The Physical Genome Mapping of Anopheles albimanus Corrected Scaffold Misassemblies and Identified Interarm Rearrangements in Genus Anopheles

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dc.contributor.authorArtemov, Gleb N.en
dc.contributor.authorPeery, Ashley N.en
dc.contributor.authorJiang, Xiaofangen
dc.contributor.authorTu, Zhijian Jakeen
dc.contributor.authorStegniy, Vladimir N.en
dc.contributor.authorSharakhova, Maria V.en
dc.contributor.authorSharakhov, Igor V.en
dc.contributor.departmentBiochemistryen
dc.contributor.departmentEntomologyen
dc.contributor.departmentFralin Life Sciences Instituteen
dc.date.accessioned2018-01-02T23:12:42Zen
dc.date.available2018-01-02T23:12:42Zen
dc.date.issued2017-01-01en
dc.description.abstractThe genome of the Neotropical malaria vector Anopheles albimanus was sequenced as part of the 16 Anopheles Genomes Project published in 2015. The draft assembly of this species consisted of 204 scaffolds with an N50 scaffold size of 18.1 Mb and a total assembly size of 170.5 Mb. It was among the smallest genomes with the longest scaffolds in the 16 Anopheles species cluster, making An. albimanus the logical choice for anchoring the genome assembly to chromosomes. In this study, we developed a high-resolution cytogenetic photomap with completely straightened polytene chromosomes from the salivary glands of the mosquito larvae. Based on this photomap, we constructed a chromosome-based genome assembly using fluorescent in situ hybridization of PCR-amplified DNA probes. Our physical mapping, assisted by an ortholog-based bioinformatics approach, identified and corrected nine misassemblies in five large genomic scaffolds.Misassemblies mostly occurred in junctions between contigs. Our comparative analysis of scaffolds with the An. gambiae genome detected multiple genetic exchanges between pericentromeric regions of chromosomal arms caused by partial-arm translocations. The finalmap consists of 40 ordered genomic scaffolds and corrected fragments ofmisassembled scaffolds. The An. albimanus physical map comprises 98.2% of the total genome assembly and represents the most complete genome map among mosquito species. This study demonstrates that physical mapping is a powerful tool for correcting errors in draft genome assemblies and for creating chromosome-anchored reference genomes.en
dc.description.versionPublished versionen
dc.format.extent155 - 164 (10) page(s)en
dc.format.mimetypeapplication/pdfen
dc.identifier.doihttps://doi.org/10.1534/g3.116.034959en
dc.identifier.issn2160-1836en
dc.identifier.issue1en
dc.identifier.orcidSharakhov, IV [0000-0003-0752-3747]en
dc.identifier.urihttp://hdl.handle.net/10919/81473en
dc.identifier.volume7en
dc.language.isoenen
dc.publisherGenetics Society of Americaen
dc.relation.urihttp://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000392200800014&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=930d57c9ac61a043676db62af60056c1en
dc.rightsCreative Commons Attribution 4.0 Internationalen
dc.rights.holderThe Author(s)en
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/en
dc.subjectGenetics & Heredityen
dc.subjectmosquito genomeen
dc.subjectfluorescence in situ hybridizationen
dc.subjectphysical mappingen
dc.subjectpolytene chromosomesen
dc.subjectAnopheles albimanusen
dc.subjectIN-SITU HYBRIDIZATIONen
dc.subjectMALARIA VECTORen
dc.subjectCHROMOSOMAL INVERSIONSen
dc.subjectPOLYTENE CHROMOSOMESen
dc.subjectCYTOGENETIC MAPen
dc.subjectAEDES-AEGYPTIen
dc.subjectLINKAGE MAPen
dc.subjectMOSQUITOen
dc.subjectFUNESTUSen
dc.subjectGAMBIAEen
dc.titleThe Physical Genome Mapping of Anopheles albimanus Corrected Scaffold Misassemblies and Identified Interarm Rearrangements in Genus Anophelesen
dc.title.serialG3-Genes Genomes Geneticsen
dc.typeArticle - Refereeden
dc.type.dcmitypeTexten
pubs.organisational-group/Virginia Techen
pubs.organisational-group/Virginia Tech/Agriculture & Life Sciencesen
pubs.organisational-group/Virginia Tech/Agriculture & Life Sciences/Biochemistryen
pubs.organisational-group/Virginia Tech/Agriculture & Life Sciences/CALS T&R Facultyen
pubs.organisational-group/Virginia Tech/Agriculture & Life Sciences/Entomologyen
pubs.organisational-group/Virginia Tech/All T&R Facultyen
pubs.organisational-group/Virginia Tech/Faculty of Health Sciencesen
pubs.organisational-group/Virginia Tech/University Research Institutesen
pubs.organisational-group/Virginia Tech/University Research Institutes/Fralin Life Sciencesen
pubs.organisational-group/Virginia Tech/University Research Institutes/Fralin Life Sciences/Fralin Affiliated Facultyen

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