title: Resources and Recommendations for Using Transcriptomics to Address Grand Challenges in Comparative Biology.
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.
authors.affiliation: *Department of Biology, Colorado State University, Fort Collins, CO 80523, USA donald.mykles@colostate.edu.
authors.forename: Donald L
authors.initials: DL
authors.lastname: Mykles
authors.affiliation: Grice Marine Laboratory, College of Charleston, Charleston, SC 29412, USA.|Hollings Marine Laboratory, Charleston, SC 29412, USA.
authors.forename: Karen G
authors.initials: KG
authors.lastname: Burnett
authors.affiliation: Department of Biology, University of Oklahoma, Norman, OK 73019, USA.
authors.forename: David S
authors.initials: DS
authors.lastname: Durica
authors.affiliation: BIO5 Institute, School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA.
authors.forename: Blake L
authors.initials: BL
authors.lastname: Joyce
authors.affiliation: School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, AZ 85721, USA.
authors.forename: Fiona M
authors.initials: FM
authors.lastname: McCarthy
authors.affiliation: Department of Animal and Food Sciences, University of Delaware, Newark, DE 19716.
authors.forename: Carl J
authors.initials: CJ
authors.lastname: Schmidt
authors.affiliation: Romberg Tiburon Center for Environmental Studies and Department of Biology, San Francisco State University, Tiburon, CA 94920, USA.|Department of Integrative Biology, University of California Berkeley, Berkeley, CA 94720, USA.
authors.forename: Jonathon H
authors.initials: JH
authors.lastname: Stillman
mesh_terms: D000818:Animals; D001695:Biology / Q000639:trends*; D019295:Computational Biology / Q000379:methods*; D003226:Congresses as Topic; D023421:Models, Animal