatics analysis resources on the CyVerse platform.

Main Results:

• Many researchers were unaware of existing bioinformatics resources on the CyVerse platform.
• Identified key challenges in applying transcriptomics to crustacean research.
• Community input revealed needs for improved gene annotation, functional analysis, and training.

Conclusions:

• Recommends integrating genomic and RNA-seq data for enhanced crustacean gene annotation and comparative expression analysis.
• Advocates for developing new methodologies for functional gene analysis in crustaceans.
• Suggests establishing information and training exchange programs to disseminate best practices.
• Proposes the cherry shrimp (Neocaridina denticulata) as a model organism for functional genomics using transgenic tools, requiring a collaborative effort.