Strategies for optimizing BioNano and Dovetail explored through a second reference quality assembly for the legume model, Medicago truncatula

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

doi:10.1186/s12864-017-3971-4

Strategies for optimizing BioNano and Dovetail explored through a second reference quality assembly for the legume model, Medicago truncatula

BMC Genomics. 2017 Aug 4;18(1):578. doi: 10.1186/s12864-017-3971-4.

Authors

Affiliations

¹ National Center for Genome Resources, 2935 Rodeo Park Drive East, Santa Fe, NM, 87505, USA.
² Montana State University, Center for Biofilm Engineering, Bozeman, MT, 59717, USA.
³ Department of Plant Biology, University of Minnesota, Saint Paul, MN, USA.
⁴ Department of Soil, Water & Climate, Plant and Microbial Biology and BioTechnology Institute, University of Minnesota, St. Paul, MN, USA.
⁵ Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN, USA.
⁶ Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, MN, USA.
⁷ J. Craig Venter Institute, Rockville, MD, USA.
⁸ Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN, USA.
⁹ National Center for Genome Resources, 2935 Rodeo Park Drive East, Santa Fe, NM, 87505, USA. jm@ncgr.org.

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.

Keywords: BioNano; Dovetail; Genome assembly; Medicago truncatula; Next generation sequencing; PacBio.

Publication types

Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

Chromosomes, Plant / genetics
Cost-Benefit Analysis
Genome, Plant / genetics
Genomics / economics
Genomics / methods*
Genomics / standards*
Medicago truncatula / genetics*
Quality Control
Reference Standards
Time Factors