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Evolutionary superscaffolding and chromosome anchoring to improve Anopheles genome assemblies

Robert Waterhouse 1, * Sergey Aganezov 2 Yoann Anselmetti 3 Jiyoung Lee 4 Livio Ruzzante 1 Maarten Reijnders 1 Romain Feron 3 Sèverine Bérard 3 Phillip George 5 Matthew Hahn 6 Paul Howell 7 Maryam Kamali 4 Sergey Koren 8 Daniel Lawson 9 Gareth Maslen 10 Ashley Peery 11 Adam Phillippy 12 Maria Sharakhova 5 Eric Tannier 13 Maria Unger 14 Simo Zhang 6 Max Alekseyev 15 Nora J Besansky 14 Cedric Chauve 16 Scott Emrich 17 Igor Sharakhov 5, * 
Abstract : 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 chromosomelevel 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.
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Submitted on : Tuesday, May 25, 2021 - 1:59:34 PM
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Robert Waterhouse, Sergey Aganezov, Yoann Anselmetti, Jiyoung Lee, Livio Ruzzante, et al.. Evolutionary superscaffolding and chromosome anchoring to improve Anopheles genome assemblies. BMC Biology, BioMed Central, 2020, 18 (1), pp.1-20. ⟨10.1186/s12915-019-0728-3⟩. ⟨hal-02455139⟩



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