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A hybrid de novo ge...
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Wallberg, AndreasUppsala universitet,Institutionen för medicinsk biokemi och mikrobiologi,Science for Life Laboratory, SciLifeLab
(author)
A hybrid de novo genome assembly of the honeybee, Apis mellifera, with chromosome-length scaffolds
- Article/chapterEnglish2019
Publisher, publication year, extent ...
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2019-04-08
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BMC,2019
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electronicrdacarrier
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LIBRIS-ID:oai:DiVA.org:uu-382559
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https://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-382559URI
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https://doi.org/10.1186/s12864-019-5642-0DOI
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Language:English
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Summary in:English
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Subject category:ref swepub-contenttype
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Subject category:art swepub-publicationtype
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Andreas Wallberg and Ignas Bunikis contributed equally to this work.
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BackgroundThe ability to generate long sequencing reads and access long-range linkage information is revolutionizing the quality and completeness of genome assemblies. Here we use a hybrid approach that combines data from four genome sequencing and mapping technologies to generate a new genome assembly of the honeybee Apis mellifera. We first generated contigs based on PacBio sequencing libraries, which were then merged with linked-read 10x Chromium data followed by scaffolding using a BioNano optical genome map and a Hi-C chromatin interaction map, complemented by a genetic linkage map.ResultsEach of the assembly steps reduced the number of gaps and incorporated a substantial amount of additional sequence into scaffolds. The new assembly (Amel_HAv3) is significantly more contiguous and complete than the previous one (Amel_4.5), based mainly on Sanger sequencing reads. N50 of contigs is 120-fold higher (5.381 Mbp compared to 0.053 Mbp) and we anchor >98% of the sequence to chromosomes. All of the 16 chromosomes are represented as single scaffolds with an average of three sequence gaps per chromosome. The improvements are largely due to the inclusion of repetitive sequence that was unplaced in previous assemblies. In particular, our assembly is highly contiguous across centromeres and telomeres and includes hundreds of AvaI and AluI repeats associated with these features.ConclusionsThe improved assembly will be of utility for refining gene models, studying genome function, mapping functional genetic variation, identification of structural variants, and comparative genomics.
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Bunikis, IgnasUppsala universitet,Institutionen för immunologi, genetik och patologi,Science for Life Laboratory, SciLifeLab(Swepub:uu)ignbu776
(author)
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Vinnere, OlgaUppsala universitet,Institutionen för immunologi, genetik och patologi,Science for Life Laboratory, SciLifeLab(Swepub:uu)olvin020
(author)
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Mosbech, Mai-BrittUppsala universitet,Institutionen för immunologi, genetik och patologi,Science for Life Laboratory, SciLifeLab(Swepub:uu)maimo985
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Childers, Anna K.USDA ARS, Insect Genet & Biochem Res Unit, Fargo, ND USA;USDA ARS, Bee Res Lab, Beltsville, MD USA
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Evans, Jay D.USDA ARS, Bee Res Lab, Beltsville, MD USA
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Mikheyev, Alexander S.Okinawa Inst Sci & Technol, Onna, Okinawa, Japan
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Robertson, Hugh M.Univ Illinois, Dept Biochem, Urbana, IL USA;Univ Illinois, Carl R Woese Inst Genom Biol, Urbana, IL USA
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Robinson, Gene E.Univ Illinois, Dept Biochem, Urbana, IL USA;Univ Illinois, Carl R Woese Inst Genom Biol, Urbana, IL USA
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Webster, Matthew ThomasUppsala universitet,Institutionen för medicinsk biokemi och mikrobiologi,Science for Life Laboratory, SciLifeLab(Swepub:uu)maweb226
(author)
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Uppsala universitetInstitutionen för medicinsk biokemi och mikrobiologi
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In:BMC Genomics: BMC201471-2164
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NATURAL SCIENCES
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and Genetics
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BMC Genomics
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