Bergman_2002_Genome.Biol_3_RESEARCH0086

Reference

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

Related information

Gene_locus related to this paper: drops-CG4390 , drowi-b4ngb5 , droya-q71d76

Citations formats

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 (2002)
Assessing the impact of comparative genomic sequence data on the functional annotation of the Drosophila genome
Genome Biol 3 :RESEARCH0086

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 (2002)
Genome Biol 3 :RESEARCH0086