TY - JOUR
T1 - A transcriptomic analysis of the phylum Nematoda
AU - Parkinson, John
AU - Mitreva, Makedonka
AU - Whitton, Claire
AU - Thomson, Marian
AU - Daub, Jennifer
AU - Martin, John
AU - Schmid, Ralf
AU - Hall, Neil
AU - Barrell, Bart
AU - Waterston, Robert H.
AU - McCarter, James P.
AU - Blaxter, Mark L.
N1 - Funding Information:
We thank all our nematology and parasitology colleagues for supplying materials (see Supplementary Methods online) and for their enthusiasm for this project and A. Anthony, J. Wasmuth and A. Hedley for trace2dbest, PartiGene and prot4EST software. The UK arm of the project was funded by the Wellcome Trust, and the US arm by the National Institutes of Health (National Institute of Allergy and Infectious Diseases). J.P.M. was supported by a Helen Hay Whitney/ Merck fellowship. Sequencing at The Wellcome Trust Sanger Institute was carried out by C. Churcher, T. Chillingworth, P. Cummings, Z. Hance, K. Jagels, S. Moule and S. Whitehead. Most of the computational analyses were done using facilities at the Center for Computational Biology, Hospital for Sick Children, Toronto.
PY - 2004/12
Y1 - 2004/12
N2 - The phylum Nematoda occupies a huge range of ecological niches, from free-living microbivores to human parasites. We analyzed the genomic biology of the phylum using 265,494 expressed-sequence tag sequences, corresponding to 93,645 putative genes, from 30 species, including 28 parasites. From 35% to 70% of each species' genes had significant similarity to proteins from the model nematode Caenorhabditis elegans. More than half of the putative genes were unique to the phylum, and 23% were unique to the species from which they were derived. We have not yet come close to exhausting the genomic diversity of the phylum. We identified more than 2,600 different known protein domains, some of which had differential abundances between major taxonomic groups of nematodes. We also defined 4,228 nematode-specific protein families from nematode-restricted genes: this class of genes probably underpins species- and higher-level taxonomic disparity. Nematode-specific families are particularly interesting as drug and vaccine targets.
AB - The phylum Nematoda occupies a huge range of ecological niches, from free-living microbivores to human parasites. We analyzed the genomic biology of the phylum using 265,494 expressed-sequence tag sequences, corresponding to 93,645 putative genes, from 30 species, including 28 parasites. From 35% to 70% of each species' genes had significant similarity to proteins from the model nematode Caenorhabditis elegans. More than half of the putative genes were unique to the phylum, and 23% were unique to the species from which they were derived. We have not yet come close to exhausting the genomic diversity of the phylum. We identified more than 2,600 different known protein domains, some of which had differential abundances between major taxonomic groups of nematodes. We also defined 4,228 nematode-specific protein families from nematode-restricted genes: this class of genes probably underpins species- and higher-level taxonomic disparity. Nematode-specific families are particularly interesting as drug and vaccine targets.
UR - http://www.scopus.com/inward/record.url?scp=9644260489&partnerID=8YFLogxK
U2 - 10.1038/ng1472
DO - 10.1038/ng1472
M3 - Article
C2 - 15543149
AN - SCOPUS:9644260489
SN - 1061-4036
VL - 36
SP - 1259
EP - 1267
JO - Nature Genetics
JF - Nature Genetics
IS - 12
ER -