Abstract
StellaBase, the Nematostella vectensis Genomics Database, is a web-based resource that will facilitate desktop and bench-top studies of the starlet sea anemone. Nematostella is an emerging model organism that has already proven useful for addressing fundamental questions in developmental evolution and evolutionary genomics. StellaBase allows users to query the assembled Nematostella genome, a confirmed gene library, and a predicted genome using both keyword and homology based search functions. Data provided by these searches will elucidate gene family evolution in early animals. Unique research tools, including a Nematostella genetic stock library, a primer library, a literature repository and a gene expression library will provide support to the burgeoning Nematostella research community. The development of StellaBase accompanies significant upgrades to CnidBase, the Cnidarian Evolutionary Genomics Database. With the completion of the first sequenced cnidarian genome, genome comparison tools have been added to CnidBase. In addition, StellaBase provides a framework for the integration of additional species-specific databases into CnidBase. StellaBase is available at http://www.stellabase.org.
MeSH Terms
Animals
Databases, Genetic
Evolution, Molecular
Gene Expression
Genomics
Internet
Oligonucleotide Probes/chemistry
Proteins/genetics
Sea Anemones/genetics,metabolism
Systems Integration
User-Computer Interface
Chemicals
Oligonucleotide Probes
Proteins
Authors & Affiliations
7 authors, click to expand affiliations / ORCID
Sullivan James C
Department of Biology, Boston University, 5 Cummington Street, Boston, MA 02215, USA.
Ryan Joseph F
Watson James A
Webb Jeramy
Mullikin James C
Rokhsar Daniel
Finnerty John R
References (26)
26 references, click to expand
-
The coral Acropora: what it can contribute to our knowledge of metazoan evolution and the evolution of developmental processes.
Bioessays. 2000 Mar;22(3):291-6
PMID: 10684589
-
The hydroid Hydractinia: a versatile, informative cnidarian representative.
Bioessays. 2001 Oct;23(10):963-71
PMID: 11598963
-
Cnidarians as a model system for understanding evolution and regeneration.
Int J Dev Biol. 2002 Jan;46(1):39-48
PMID: 11902686
-
Developmental signaling in Hydra: what does it take to build a "simple" animal?
Dev Biol. 2002 Aug 15;248(2):199-219
PMID: 12167399
-
CnidBase: The Cnidarian Evolutionary Genomics Database.
Nucleic Acids Res. 2003 Jan 1;31(1):159-63
PMID: 12519972
-
The phusion assembler.
Genome Res. 2003 Jan;13(1):81-90
PMID: 12529309
-
The ancestral role of Brachyury: expression of NemBra1 in the basal cnidarian Nematostella vectensis (Anthozoa).
Dev Genes Evol. 2003 Jan;212(12):563-70
PMID: 12536320
-
EST analysis of gene expression in the tentacle of Cyanea capillata.
FEBS Lett. 2003 Mar 13;538(1-3):183-91
PMID: 12633876
-
Early evolution of a homeobox gene: the parahox gene Gsx in the Cnidaria and the Bilateria.
Evol Dev. 2003 Jul-Aug;5(4):331-45
PMID: 12823450
-
An ancient role for nuclear beta-catenin in the evolution of axial polarity and germ layer segregation.
Nature. 2003 Nov 27;426(6965):446-50
PMID: 14647383
-
EST analysis of the cnidarian Acropora millepora reveals extensive gene loss and rapid sequence divergence in the model invertebrates.
Curr Biol. 2003 Dec 16;13(24):2190-5
PMID: 14680636
-
The Pfam protein families database.
Nucleic Acids Res. 2004 Jan 1;32(Database issue):D138-41
PMID: 14681378
-
The ancestral role of COE genes may have been in chemoreception: evidence from the development of the sea anemone, Nematostella vectensis (Phylum Cnidaria; Class Anthozoa).
Dev Genes Evol. 2004 Mar;214(3):134-8
PMID: 14752662
-
Investigating the origins of triploblasty: 'mesodermal' gene expression in a diploblastic animal, the sea anemone Nematostella vectensis (phylum, Cnidaria; class, Anthozoa).
Development. 2004 May;131(10):2463-74
PMID: 15128674
-
Origins of bilateral symmetry: Hox and dpp expression in a sea anemone.
Science. 2004 May 28;304(5675):1335-7
PMID: 15131263
-
Regional population structure of a widely introduced estuarine invertebrate: Nematostella vectensis Stephenson in New England.
Mol Ecol. 2004 Oct;13(10):2969-81
PMID: 15367113
-
Unexpected complexity of the Wnt gene family in a sea anemone.
Nature. 2005 Jan 13;433(7022):156-60
PMID: 15650739
-
Rising starlet: the starlet sea anemone, Nematostella vectensis.
Bioessays. 2005 Feb;27(2):211-21
PMID: 15666346
-
Databases in peril.
Nature. 2005 Jun 23;435(7045):1010-1
PMID: 15973369
-
Origin of the Eumetazoa: testing ecological predictions of molecular clocks against the Proterozoic fossil record.
Proc Natl Acad Sci U S A. 2005 Jul 5;102(27):9547-52
PMID: 15983372
-
Basic local alignment search tool.
J Mol Biol. 1990 Oct 5;215(3):403-10
PMID: 2231712
-
The Culture, Sexual and Asexual Reproduction, and Growth of the Sea Anemone Nematostella vectensis.
Biol Bull. 1992 Apr;182(2):169-176
PMID: 29303672
-
Evaluation of gene structure prediction programs.
Genomics. 1996 Jun 15;34(3):353-67
PMID: 8786136
-
Prediction of complete gene structures in human genomic DNA.
J Mol Biol. 1997 Apr 25;268(1):78-94
PMID: 9149143
-
Homeoboxes in sea anemones (Cnidaria:Anthozoa): a PCR-based survey of Nematostella vectensis and Metridium senile.
Biol Bull. 1997 Aug;193(1):62-76
PMID: 9290214
-
Finding the genes in genomic DNA.
Curr Opin Struct Biol. 1998 Jun;8(3):346-54
PMID: 9666331