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

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العنوان: Strategies for optimizing BioNano and Dovetail explored through a second reference quality assembly for the legume model, Medicago truncatula
المؤلفون: Michael J. Sadowsky, Peter Tiffin, Robert M. Stupar, Nicholas P. Devitt, Jason R. Miller, Diego Fajardo, Kevin A. T. Silverstein, Nevin D. Young, Thiruvarangan Ramaraj, Peng Zhou, Joann Mudge, Karen M. Moll
المصدر: BMC Genomics
BMC Genomics, Vol 18, Iss 1, Pp 1-16 (2017)
سنة النشر: 2017
مصطلحات موضوعية: 0106 biological sciences, 0301 basic medicine, Quality Control, Time Factors, lcsh:QH426-470, lcsh:Biotechnology, Cost-Benefit Analysis, Dovetail, Sequence assembly, BioNano, Computational biology, Biology, 01 natural sciences, Genome, DNA sequencing, Chromosomes, Plant, 03 medical and health sciences, lcsh:TP248.13-248.65, Next generation sequencing, Medicago truncatula, Genetics, 2. Zero hunger, Whole genome sequencing, PacBio, Genome assembly, Genomics, Reference Standards, biology.organism_classification, Dovetail joint, lcsh:Genetics, 030104 developmental biology, DNA microarray, Functional genomics, Genome, Plant, 010606 plant biology & botany, Biotechnology, Research Article
الوصف: 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. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3971-4) contains supplementary material, which is available to authorized users.
تدمد: 1471-2164
URL الوصول: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::f18b3abfe7a549ae61082fccd57ff4de
https://pubmed.ncbi.nlm.nih.gov/28778149
حقوق: OPEN
رقم الأكسشن: edsair.doi.dedup.....f18b3abfe7a549ae61082fccd57ff4de
قاعدة البيانات: OpenAIRE
الوصف
تدمد:14712164