title: EchinoDB, an application for comparative transcriptomics of deeply-sampled clades of echinoderms.
abstract: BACKGROUND
  One of our goals for the echinoderm tree of life project (http://echinotol.org) is to identify orthologs suitable for phylogenetic analysis from next-generation transcriptome data. The current dataset is the largest assembled for echinoderm phylogeny and transcriptomics. We used RNA-Seq to profile adult tissues from 42 echinoderm specimens from 24 orders and 37 families. In order to achieve sampling members of clades that span key evolutionary divergence, many of our exemplars were collected from deep and polar seas.
  
  
  METHODS
  A small fraction of the transcriptome data we produced is being used for phylogenetic reconstruction. Thus to make a larger dataset available to researchers with a wide variety of interests, we made a web-based application, EchinoDB (http://echinodb.uncc.edu). EchinoDB is a repository of orthologous transcripts from echinoderms that is searchable via keywords and sequence similarity.
  
  
  CONCLUSIONS
  From transcripts we identified 749,397 clusters of orthologous loci. We have developed the information technology to manage and search the loci their annotations with respect to the Sea Urchin (Strongylocentrotus purpuratus) genome. Several users have already taken advantage of these data for spin-off projects in developmental biology, gene family studies, and neuroscience. We hope others will search EchinoDB to discover datasets relevant to a variety of additional questions in comparative biology.
authors.affiliation: Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, 9201 University City Blvd, Charlotte, NC, 28223-0001, USA. djanies@uncc.edu.
authors.forename: Daniel A
authors.initials: DA
authors.lastname: Janies
authors.affiliation: Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, 9201 University City Blvd, Charlotte, NC, 28223-0001, USA.
authors.forename: Zach
authors.initials: Z
authors.lastname: Witter
authors.affiliation: Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, 9201 University City Blvd, Charlotte, NC, 28223-0001, USA.
authors.forename: Gregorio V
authors.initials: GV
authors.lastname: Linchangco
authors.affiliation: Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, 70803, USA.
authors.forename: David W
authors.initials: DW
authors.lastname: Foltz
authors.affiliation: Marine Laboratory, University of Guam, University Dr, Mangilao, 96923, Guam.
authors.forename: Allison K
authors.initials: AK
authors.lastname: Miller
authors.affiliation: Marine Laboratory, University of Guam, University Dr, Mangilao, 96923, Guam.
authors.forename: Alexander M
authors.initials: AM
authors.lastname: Kerr
authors.affiliation: Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, 9201 University City Blvd, Charlotte, NC, 28223-0001, USA.
authors.forename: Jeremy
authors.initials: J
authors.lastname: Jay
authors.affiliation: Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, 9201 University City Blvd, Charlotte, NC, 28223-0001, USA.
authors.forename: Robert W
authors.initials: RW
authors.lastname: Reid
authors.affiliation: Department of Biology, Duke University, Durham, NC, 27708, USA.
authors.forename: Gregory A
authors.initials: GA
authors.lastname: Wray
mesh_terms: D000818:Animals; D016208:Databases, Factual; D016678:Genome; D059014:High-Throughput Nucleotide Sequencing; D010802:Phylogeny; D012617:Sea Urchins / Q000145:classification / Q000235:genetics*; D059467:Transcriptome