The Drosophila gene collection: identification of putative full-length cDNAs for 70% of D. melanogaster genes.
Collections of full-length nonredundant cDNA clones are critical reagents for functional genomics. The first step toward these resources is the generation and single-pass sequencing of cDNA libraries that contain a high proportion of full-length clones. The first release of the Drosophila Gene Collection Release 1 (DGCr1) was produced from six libraries representing various tissues, developmental stages, and the cultured S2 cell line. Nearly 80,000 random 5' expressed sequence tags (5' expressed sequence tags [ESTs]from these libraries were collapsed into a nonredundant set of 5849 cDNAs, corresponding to ~40% of the 13,474 predicted genes in Drosophila. To obtain cDNA clones representing the remaining genes, we have generated an additional 157,835 5' ESTs from two previously existing and three new libraries. One new library is derived from adult testis, a tissue we previously did not exploit for gene discovery; two new cap-trapped normalized libraries are derived from 0-22-h embryos and adult heads. Taking advantage of the annotated D. melanogaster genome sequence, we clustered the ESTs by aligning them to the genome. Clusters that overlap genes not already represented by cDNA clones in the DGCr1 were analyzed further, and putative full-length clones were selected for inclusion in the new DGC. This second release of the DGC (DGCr2) contains 5061 additional clones, extending the collection to 10,910 cDNAs representing >70% of the predicted genes in Drosophila.
Stapleton
Mark
M
Berkeley Drosophila Genome Project, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA. staple@fruitfly.org
Liao
Guochun
G
Brokstein
Peter
P
Hong
Ling
L
Carninci
Piero
P
Shiraki
Toshiyuki
T
Hayashizaki
Yoshihide
Y
Champe
Mark
M
Pacleb
Joanne
J
Wan
Ken
K
Yu
Charles
C
Carlson
Joe
J
George
Reed
R
Celniker
Susan
S
Rubin
Gerald M
GM
D000818:Animals; D002460:Cell Line; D016000:Cluster Analysis; D018076:DNA, Complementary / Q000235:genetics*; D004331:Drosophila melanogaster / Q000166:cytology / Q000235:genetics*; D020224:Expressed Sequence Tags; D015723:Gene Library; D017344:Genes, Insect / Q000235:genetics*; D008297:Male; D008562:Membrane Glycoproteins; D008565:Membrane Proteins; D008969:Molecular Sequence Data; D019038:Platelet Glycoprotein GPIb-IX Complex; D012313:RNA / Q000302:isolation & purification; D016415:Sequence Alignment / Q000379:methods; D017422:Sequence Analysis, DNA / Q000379:methods; D013737:Testis / Q000737:chemistry
D018076:DNA, Complementary; D008562:Membrane Glycoproteins; D008565:Membrane Proteins; D019038:Platelet Glycoprotein GPIb-IX Complex; C094990:adhesion receptor; D012313:RNA