title: Update of the Anopheles gambiae PEST genome assembly.
abstract: BACKGROUND
  The genome of Anopheles gambiae, the major vector of malaria, was sequenced and assembled in 2002. This initial genome assembly and analysis made available to the scientific community was complicated by the presence of assembly issues, such as scaffolds with no chromosomal location, no sequence data for the Y chromosome, haplotype polymorphisms resulting in two different genome assemblies in limited regions and contaminating bacterial DNA.
  
  
  RESULTS
  Polytene chromosome in situ hybridization with cDNA clones was used to place 15 unmapped scaffolds (sizes totaling 5.34 Mbp) in the pericentromeric regions of the chromosomes and oriented a further 9 scaffolds. Additional analysis by in situ hybridization of bacterial artificial chromosome (BAC) clones placed 1.32 Mbp (5 scaffolds) in the physical gaps between scaffolds on euchromatic parts of the chromosomes. The Y chromosome sequence information (0.18 Mbp) remains highly incomplete and fragmented among 55 short scaffolds. Analysis of BAC end sequences showed that 22 inter-scaffold gaps were spanned by BAC clones. Unmapped scaffolds were also aligned to the chromosome assemblies in silico, identifying regions totaling 8.18 Mbp (144 scaffolds) that are probably represented in the genome project by two alternative assemblies. An additional 3.53 Mbp of alternative assembly was identified within mapped scaffolds. Scaffolds comprising 1.97 Mbp (679 small scaffolds) were identified as probably derived from contaminating bacterial DNA. In total, about 33% of previously unmapped sequences were placed on the chromosomes.
  
  
  CONCLUSIONS
  This study has used new approaches to improve the physical map and assembly of the A. gambiae genome.
authors.affiliation: Center for Global Health and Infectious Diseases, University of Notre Dame, Galvin Life Sciences Building, Notre Dame, IN 46556-0369, USA. msharakh@vt.edu
authors.forename: Maria V
authors.initials: MV
authors.lastname: Sharakhova
authors.forename: Martin P
authors.initials: MP
authors.lastname: Hammond
authors.forename: Neil F
authors.initials: NF
authors.lastname: Lobo
authors.forename: Jaroslaw
authors.initials: J
authors.lastname: Krzywinski
authors.forename: Maria F
authors.initials: MF
authors.lastname: Unger
authors.forename: Maureen E
authors.initials: ME
authors.lastname: Hillenmeyer
authors.forename: Robert V
authors.initials: RV
authors.lastname: Bruggner
authors.forename: Ewan
authors.initials: E
authors.lastname: Birney
authors.forename: Frank H
authors.initials: FH
authors.lastname: Collins
mesh_terms: D000818:Animals; D000852:Anopheles / Q000235:genetics*; D001419:Bacteria / Q000235:genetics; D002503:Centromere / Q000235:genetics; D002875:Chromosomes / Q000235:genetics; D022041:Euchromatin / Q000235:genetics; D049750:Genome, Insect / Q000235:genetics*; D020161:Physical Chromosome Mapping; D011110:Polymorphism, Genetic; D013045:Species Specificity
chemical_list: D022041:Euchromatin