TRITEX: chromosome-scale sequence assembly of Triticeae genomes with open-source tools

C. Monat; S. Padmarasu; T. Lux; T. Wicker; H. Gundlach; A. Himmelbach; J. Ens; C. Li; G.J. Muehlbauer; A.H. Schulman; R. Waugh; I. Braumann; C. Pozniak; U. Scholz; K.F.X. Mayer; M. Spannagl; N. Stein; M. Mascher

doi:10.1186/s13059-019-1899-5

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TRITEX: chromosome-scale sequence assembly of Triticeae genomes with open-source tools

Journal article

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TRITEX: chromosome-scale sequence assembly of Triticeae genomes with open-source tools

C. Monat, S. Padmarasu, T. Lux, T. Wicker, H. Gundlach, A. Himmelbach, J. Ens, C. Li, G.J. Muehlbauer, A.H. Schulman, …

Genome Biology, Vol.20(1)

2019

DOI: https://doi.org/10.1186/s13059-019-1899-5

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Abstract

Chromosome-scale genome sequence assemblies underpin pan-genomic studies. Recent genome assembly efforts in the large-genome Triticeae crops wheat and barley have relied on the commercial closed-source assembly algorithm DeNovoMagic. We present TRITEX, an open-source computational workflow that combines paired-end, mate-pair, 10X Genomics linked-read with chromosome conformation capture sequencing data to construct sequence scaffolds with megabase-scale contiguity ordered into chromosomal pseudomolecules. We evaluate the performance of TRITEX on publicly available sequence data of tetraploid wild emmer and hexaploid bread wheat, and construct an improved annotated reference genome sequence assembly of the barley cultivar Morex as a community resource.

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Title: TRITEX: chromosome-scale sequence assembly of Triticeae genomes with open-source tools
Authors/Creators: C. Monat (Author/Creator) - Leibniz-Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK)
S. Padmarasu (Author/Creator) - Leibniz-Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK)
T. Lux (Author/Creator) - Helmholtz Zentrum München
T. Wicker (Author/Creator) - University of Zurich
H. Gundlach (Author/Creator) - Helmholtz Zentrum München
A. Himmelbach (Author/Creator) - Leibniz-Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK)
J. Ens (Author/Creator) - University of Saskatchewan
C. Li (Author/Creator) - Yangtze University
G.J. Muehlbauer (Author/Creator) - University of Minnesota
A.H. Schulman (Author/Creator) - Natural Resources Institute Finland
R. Waugh (Author/Creator) - University of Dundee
I. Braumann (Author/Creator) - Carlsberg Laboratory
C. Pozniak (Author/Creator) - University of Saskatchewan
U. Scholz (Author/Creator) - Leibniz-Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK)
K.F.X. Mayer (Author/Creator) - Technical University Munich
M. Spannagl (Author/Creator) - Helmholtz Zentrum München
N. Stein (Author/Creator) - Leibniz-Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK)
M. Mascher (Author/Creator) - Leibniz-Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK)
Publication Details: Genome Biology, Vol.20(1)
Publisher: BioMed Central
Identifiers: 991005542298207891
Copyright: © 2019 The Author(s).
Murdoch Affiliation: Western Barley Genetics Alliance; School of Veterinary and Life Sciences
Language: English
Resource Type: Journal article

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Collaboration types: Domestic collaboration; International collaboration
Citation topics: 3 Agriculture, Environment & Ecology; 3.4 Crop Science; 3.4.96 QTL
Web Of Science research areas: Biotechnology & Applied Microbiology; Genetics & Heredity
ESI research areas: Molecular Biology & Genetics