Evolutionary superscaffolding and chromosome anchoring to improve Anopheles genome assemblies

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dc.contributor.authorWaterhouse, Robert M.en
dc.contributor.authorAganezov, Sergeyen
dc.contributor.authorAnselmetti, Yoannen
dc.contributor.authorLee, Jiyoungen
dc.contributor.authorRuzzante, Livioen
dc.contributor.authorReijnders, Maarten J. M. F.en
dc.contributor.authorFeron, Romainen
dc.contributor.authorBérard, Sèverineen
dc.contributor.authorGeorge, Phillipen
dc.contributor.authorHahn, Matthew W.en
dc.contributor.authorHowell, Paul I.en
dc.contributor.authorKamali, Maryamen
dc.contributor.authorKoren, Sergeyen
dc.contributor.authorLawson, Danielen
dc.contributor.authorMaslen, Garethen
dc.contributor.authorPeery, Ashleyen
dc.contributor.authorPhillippy, Adam M.en
dc.contributor.authorSharakhova, Maria V.en
dc.contributor.authorTannier, Ericen
dc.contributor.authorUnger, Maria F.en
dc.contributor.authorZhang, Simo V.en
dc.contributor.authorAlekseyev, Max A.en
dc.contributor.authorBesansky, Nora J.en
dc.contributor.authorChauve, Cedricen
dc.contributor.authorEmrich, Scott J.en
dc.contributor.authorSharakhov, Igor V.en
dc.contributor.departmentEntomologyen
dc.date.accessioned2020-01-06T13:39:17Zen
dc.date.available2020-01-06T13:39:17Zen
dc.date.issued2020-01-02en
dc.date.updated2020-01-05T04:16:01Zen
dc.description.abstractBackground New sequencing technologies have lowered financial barriers to whole genome sequencing, but resulting assemblies are often fragmented and far from ‘finished’. Updating multi-scaffold drafts to chromosome-level status can be achieved through experimental mapping or re-sequencing efforts. Avoiding the costs associated with such approaches, comparative genomic analysis of gene order conservation (synteny) to predict scaffold neighbours (adjacencies) offers a potentially useful complementary method for improving draft assemblies. Results We evaluated and employed 3 gene synteny-based methods applied to 21 Anopheles mosquito assemblies to produce consensus sets of scaffold adjacencies. For subsets of the assemblies, we integrated these with additional supporting data to confirm and complement the synteny-based adjacencies: 6 with physical mapping data that anchor scaffolds to chromosome locations, 13 with paired-end RNA sequencing (RNAseq) data, and 3 with new assemblies based on re-scaffolding or long-read data. Our combined analyses produced 20 new superscaffolded assemblies with improved contiguities: 7 for which assignments of non-anchored scaffolds to chromosome arms span more than 75% of the assemblies, and a further 7 with chromosome anchoring including an 88% anchored Anopheles arabiensis assembly and, respectively, 73% and 84% anchored assemblies with comprehensively updated cytogenetic photomaps for Anopheles funestus and Anopheles stephensi. Conclusions Experimental data from probe mapping, RNAseq, or long-read technologies, where available, all contribute to successful upgrading of draft assemblies. Our evaluations show that gene synteny-based computational methods represent a valuable alternative or complementary approach. Our improved Anopheles reference assemblies highlight the utility of applying comparative genomics approaches to improve community genomic resources.en
dc.description.versionPublished versionen
dc.format.mimetypeapplication/pdfen
dc.identifier.citationBMC Biology. 2020 Jan 02;18(1):1en
dc.identifier.doihttps://doi.org/10.1186/s12915-019-0728-3en
dc.identifier.urihttp://hdl.handle.net/10919/96295en
dc.language.isoenen
dc.rightsCreative Commons Attribution 4.0 Internationalen
dc.rights.holderThe Author(s)en
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/en
dc.titleEvolutionary superscaffolding and chromosome anchoring to improve Anopheles genome assembliesen
dc.title.serialBMC Biologyen
dc.typeArticle - Refereeden
dc.type.dcmitypeTexten

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