Members of the Animal Genome to Phenome Research Coordination Network discussed best practices for the de novo assembly, annotation, and expression analysis of RNA-seq data. The AG2P RCN 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. Discussion participants studied a great variety of organisms, and represented laboratories present in both the US and abroad (see above figure). A policy paper summarizing community needs, computational pipelines, current resources and future directions has recently been published in Integrative and Comparative Biology.
The NSF’s “Genomes to Phenomes (G2P)” initiative is identifying key questions, such as how genetic mechanisms produce more fit phenotypes (adaptive evolution) and how genotype affects non-linear or non-additive molecular changes to produce a different phenotype. There is an emerging consensus behind the need to understand the mechanisms that govern the genome to phenome continuum, which requires integration across all levels of biological organization. As the product of the genome, a transcriptome is a key driver of phenotype and thus serves as a vital link between genes and the environment. A relatively small number of decapod crustacean species have been intensively studied at the molecular level; their availability, experimental tractability, and economic relevance factor into the selection of a particular species as a model. Transcriptomics, using high-throughput next generation sequencing (NGS, coupled with RNA sequencing or RNA-seq) is revolutionizing crustacean biology. The eleven symposium presentations presented at this symposium illustrated how RNA-seq is being used to study stress response, molting and limb regeneration, immunity and disease, reproduction and development, neurobiology, and ecology and evolution. A summary of the symposium has been recently been published in Integrative and Comparative Biology.