A hybrid de novo genome assembly of the honeybee, Apis mellifera, with chromosome-length scaffolds
Abstract 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 ge...
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doaj-51c888da991d4db886d2c3dd8c82d76f2020-11-25T02:01:13ZengBMCBMC Genomics1471-21642019-04-0120111910.1186/s12864-019-5642-0A hybrid de novo genome assembly of the honeybee, Apis mellifera, with chromosome-length scaffoldsAndreas Wallberg0Ignas Bunikis1Olga Vinnere Pettersson2Mai-Britt Mosbech3Anna K. Childers4Jay D. Evans5Alexander S. Mikheyev6Hugh M. Robertson7Gene E. Robinson8Matthew T. Webster9Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala UniversityDepartment of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala UniversityDepartment of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala UniversityDepartment of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala UniversityUSDA-ARS Insect Genetics and Biochemistry Research UnitUSDA-ARS Bee Research LabOkinawa Institute of Science and TechnologyDepartment of Entomology and Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-ChampaignDepartment of Entomology and Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-ChampaignDepartment of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala UniversityAbstract 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.http://link.springer.com/article/10.1186/s12864-019-5642-0Genome assemblySingle-molecule real-time (SMRT) sequencingLinked-read sequencingOptical mappingHi-CTelomeres |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Andreas Wallberg Ignas Bunikis Olga Vinnere Pettersson Mai-Britt Mosbech Anna K. Childers Jay D. Evans Alexander S. Mikheyev Hugh M. Robertson Gene E. Robinson Matthew T. Webster |
spellingShingle |
Andreas Wallberg Ignas Bunikis Olga Vinnere Pettersson Mai-Britt Mosbech Anna K. Childers Jay D. Evans Alexander S. Mikheyev Hugh M. Robertson Gene E. Robinson Matthew T. Webster A hybrid de novo genome assembly of the honeybee, Apis mellifera, with chromosome-length scaffolds BMC Genomics Genome assembly Single-molecule real-time (SMRT) sequencing Linked-read sequencing Optical mapping Hi-C Telomeres |
author_facet |
Andreas Wallberg Ignas Bunikis Olga Vinnere Pettersson Mai-Britt Mosbech Anna K. Childers Jay D. Evans Alexander S. Mikheyev Hugh M. Robertson Gene E. Robinson Matthew T. Webster |
author_sort |
Andreas Wallberg |
title |
A hybrid de novo genome assembly of the honeybee, Apis mellifera, with chromosome-length scaffolds |
title_short |
A hybrid de novo genome assembly of the honeybee, Apis mellifera, with chromosome-length scaffolds |
title_full |
A hybrid de novo genome assembly of the honeybee, Apis mellifera, with chromosome-length scaffolds |
title_fullStr |
A hybrid de novo genome assembly of the honeybee, Apis mellifera, with chromosome-length scaffolds |
title_full_unstemmed |
A hybrid de novo genome assembly of the honeybee, Apis mellifera, with chromosome-length scaffolds |
title_sort |
hybrid de novo genome assembly of the honeybee, apis mellifera, with chromosome-length scaffolds |
publisher |
BMC |
series |
BMC Genomics |
issn |
1471-2164 |
publishDate |
2019-04-01 |
description |
Abstract 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. |
topic |
Genome assembly Single-molecule real-time (SMRT) sequencing Linked-read sequencing Optical mapping Hi-C Telomeres |
url |
http://link.springer.com/article/10.1186/s12864-019-5642-0 |
work_keys_str_mv |
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