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Title: The Drosophila gene collection: Identification of putative full-length cDNAs for 70 percent of D. melanogaster genes

Abstract

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 5prime expressed sequence tags (EST) from these libraries were collapsed into a nonredundant set of 5849 cDNAs, corresponding to {approx}40 percent of the 13,474 predicted genes in Drosophila. To obtain cDNA clones representing the remaining genes, we have generated an additional 157,835 5prime 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 0-22hr 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 themore » DGC (DGCr2) contains 5061 additional clones, extending the collection to 10,910 cDNAs representing >70 percent of the predicted genes in Drosophila.« less

Authors:
; ; ; ; ; ; ; ; ; ; ; ; ; ;
Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
Functional Genomics; National Institutes of Health (US)
OSTI Identifier:
801954
Report Number(s):
LBNL-50121
R&D Project: 80ADLE; B& R 600305000; TRN: US200223%%473
DOE Contract Number:  
AC03-76SF00098
Resource Type:
Journal Article
Journal Name:
Genome Research
Additional Journal Information:
Journal Volume: 12; Journal Issue: 8; Other Information: Journal Publication Date: August, 2002; PBD: 12 Aug 2002
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; ADULTS; DROSOPHILA; EMBRYOS; FUNCTIONALS; GENES; DROSOPHILA EST GENE COLLECTION SIM4 ALIGNMENTS

Citation Formats

Stapleton, Mark, Liao, Guochun, Brokstein, Peter, Hong, Ling, Carninci, Piero, Shiraki, Toshiyuki, Hayashizaki, Yoshihide, Champe, Mark, Pacleb, Joanne, Wan, Ken, Yu, Charles, Carlson, Joe, George, Reed, Celniker, Susan, and Rubin, Gerald M. The Drosophila gene collection: Identification of putative full-length cDNAs for 70 percent of D. melanogaster genes. United States: N. p., 2002. Web. doi:10.1101/gr.269102.
Stapleton, Mark, Liao, Guochun, Brokstein, Peter, Hong, Ling, Carninci, Piero, Shiraki, Toshiyuki, Hayashizaki, Yoshihide, Champe, Mark, Pacleb, Joanne, Wan, Ken, Yu, Charles, Carlson, Joe, George, Reed, Celniker, Susan, & Rubin, Gerald M. The Drosophila gene collection: Identification of putative full-length cDNAs for 70 percent of D. melanogaster genes. United States. https://doi.org/10.1101/gr.269102
Stapleton, Mark, Liao, Guochun, Brokstein, Peter, Hong, Ling, Carninci, Piero, Shiraki, Toshiyuki, Hayashizaki, Yoshihide, Champe, Mark, Pacleb, Joanne, Wan, Ken, Yu, Charles, Carlson, Joe, George, Reed, Celniker, Susan, and Rubin, Gerald M. Mon . "The Drosophila gene collection: Identification of putative full-length cDNAs for 70 percent of D. melanogaster genes". United States. https://doi.org/10.1101/gr.269102.
@article{osti_801954,
title = {The Drosophila gene collection: Identification of putative full-length cDNAs for 70 percent of D. melanogaster genes},
author = {Stapleton, Mark and Liao, Guochun and Brokstein, Peter and Hong, Ling and Carninci, Piero and Shiraki, Toshiyuki and Hayashizaki, Yoshihide and Champe, Mark and Pacleb, Joanne and Wan, Ken and Yu, Charles and Carlson, Joe and George, Reed and Celniker, Susan and Rubin, Gerald M},
abstractNote = {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 5prime expressed sequence tags (EST) from these libraries were collapsed into a nonredundant set of 5849 cDNAs, corresponding to {approx}40 percent of the 13,474 predicted genes in Drosophila. To obtain cDNA clones representing the remaining genes, we have generated an additional 157,835 5prime 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 0-22hr 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 percent of the predicted genes in Drosophila.},
doi = {10.1101/gr.269102},
url = {https://www.osti.gov/biblio/801954}, journal = {Genome Research},
number = 8,
volume = 12,
place = {United States},
year = {2002},
month = {8}
}