PT - JOURNAL ARTICLE AU - Robert M. Waterhouse AU - Sergey Aganezov AU - Yoann Anselmetti AU - Jiyoung Lee AU - Livio Ruzzante AU - Maarten J.M.F. Reijnders AU - Romain Feron AU - Sèverine Bérard AU - Phillip George AU - Matthew W. Hahn AU - Paul I. Howell AU - Maryam Kamali AU - Sergey Koren AU - Daniel Lawson AU - Gareth Maslen AU - Ashley Peery AU - Adam M. Phillippy AU - Maria V. Sharakhova AU - Eric Tannier AU - Maria F. Unger AU - Simo V. Zhang AU - Max A. Alekseyev AU - Nora J. Besansky AU - Cedric Chauve AU - Scott J. Emrich AU - Igor V. Sharakhov TI - Evolutionary superscaffolding and chromosome anchoring to improve <em>Anopheles</em> genome assemblies AID - 10.1101/434670 DP - 2019 Jan 01 TA - bioRxiv PG - 434670 4099 - http://biorxiv.org/content/early/2019/03/05/434670.short 4100 - http://biorxiv.org/content/early/2019/03/05/434670.full AB - Background 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 employed three 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: six with physical mapping data that anchor scaffolds to chromosome locations, 13 with paired-end RNA sequencing (RNAseq) data, and three with new assemblies based on re-scaffolding or Pacific Biosciences long-read data. Our combined analyses produced 20 new superscaffolded assemblies with improved contiguities: seven for which assignments of non-anchored scaffolds to chromosome arms span more than 75% of the assemblies, and a further seven 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 comparisons 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.ADADSEQAGOAGOUTI-basedAGOUTIannotated genome optimization using transcriptome information toolALNalignment-basedCAMSAcomparative analysis and merging of scaffold assemblies toolDPdynamic programmingFISHfluorescence in situ hybridizationGAGOS-ASMGOS-ASMGene order scaffold assemblerKbpkilobasepairsMbpmegabasepairsOSORTHOSTITCHPacBioPacific BiosciencesPBPacBio-basedPHYphysical-mapping-basedRNAseqRNA sequencingQTLquantitative trait lociSYNsynteny-based.