Resources and recommendations for using transcriptomics to address grand challenges in comparative biology

Donald L. Mykles, Karen G. Burnett, David S. Durica, Blake L. Joyce, Fiona M McCarthy, Carl J. Schmidt, Jonathon H. Stillman

Research output: Contribution to journalArticle

5 Citations (Scopus)

Abstract

High-throughput RNA sequencing (RNA-seq) technology has become an important tool for studying physiological responses of organisms to changes in their environment. De novo assembly of RNA-seq data has allowed researchers to create a comprehensive catalog of genes expressed in a tissue and to quantify their expression without a complete genome sequence. The contributions from the "Tapping the Power of Crustacean Transcriptomics to Address Grand Challenges in Comparative Biology" symposium in this issue show the successes and limitations of using RNA-seq in the study of crustaceans. In conjunction with the symposium, the Animal Genome to Phenome Research Coordination Network collated comments from participants at the meeting regarding the challenges encountered when using transcriptomics in their research. Input came from novices and experts ranging from graduate students to principal investigators. Many were unaware of the bioinformatics analysis resources currently available on the CyVerse platform. Our analysis of community responses led to three recommendations for advancing the field: (1) integration of genomic and RNA-seq sequence assemblies for crustacean gene annotation and comparative expression; (2) development of methodologies for the functional analysis of genes; and (3) information and training exchange among laboratories for transmission of best practices. The field lacks the methods for manipulating tissue-specific gene expression. The decapod crustacean research community should consider the cherry shrimp, Neocaridina denticulata, as a decapod model for the application of transgenic tools for functional genomics. This would require a multi-investigator effort.

Original languageEnglish (US)
Pages (from-to)1183-1191
Number of pages9
JournalIntegrative and Comparative Biology
Volume56
Issue number6
DOIs
StatePublished - Dec 1 2016

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transcriptomics
Crustacea
Biological Sciences
sequence analysis
Decapoda
research coordination
principal investigators
genomics
genome
genes
bioinformatics
physiological response
students
shrimp
researchers
genetically modified organisms
gene expression
organisms
methodology
animals

ASJC Scopus subject areas

  • Animal Science and Zoology
  • Plant Science

Cite this

Resources and recommendations for using transcriptomics to address grand challenges in comparative biology. / Mykles, Donald L.; Burnett, Karen G.; Durica, David S.; Joyce, Blake L.; McCarthy, Fiona M; Schmidt, Carl J.; Stillman, Jonathon H.

In: Integrative and Comparative Biology, Vol. 56, No. 6, 01.12.2016, p. 1183-1191.

Research output: Contribution to journalArticle

Mykles, Donald L. ; Burnett, Karen G. ; Durica, David S. ; Joyce, Blake L. ; McCarthy, Fiona M ; Schmidt, Carl J. ; Stillman, Jonathon H. / Resources and recommendations for using transcriptomics to address grand challenges in comparative biology. In: Integrative and Comparative Biology. 2016 ; Vol. 56, No. 6. pp. 1183-1191.
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