title: Full-length messenger RNA sequences greatly improve genome annotation.
abstract: BACKGROUND
  Annotation of eukaryotic genomes is a complex endeavor that requires the integration of evidence from multiple, often contradictory, sources. With the ever-increasing amount of genome sequence data now available, methods for accurate identification of large numbers of genes have become urgently needed. In an effort to create a set of very high-quality gene models, we used the sequence of 5,000 full-length gene transcripts from Arabidopsis to re-annotate its genome. We have mapped these transcripts to their exact chromosomal locations and, using alignment programs, have created gene models that provide a reference set for this organism.
  
  
  RESULTS
  Approximately 35% of the transcripts indicated that previously annotated genes needed modification, and 5% of the transcripts represented newly discovered genes. We also discovered that multiple transcription initiation sites appear to be much more common than previously known, and we report numerous cases of alternative mRNA splicing. We include a comparison of different alignment software and an analysis of how the transcript data improved the previously published annotation.
  
  
  CONCLUSIONS
  Our results demonstrate that sequencing of large numbers of full-length transcripts followed by computational mapping greatly improves identification of the complete exon structures of eukaryotic genes. In addition, we are able to find numerous introns in the untranslated regions of the genes.
authors.affiliation: The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA. salzberg@tigr.org
authors.forename: Brian J
authors.initials: BJ
authors.lastname: Haas
authors.forename: Natalia
authors.initials: N
authors.lastname: Volfovsky
authors.forename: Christopher D
authors.initials: CD
authors.lastname: Town
authors.forename: Maxim
authors.initials: M
authors.lastname: Troukhan
authors.forename: Nickolai
authors.initials: N
authors.lastname: Alexandrov
authors.forename: Kenneth A
authors.initials: KA
authors.lastname: Feldmann
authors.forename: Richard B
authors.initials: RB
authors.lastname: Flavell
authors.forename: Owen
authors.initials: O
authors.lastname: White
authors.forename: Steven L
authors.initials: SL
authors.lastname: Salzberg
mesh_terms: D017398:Alternative Splicing / Q000235:genetics; D017360:Arabidopsis / Q000235:genetics*; D019295:Computational Biology; D030541:Databases, Genetic; D005091:Exons / Q000235:genetics; D017343:Genes, Plant / Q000235:genetics; D018745:Genome, Plant; D012326:RNA Splicing / Q000235:genetics; D012333:RNA, Messenger / Q000145:classification / Q000235:genetics*; D018749:RNA, Plant / Q000145:classification / Q000235:genetics
chemical_list: D012333:RNA, Messenger; D018749:RNA, Plant