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A hybrid de novo ge...
A hybrid de novo genome assembly of the honeybee, Apis mellifera, with chromosome-length scaffolds
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- Wallberg, Andreas (författare)
- Uppsala universitet,Institutionen för medicinsk biokemi och mikrobiologi,Science for Life Laboratory, SciLifeLab
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- Bunikis, Ignas (författare)
- Uppsala universitet,Institutionen för immunologi, genetik och patologi,Science for Life Laboratory, SciLifeLab
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- Vinnere, Olga (författare)
- Uppsala universitet,Institutionen för immunologi, genetik och patologi,Science for Life Laboratory, SciLifeLab
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- Mosbech, Mai-Britt (författare)
- Uppsala universitet,Institutionen för immunologi, genetik och patologi,Science for Life Laboratory, SciLifeLab
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- Childers, Anna K. (författare)
- 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. (författare)
- USDA ARS, Bee Res Lab, Beltsville, MD USA
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- Mikheyev, Alexander S. (författare)
- Okinawa Inst Sci & Technol, Onna, Okinawa, Japan
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- Robertson, Hugh M. (författare)
- 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. (författare)
- Univ Illinois, Dept Biochem, Urbana, IL USA;Univ Illinois, Carl R Woese Inst Genom Biol, Urbana, IL USA
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- Webster, Matthew Thomas (författare)
- Uppsala universitet,Institutionen för medicinsk biokemi och mikrobiologi,Science for Life Laboratory, SciLifeLab
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(creator_code:org_t)
- 2019-04-08
- 2019
- Engelska.
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Ingår i: BMC Genomics. - : BMC. - 1471-2164. ; 20
- Relaterad länk:
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https://doi.org/10.1...
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https://uu.diva-port... (primary) (Raw object)
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https://bmcgenomics....
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https://urn.kb.se/re...
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https://doi.org/10.1...
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Abstract
Ämnesord
Stäng
- 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.
Ämnesord
- NATURVETENSKAP -- Biologi -- Genetik (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences -- Genetics (hsv//eng)
Nyckelord
- Genome assembly
- Single-molecule real-time (SMRT) sequencing
- Linked-read sequencing
- Optical mapping
- Hi-C
- Telomeres
- Centromeres
Publikations- och innehållstyp
- ref (ämneskategori)
- art (ämneskategori)
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Wallberg, Andrea ...
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Bunikis, Ignas
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Vinnere, Olga
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Mosbech, Mai-Bri ...
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Childers, Anna K ...
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Evans, Jay D.
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Mikheyev, Alexan ...
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Robertson, Hugh ...
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Robinson, Gene E ...
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Webster, Matthew ...
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BMC Genomics
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Uppsala universitet