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EchinoDB, an application for comparative transcriptomics of deeply-sampled clades of echinoderms.

Publication ,  Journal Article
Janies, DA; Witter, Z; Linchangco, GV; Foltz, DW; Miller, AK; Kerr, AM; Jay, J; Reid, RW; Wray, GA
Published in: BMC bioinformatics
January 2016

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.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.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.

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Published In

BMC bioinformatics

DOI

EISSN

1471-2105

ISSN

1471-2105

Publication Date

January 2016

Volume

17

Start / End Page

48

Related Subject Headings

  • Transcriptome
  • Sea Urchins
  • Phylogeny
  • High-Throughput Nucleotide Sequencing
  • Genome
  • Databases, Factual
  • Bioinformatics
  • Animals
  • 49 Mathematical sciences
  • 46 Information and computing sciences
 

Citation

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Janies, D. A., Witter, Z., Linchangco, G. V., Foltz, D. W., Miller, A. K., Kerr, A. M., … Wray, G. A. (2016). EchinoDB, an application for comparative transcriptomics of deeply-sampled clades of echinoderms. BMC Bioinformatics, 17, 48. https://doi.org/10.1186/s12859-016-0883-2
Janies, Daniel A., Zach Witter, Gregorio V. Linchangco, David W. Foltz, Allison K. Miller, Alexander M. Kerr, Jeremy Jay, Robert W. Reid, and Gregory A. Wray. “EchinoDB, an application for comparative transcriptomics of deeply-sampled clades of echinoderms.BMC Bioinformatics 17 (January 2016): 48. https://doi.org/10.1186/s12859-016-0883-2.
Janies DA, Witter Z, Linchangco GV, Foltz DW, Miller AK, Kerr AM, et al. EchinoDB, an application for comparative transcriptomics of deeply-sampled clades of echinoderms. BMC bioinformatics. 2016 Jan;17:48.
Janies, Daniel A., et al. “EchinoDB, an application for comparative transcriptomics of deeply-sampled clades of echinoderms.BMC Bioinformatics, vol. 17, Jan. 2016, p. 48. Epmc, doi:10.1186/s12859-016-0883-2.
Janies DA, Witter Z, Linchangco GV, Foltz DW, Miller AK, Kerr AM, Jay J, Reid RW, Wray GA. EchinoDB, an application for comparative transcriptomics of deeply-sampled clades of echinoderms. BMC bioinformatics. 2016 Jan;17:48.
Journal cover image

Published In

BMC bioinformatics

DOI

EISSN

1471-2105

ISSN

1471-2105

Publication Date

January 2016

Volume

17

Start / End Page

48

Related Subject Headings

  • Transcriptome
  • Sea Urchins
  • Phylogeny
  • High-Throughput Nucleotide Sequencing
  • Genome
  • Databases, Factual
  • Bioinformatics
  • Animals
  • 49 Mathematical sciences
  • 46 Information and computing sciences