Strategies for optimizing BioNano and Dovetail explored through a second reference quality assembly for the legume model, Medicago truncatula
Abstract Background Third generation sequencing technologies, with sequencing reads in the tens- of kilo-bases, facilitate genome assembly by spanning ambiguous regions and improving continuity. This has been critical for plant genomes, which are difficult to assemble due to high repeat content, gen...
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doaj-c7461827cd534a32ad183f5e1d464f062020-11-24T21:51:47ZengBMCBMC Genomics1471-21642017-08-0118111610.1186/s12864-017-3971-4Strategies for optimizing BioNano and Dovetail explored through a second reference quality assembly for the legume model, Medicago truncatulaKaren M. Moll0Peng Zhou1Thiruvarangan Ramaraj2Diego Fajardo3Nicholas P. Devitt4Michael J. Sadowsky5Robert M. Stupar6Peter Tiffin7Jason R. Miller8Nevin D. Young9Kevin A. T. Silverstein10Joann Mudge11National Center for Genome ResourcesDepartment of Plant Biology, University of MinnesotaNational Center for Genome ResourcesNational Center for Genome ResourcesNational Center for Genome ResourcesDepartment of Soil, Water & Climate, Plant and Microbial Biology and BioTechnology Institute, University of MinnesotaDepartment of Agronomy and Plant Genetics, University of MinnesotaDepartment of Plant and Microbial Biology, University of MinnesotaJ. Craig Venter InstituteDepartment of Plant and Microbial Biology, University of MinnesotaMinnesota Supercomputing Institute, University of MinnesotaNational Center for Genome ResourcesAbstract Background Third generation sequencing technologies, with sequencing reads in the tens- of kilo-bases, facilitate genome assembly by spanning ambiguous regions and improving continuity. This has been critical for plant genomes, which are difficult to assemble due to high repeat content, gene family expansions, segmental and tandem duplications, and polyploidy. Recently, high-throughput mapping and scaffolding strategies have further improved continuity. Together, these long-range technologies enable quality draft assemblies of complex genomes in a cost-effective and timely manner. Results Here, we present high quality genome assemblies of the model legume plant, Medicago truncatula (R108) using PacBio, Dovetail Chicago (hereafter, Dovetail) and BioNano technologies. To test these technologies for plant genome assembly, we generated five assemblies using all possible combinations and ordering of these three technologies in the R108 assembly. While the BioNano and Dovetail joins overlapped, they also showed complementary gains in continuity and join numbers. Both technologies spanned repetitive regions that PacBio alone was unable to bridge. Combining technologies, particularly Dovetail followed by BioNano, resulted in notable improvements compared to Dovetail or BioNano alone. A combination of PacBio, Dovetail, and BioNano was used to generate a high quality draft assembly of R108, a M. truncatula accession widely used in studies of functional genomics. As a test for the usefulness of the resulting genome sequence, the new R108 assembly was used to pinpoint breakpoints and characterize flanking sequence of a previously identified translocation between chromosomes 4 and 8, identifying more than 22.7 Mb of novel sequence not present in the earlier A17 reference assembly. Conclusions Adding Dovetail followed by BioNano data yielded complementary improvements in continuity over the original PacBio assembly. This strategy proved efficient and cost-effective for developing a quality draft assembly compared to traditional reference assemblies.http://link.springer.com/article/10.1186/s12864-017-3971-4Genome assemblyNext generation sequencingBioNanoDovetailPacBioMedicago truncatula |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Karen M. Moll Peng Zhou Thiruvarangan Ramaraj Diego Fajardo Nicholas P. Devitt Michael J. Sadowsky Robert M. Stupar Peter Tiffin Jason R. Miller Nevin D. Young Kevin A. T. Silverstein Joann Mudge |
spellingShingle |
Karen M. Moll Peng Zhou Thiruvarangan Ramaraj Diego Fajardo Nicholas P. Devitt Michael J. Sadowsky Robert M. Stupar Peter Tiffin Jason R. Miller Nevin D. Young Kevin A. T. Silverstein Joann Mudge Strategies for optimizing BioNano and Dovetail explored through a second reference quality assembly for the legume model, Medicago truncatula BMC Genomics Genome assembly Next generation sequencing BioNano Dovetail PacBio Medicago truncatula |
author_facet |
Karen M. Moll Peng Zhou Thiruvarangan Ramaraj Diego Fajardo Nicholas P. Devitt Michael J. Sadowsky Robert M. Stupar Peter Tiffin Jason R. Miller Nevin D. Young Kevin A. T. Silverstein Joann Mudge |
author_sort |
Karen M. Moll |
title |
Strategies for optimizing BioNano and Dovetail explored through a second reference quality assembly for the legume model, Medicago truncatula |
title_short |
Strategies for optimizing BioNano and Dovetail explored through a second reference quality assembly for the legume model, Medicago truncatula |
title_full |
Strategies for optimizing BioNano and Dovetail explored through a second reference quality assembly for the legume model, Medicago truncatula |
title_fullStr |
Strategies for optimizing BioNano and Dovetail explored through a second reference quality assembly for the legume model, Medicago truncatula |
title_full_unstemmed |
Strategies for optimizing BioNano and Dovetail explored through a second reference quality assembly for the legume model, Medicago truncatula |
title_sort |
strategies for optimizing bionano and dovetail explored through a second reference quality assembly for the legume model, medicago truncatula |
publisher |
BMC |
series |
BMC Genomics |
issn |
1471-2164 |
publishDate |
2017-08-01 |
description |
Abstract Background Third generation sequencing technologies, with sequencing reads in the tens- of kilo-bases, facilitate genome assembly by spanning ambiguous regions and improving continuity. This has been critical for plant genomes, which are difficult to assemble due to high repeat content, gene family expansions, segmental and tandem duplications, and polyploidy. Recently, high-throughput mapping and scaffolding strategies have further improved continuity. Together, these long-range technologies enable quality draft assemblies of complex genomes in a cost-effective and timely manner. Results Here, we present high quality genome assemblies of the model legume plant, Medicago truncatula (R108) using PacBio, Dovetail Chicago (hereafter, Dovetail) and BioNano technologies. To test these technologies for plant genome assembly, we generated five assemblies using all possible combinations and ordering of these three technologies in the R108 assembly. While the BioNano and Dovetail joins overlapped, they also showed complementary gains in continuity and join numbers. Both technologies spanned repetitive regions that PacBio alone was unable to bridge. Combining technologies, particularly Dovetail followed by BioNano, resulted in notable improvements compared to Dovetail or BioNano alone. A combination of PacBio, Dovetail, and BioNano was used to generate a high quality draft assembly of R108, a M. truncatula accession widely used in studies of functional genomics. As a test for the usefulness of the resulting genome sequence, the new R108 assembly was used to pinpoint breakpoints and characterize flanking sequence of a previously identified translocation between chromosomes 4 and 8, identifying more than 22.7 Mb of novel sequence not present in the earlier A17 reference assembly. Conclusions Adding Dovetail followed by BioNano data yielded complementary improvements in continuity over the original PacBio assembly. This strategy proved efficient and cost-effective for developing a quality draft assembly compared to traditional reference assemblies. |
topic |
Genome assembly Next generation sequencing BioNano Dovetail PacBio Medicago truncatula |
url |
http://link.springer.com/article/10.1186/s12864-017-3971-4 |
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