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Update of the Anopheles gambiaePEST genome assembly

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dc.contributor.authorSharakhova, Maria V.en
dc.contributor.authorHammond, Martin P.en
dc.contributor.authorLobo, Neil F.en
dc.contributor.authorKrzywinski, Jaroslawen
dc.contributor.authorUnger, Maria F.en
dc.contributor.authorHillenmeyer, Maureen E.en
dc.contributor.authorBruggner, Robert V.en
dc.contributor.authorBirney, Ewanen
dc.contributor.authorCollins, Frank H.en
dc.contributor.departmentEntomologyen
dc.date.accessioned2012-08-24T12:13:19Zen
dc.date.available2012-08-24T12:13:19Zen
dc.date.issued2007-01-08en
dc.date.updated2012-08-24T12:13:19Zen
dc.description.abstractBackground 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. Conclusion This study has used new approaches to improve the physical map and assembly of the A. gambiae genome.en
dc.description.versionPublished versionen
dc.format.mimetypeapplication/pdfen
dc.identifier.citationGenome Biology. 2007 Jan 08;8(1):R5en
dc.identifier.doihttps://doi.org/10.1186/gb-2007-8-1-r5en
dc.identifier.urihttp://hdl.handle.net/10919/18936en
dc.language.isoenen
dc.rightsCreative Commons Attribution 4.0 Internationalen
dc.rights.holderMaria V Sharakhova et al.; licensee BioMed Central Ltd.en
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/en
dc.titleUpdate of the Anopheles gambiaePEST genome assemblyen
dc.title.serialGenome Biologyen
dc.typeArticle - Refereeden
dc.type.dcmitypeTexten

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