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PMID: 28724409 Published · epublish English Journal Article Research Support, U.S. Gov't, Non-P.H.S.

Hybrid assembly with long and short reads improves discovery of gene family expansions.

BMC genomics ·Vol. 18 ·No. 1 ·2017-00-19 ·Pages 541

Miller JR, Zhou P, Mudge J, Gurtowski J, Lee H, Ramaraj T, Walenz BP, Liu J, Stupar RM, Denny R, Song L, Singh N, Maron LG, McCouch SR, McCombie WR, Schatz MC, Tiffin P, Young ND, Silverstein KAT

Abstract

Long-read and short-read sequencing technologies offer competing advantages for eukaryotic genome sequencing projects. Combinations of both may be appropriate for surveys of within-species genomic variation. We developed a hybrid assembly pipeline called "Alpaca" that can operate on 20X long-read coverage plus about 50X short-insert and 50X long-insert short-read coverage. To preclude collapse of tandem repeats, Alpaca relies on base-call-corrected long reads for contig formation. Compared to two other assembly protocols, Alpaca demonstrated the most reference agreement and repeat capture on the rice genome. On three accessions of the model legume Medicago truncatula, Alpaca generated the most agreement to a conspecific reference and predicted tandemly repeated genes absent from the other assemblies. Our results suggest Alpaca is a useful tool for investigating structural and copy number variation within de novo assemblies of sampled populations.

Keywords
Genome assembly Hybrid assembly pipeline Medicago truncatula Tandem repeats
MeSH Terms
DNA Copy Number Variations Genes, Plant/genetics Genomics/methods Medicago truncatula/genetics Multigene Family/genetics Oryza/genetics Phenotype Tandem Repeat Sequences/genetics
Authors & Affiliations
19 authors, click to expand affiliations / ORCID
Miller Jason R
J. Craig Venter Institute, 9714 Medical Center Drive, Rockville, MD, 20850, USA. [email protected].
Zhou Peng
Department of Plant Biology, University of Minnesota, Saint Paul, MN, USA.
Mudge Joann
National Center for Genome Resources, Santa Fe, NM, USA.
Gurtowski James
Cold Spring Harbor Laboratory, Harbor, Cold Spring, NY, USA.
Lee Hayan
Stanford School of Medicine, Stanford, CA, USA.
Ramaraj Thiruvarangan
National Center for Genome Resources, Santa Fe, NM, USA.
Walenz Brian P
National Human Genome Research Institute, Bethesda, MD, USA.
Liu Junqi
Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, USA.
Stupar Robert M
Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, USA.
Denny Roxanne
Department of Plant Pathology, University of Minnesota, St. Paul, MN, USA.
Song Li
Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA.
Singh Namrata
School of Integrative Plant Sciences, Plant Breeding and Genetics section, Cornell University, Ithaca, NY, 14850, USA.
Maron Lyza G
School of Integrative Plant Sciences, Plant Breeding and Genetics section, Cornell University, Ithaca, NY, 14850, USA.
McCouch Susan R
School of Integrative Plant Sciences, Plant Breeding and Genetics section, Cornell University, Ithaca, NY, 14850, USA.
McCombie W Richard
Cold Spring Harbor Laboratory, Harbor, Cold Spring, NY, USA.
Schatz Michael C
Departments of Computer Science and Biology, Johns Hopkins University, Baltimore, MD, USA.
Tiffin Peter
Department of Plant Biology, University of Minnesota, Saint Paul, MN, USA.
Young Nevin D
Department of Plant Biology, University of Minnesota, Saint Paul, MN, USA.
Silverstein Kevin A T
Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN, USA.
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Article Info
Journal
BMC genomics
Abbr.
BMC Genomics
ISSN
1471-2164
DOI
10.1186/s12864-017-3927-8
Email
[email protected]
Published
2017-00-19
Epub
2017-00-19
Pages
541
Language
English
Region
England
NLM ID
100965258
PMCID
PMC5518131
Subset
IM
Grants
NCI NIH HHS · P30 CA045508 · United States
External Links
PubMed source DOI: 10.1186/s12864-017-3927-8 PMC Full Text View journal details
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