title: Evaluation of the chicken transcriptome by SAGE of B cells and the DT40 cell line.
abstract: BACKGROUND
  The understanding of whole genome sequences in higher eukaryotes depends to a large degree on the reliable definition of transcription units including exon/intron structures, translated open reading frames (ORFs) and flanking untranslated regions. The best currently available chicken transcript catalog is the Ensembl build based on the mappings of a relatively small number of full length cDNAs and ESTs to the genome as well as genome sequence derived in silico gene predictions.
  
  
  RESULTS
  We use Long Serial Analysis of Gene Expression (LongSAGE) in bursal lymphocytes and the DT40 cell line to verify the quality and completeness of the annotated transcripts. 53.6% of the more than 38,000 unique SAGE tags (unitags) match to full length bursal cDNAs, the Ensembl transcript build or the genome sequence. The majority of all matching unitags show single matches to the genome, but no matches to the genome derived Ensembl transcript build. Nevertheless, most of these tags map close to the 3' boundaries of annotated Ensembl transcripts.
  
  
  CONCLUSIONS
  These results suggests that rather few genes are missing in the current Ensembl chicken transcript build, but that the 3' ends of many transcripts may not have been accurately predicted. The tags with no match in the transcript sequences can now be used to improve gene predictions, pinpoint the genomic location of entirely missed transcripts and optimize the accuracy of gene finder software.
authors.affiliation: Institute of Molecular Radiobiology, GSF, Ingolstädter Landstr, 1, D-85764 Neuherberg, Germany. mbw@stowers-institute.org <mbw@stowers-institute.org>
authors.forename: Matthias B
authors.initials: MB
authors.lastname: Wahl
authors.forename: Randolph B
authors.initials: RB
authors.lastname: Caldwell
authors.forename: Andrzej M
authors.initials: AM
authors.lastname: Kierzek
authors.forename: Hiroshi
authors.initials: H
authors.lastname: Arakawa
authors.forename: Eduardo
authors.initials: E
authors.lastname: Eyras
authors.forename: Nina
authors.initials: N
authors.lastname: Hubner
authors.forename: Christian
authors.initials: C
authors.lastname: Jung
authors.forename: Manuel
authors.initials: M
authors.lastname: Soeldenwagner
authors.forename: Manuela
authors.initials: M
authors.lastname: Cervelli
authors.forename: Yan-Dong
authors.initials: YD
authors.lastname: Wang
authors.forename: Volkmar
authors.initials: V
authors.lastname: Liebscher
authors.forename: Jean-Marie
authors.initials: JM
authors.lastname: Buerstedde
mesh_terms: D000818:Animals; D001402:B-Lymphocytes / Q000378:metabolism*; D002060:Bursa of Fabricius / Q000166:cytology; D002460:Cell Line; D002645:Chickens / Q000235:genetics*; D002874:Chromosome Mapping; D018076:DNA, Complementary; D020869:Gene Expression Profiling / Q000379:methods; D015723:Gene Library; D016678:Genome; D023281:Genomics; D012333:RNA, Messenger; D014158:Transcription, Genetic
chemical_list: D018076:DNA, Complementary; D012333:RNA, Messenger