Pacleb J

References (2)

Title : A Drosophila full-length cDNA resource - Stapleton_2002_Genome.Biol_3_RESEARCH0080
Author(s) : Stapleton M , Carlson J , Brokstein P , Yu C , Champe M , George R , Guarin H , Kronmiller B , Pacleb J , Park S , Wan K , Rubin GM , Celniker SE
Ref : Genome Biol , 3 :RESEARCH0080 , 2002
Abstract : BACKGROUND: A collection of sequenced full-length cDNAs is an important resource both for functional genomics studies and for the determination of the intron-exon structure of genes. Providing this resource to the Drosophila melanogaster research community has been a long-term goal of the Berkeley Drosophila Genome Project. We have previously described the Drosophila Gene Collection (DGC), a set of putative full-length cDNAs that was produced by generating and analyzing over 250,000 expressed sequence tags (ESTs) derived from a variety of tissues and developmental stages.
RESULTS: We have generated high-quality full-insert sequence for 8,921 clones in the DGC. We compared the sequence of these clones to the annotated Release 3 genomic sequence, and identified more than 5,300 cDNAs that contain a complete and accurate protein-coding sequence. This corresponds to at least one splice form for 40% of the predicted D. melanogaster genes. We also identified potential new cases of RNA editing.
CONCLUSIONS: We show that comparison of cDNA sequences to a high-quality annotated genomic sequence is an effective approach to identifying and eliminating defective clones from a cDNA collection and ensure its utility for experimentation. Clones were eliminated either because they carry single nucleotide discrepancies, which most probably result from reverse transcriptase errors, or because they are truncated and contain only part of the protein-coding sequence.
ESTHER : Stapleton_2002_Genome.Biol_3_RESEARCH0080
PubMedSearch : Stapleton_2002_Genome.Biol_3_RESEARCH0080
PubMedID: 12537569
Gene_locus related to this paper: drome-KRAKEN

Title : Assessing the impact of comparative genomic sequence data on the functional annotation of the Drosophila genome - Bergman_2002_Genome.Biol_3_RESEARCH0086
Author(s) : Bergman CM , Pfeiffer BD , Rincon-Limas DE , Hoskins RA , Gnirke A , Mungall CJ , Wang AM , Kronmiller B , Pacleb J , Park S , Stapleton M , Wan K , George RA , de Jong PJ , Botas J , Rubin GM , Celniker SE
Ref : Genome Biol , 3 :RESEARCH0086 , 2002
Abstract : BACKGROUND: It is widely accepted that comparative sequence data can aid the functional annotation of genome sequences; however, the most informative species and features of genome evolution for comparison remain to be determined.
RESULTS: We analyzed conservation in eight genomic regions (apterous, even-skipped, fushi tarazu, twist, and Rhodopsins 1, 2, 3 and 4) from four Drosophila species (D. erecta, D. pseudoobscura, D. willistoni, and D. littoralis) covering more than 500 kb of the D. melanogaster genome. All D. melanogaster genes (and 78-82% of coding exons) identified in divergent species such as D. pseudoobscura show evidence of functional constraint. Addition of a third species can reveal functional constraint in otherwise non-significant pairwise exon comparisons. Microsynteny is largely conserved, with rearrangement breakpoints, novel transposable element insertions, and gene transpositions occurring in similar numbers. Rates of amino-acid substitution are higher in uncharacterized genes relative to genes that have previously been studied. Conserved non-coding sequences (CNCSs) tend to be spatially clustered with conserved spacing between CNCSs, and clusters of CNCSs can be used to predict enhancer sequences.
CONCLUSIONS: Our results provide the basis for choosing species whose genome sequences would be most useful in aiding the functional annotation of coding and cis-regulatory sequences in Drosophila. Furthermore, this work shows how decoding the spatial organization of conserved sequences, such as the clustering of CNCSs, can complement efforts to annotate eukaryotic genomes on the basis of sequence conservation alone.
ESTHER : Bergman_2002_Genome.Biol_3_RESEARCH0086
PubMedSearch : Bergman_2002_Genome.Biol_3_RESEARCH0086
PubMedID: 12537575
Gene_locus related to this paper: drops-CG4390 , drowi-b4ngb5 , droya-q71d76