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A hybrid de novo genome assembly of the honeybee, Apis mellifera, with chromosome-length scaffolds
Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Uppsala University, Science for Life Laboratory, SciLifeLab.
Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology. Uppsala University, Science for Life Laboratory, SciLifeLab.
Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology. Uppsala University, Science for Life Laboratory, SciLifeLab.
Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology. Uppsala University, Science for Life Laboratory, SciLifeLab.
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2019 (English)In: BMC Genomics, ISSN 1471-2164, E-ISSN 1471-2164, Vol. 20, article id 275Article in journal (Refereed) Published
Abstract [en]

Background

The 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.

Results

Each 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.

Conclusions

The improved assembly will be of utility for refining gene models, studying genome function, mapping functional genetic variation, identification of structural variants, and comparative genomics.

Place, publisher, year, edition, pages
BMC , 2019. Vol. 20, article id 275
Keywords [en]
Genome assembly, Single-molecule real-time (SMRT) sequencing, Linked-read sequencing, Optical mapping, Hi-C, Telomeres, Centromeres
National Category
Genetics
Identifiers
URN: urn:nbn:se:uu:diva-382559DOI: 10.1186/s12864-019-5642-0ISI: 000464118800001PubMedID: 30961563OAI: oai:DiVA.org:uu-382559DiVA, id: diva2:1313567
Funder
Swedish Research Council Formas, 2013-722Swedish Research Council, 2014-5096
Note

Andreas Wallberg and Ignas Bunikis contributed equally to this work.

Available from: 2019-05-03 Created: 2019-05-03 Last updated: 2019-05-03Bibliographically approved

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Wallberg, AndreasBunikis, IgnasVinnere, OlgaMosbech, Mai-BrittWebster, Matthew Thomas
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