Improving Illumina assemblies with Hi-C and long reads : An example with the North African dromedary

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dc.contributor.author Elbers, Jean P.
dc.contributor.author Rogers, Mark F.
dc.contributor.author Perelman, Polina L.
dc.contributor.author Proskuryakova, Anastasia A.
dc.contributor.author Serdyukova, Natalia A.
dc.contributor.author Johnson, Warren E.
dc.contributor.author Horin, Petr
dc.contributor.author Corander, Jukka
dc.contributor.author Murphy, David
dc.contributor.author Burger, Pamela A.
dc.date.accessioned 2019-07-01T07:03:01Z
dc.date.available 2019-07-01T07:03:01Z
dc.date.issued 2019-07
dc.identifier.citation Elbers , J P , Rogers , M F , Perelman , P L , Proskuryakova , A A , Serdyukova , N A , Johnson , W E , Horin , P , Corander , J , Murphy , D & Burger , P A 2019 , ' Improving Illumina assemblies with Hi-C and long reads : An example with the North African dromedary ' , Molecular Ecology Resources , vol. 19 , no. 4 , pp. 1015-1026 . https://doi.org/10.1111/1755-0998.13020
dc.identifier.other PURE: 123936661
dc.identifier.other PURE UUID: 2bf206f1-2a0d-4015-bba6-26f10551c424
dc.identifier.other RIS: urn:22B4350C5A03409EEB052803726F584C
dc.identifier.other WOS: 000471830200016
dc.identifier.uri http://hdl.handle.net/10138/303677
dc.description.abstract Researchers have assembled thousands of eukaryotic genomes using Illumina reads, but traditional mate-pair libraries cannot span all repetitive elements, resulting in highly fragmented assemblies. However, both chromosome conformation capture techniques, such as Hi-C and Dovetail Genomics Chicago libraries and long-read sequencing, such as Pacific Biosciences and Oxford Nanopore, help span and resolve repetitive regions and therefore improve genome assemblies. One important livestock species of arid regions that does not have a high-quality contiguous reference genome is the dromedary (Camelus dromedarius). Draft genomes exist but are highly fragmented, and a high-quality reference genome is needed to understand adaptation to desert environments and artificial selection during domestication. Dromedaries are among the last livestock species to have been domesticated, and together with wild and domestic Bactrian camels, they are the only representatives of the Camelini tribe, which highlights their evolutionary significance. Here we describe our efforts to improve the North African dromedary genome. We used Chicago and Hi-C sequencing libraries from Dovetail Genomics to resolve the order of previously assembled contigs, producing almost chromosome-level scaffolds. Remaining gaps were filled with Pacific Biosciences long reads, and then scaffolds were comparatively mapped to chromosomes. Long reads added 99.32 Mbp to the total length of the new assembly. Dovetail Chicago and Hi-C libraries increased the longest scaffold over 12-fold, from 9.71 Mbp to 124.99 Mbp and the scaffold N50 over 50-fold, from 1.48 Mbp to 75.02 Mbp. We demonstrate that Illumina de novo assemblies can be substantially upgraded by combining chromosome conformation capture and long-read sequencing. en
dc.format.extent 12
dc.language.iso eng
dc.relation.ispartof Molecular Ecology Resources
dc.rights cc_by
dc.rights.uri info:eu-repo/semantics/openAccess
dc.subject 1181 Ecology, evolutionary biology
dc.subject 1184 Genetics, developmental biology, physiology
dc.subject chromosome mapping
dc.subject chromosome conformation capture
dc.subject dromedary
dc.subject genome assembly
dc.subject scaffolding
dc.subject genome annotation
dc.subject PLANT
dc.subject CATTLE
dc.subject ABYSS
dc.subject PRODUCTION TRAITS
dc.subject ANNOTATION
dc.subject SEQUENCE
dc.subject ARCHITECTURE
dc.subject GENOME-WIDE ASSOCIATION
dc.subject RESOURCE
dc.subject MAKER
dc.title Improving Illumina assemblies with Hi-C and long reads : An example with the North African dromedary en
dc.type Article
dc.contributor.organization Jukka Corander / Principal Investigator
dc.contributor.organization Department of Mathematics and Statistics
dc.contributor.organization Biostatistics Helsinki
dc.description.reviewstatus Peer reviewed
dc.relation.doi https://doi.org/10.1111/1755-0998.13020
dc.relation.issn 1755-098X
dc.rights.accesslevel openAccess
dc.type.version publishedVersion

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