title: Analysis of 14 BAC sequences from the Aedes aegypti genome: a benchmark for genome annotation and assembly.
abstract: BACKGROUND
  Aedes aegypti is the principal vector of yellow fever and dengue viruses throughout the tropical world. To provide a set of manually curated and annotated sequences from the Ae. aegypti genome, 14 mapped bacterial artificial chromosome (BAC) clones encompassing 1.57 Mb were sequenced, assembled and manually annotated using a combination of computational gene-finding, expressed sequence tag (EST) matches and comparative protein homology. PCR and sequencing were used to experimentally confirm expression and sequence of a subset of these transcripts.
  
  
  RESULTS
  Of the 51 manual annotations, 50 and 43 demonstrated a high level of similarity to Anopheles gambiae and Drosophila melanogaster genes, respectively. Ten of the 12 BAC sequences with more than one annotated gene exhibited synteny with the A. gambiae genome. Putative transcripts from eight BAC clones were found in multiple copies (two copies in most cases) in the Aedes genome assembly, which point to the probable presence of haplotype polymorphisms and/or misassemblies.
  
  
  CONCLUSIONS
  This study not only provides a benchmark set of manually annotated transcripts for this genome that can be used to assess the quality of the auto-annotation pipeline and the assembly, but it also looks at the effect of a high repeat content on the genome assembly and annotation pipeline.
authors.affiliation: Center for Global Health and Infectious Diseases, Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556-0369, USA. nlobo@nd.edu
authors.forename: Neil F
authors.initials: NF
authors.lastname: Lobo
authors.forename: Kathy S
authors.initials: KS
authors.lastname: Campbell
authors.forename: Daniel
authors.initials: D
authors.lastname: Thaner
authors.forename: Becky
authors.initials: B
authors.lastname: Debruyn
authors.forename: Hean
authors.initials: H
authors.lastname: Koo
authors.forename: William M
authors.initials: WM
authors.lastname: Gelbart
authors.forename: Brendan J
authors.initials: BJ
authors.lastname: Loftus
authors.forename: David W
authors.initials: DW
authors.lastname: Severson
authors.forename: Frank H
authors.initials: FH
authors.lastname: Collins
mesh_terms: D000330:Aedes / Q000235:genetics*; D000818:Animals; D001483:Base Sequence; D022202:Chromosomes, Artificial, Bacterial / Q000235:genetics*; D030561:Databases, Nucleic Acid; D016678:Genome; D023281:Genomics / Q000379:methods; D011110:Polymorphism, Genetic; D012333:RNA, Messenger
chemical_list: D012333:RNA, Messenger