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

Cécile Monat; Sudharsan Padmarasu; Thomas Lux; Thomas Wicker; Heidrun Gundlach; Axel Himmelbach; Jennifer Ens; Chengdao Li; Gary J. Muehlbauer; Alan H. Schulman; Robbie Waugh; Ilka Braumann; Curtis Pozniak; Uwe Scholz; Klaus F. X. Mayer; Manuel Spannagl; Nils Stein; Martin Mascher

doi:10.1186/s13059-019-1899-5

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

Cécile Monat, Sudharsan Padmarasu, Thomas Lux, Thomas Wicker, Heidrun Gundlach, Axel Himmelbach, Jennifer Ens, Chengdao Li, Gary J. Muehlbauer, Alan H. Schulman, Robbie Waugh, Ilka Braumann, Curtis Pozniak, Uwe Scholz, Klaus F. X. Mayer, Manuel Spannagl, Nils Stein (Lead / Corresponding author), Martin Mascher (Lead / Corresponding author)

Plant Sciences

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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.

Original language	English
Article number	284
Pages (from-to)	1-18
Number of pages	18
Journal	Genome Biology
Volume	20
Issue number	1
DOIs	https://doi.org/10.1186/s13059-019-1899-5
Publication status	Published - 18 Dec 2019

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10.1186/s13059-019-1899-5Licence: CC BY

Final Published VersionFinal published version, 2.96 MBLicence: CC BY

A Reference Transcript Database for Improved Analysis of RNA-seq Data from Barley
Brown, J. (Investigator) & Waugh, R. (Investigator)
Biotechnology and Biological Sciences Research Council
1/10/18 → 30/09/20
Project: Research

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Monat, C., Padmarasu, S., Lux, T., Wicker, T., Gundlach, H., Himmelbach, A., Ens, J., Li, C., Muehlbauer, G. J., Schulman, A. H., Waugh, R., Braumann, I., Pozniak, C., Scholz, U., Mayer, K. F. X., Spannagl, M., Stein, N., & Mascher, M. (2019). TRITEX: chromosome-scale sequence assembly of Triticeae genomes with open-source tools. Genome Biology, 20(1), 1-18. Article 284. https://doi.org/10.1186/s13059-019-1899-5

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title = "TRITEX: chromosome-scale sequence assembly of Triticeae genomes with open-source tools",

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.",

author = "C{\'e}cile Monat and Sudharsan Padmarasu and Thomas Lux and Thomas Wicker and Heidrun Gundlach and Axel Himmelbach and Jennifer Ens and Chengdao Li and Muehlbauer, {Gary J.} and Schulman, {Alan H.} and Robbie Waugh and Ilka Braumann and Curtis Pozniak and Uwe Scholz and Mayer, {Klaus F. X.} and Manuel Spannagl and Nils Stein and Martin Mascher",

note = "This research was supported by grants from the German Federal Ministry of Education and Research to NS, MM, US, MS, and KFXM (“SHAPE,” FKZ 031B0190), to US and KFXM (“De.NBI,” FKZ 031A536) and from the German Federal Ministry of Food and Agriculture to KFXM (grant 2819103915, “Wheatseq”). Support for 10X sequencing was provided by a research grant from Genome Canada and Genome Prairie (to CP and JE). Tim Close (University of California, Riverside) contributed funds from Hatch Project CA-R-BPS-5306-H to the Dovetail assembly. The Dovetail assembly was also supported by the Carlsberg Foundation.",

year = "2019",

month = dec,

day = "18",

doi = "10.1186/s13059-019-1899-5",

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Monat, C, Padmarasu, S, Lux, T, Wicker, T, Gundlach, H, Himmelbach, A, Ens, J, Li, C, Muehlbauer, GJ, Schulman, AH, Waugh, R, Braumann, I, Pozniak, C, Scholz, U, Mayer, KFX, Spannagl, M, Stein, N & Mascher, M 2019, 'TRITEX: chromosome-scale sequence assembly of Triticeae genomes with open-source tools', Genome Biology, vol. 20, no. 1, 284, pp. 1-18. https://doi.org/10.1186/s13059-019-1899-5

TY - JOUR

T1 - TRITEX

T2 - chromosome-scale sequence assembly of Triticeae genomes with open-source tools

AU - Monat, Cécile

AU - Padmarasu, Sudharsan

AU - Lux, Thomas

AU - Wicker, Thomas

AU - Gundlach, Heidrun

AU - Himmelbach, Axel

AU - Ens, Jennifer

AU - Li, Chengdao

AU - Muehlbauer, Gary J.

AU - Schulman, Alan H.

AU - Waugh, Robbie

AU - Braumann, Ilka

AU - Pozniak, Curtis

AU - Scholz, Uwe

AU - Mayer, Klaus F. X.

AU - Spannagl, Manuel

AU - Stein, Nils

AU - Mascher, Martin

N1 - This research was supported by grants from the German Federal Ministry of Education and Research to NS, MM, US, MS, and KFXM (“SHAPE,” FKZ 031B0190), to US and KFXM (“De.NBI,” FKZ 031A536) and from the German Federal Ministry of Food and Agriculture to KFXM (grant 2819103915, “Wheatseq”). Support for 10X sequencing was provided by a research grant from Genome Canada and Genome Prairie (to CP and JE). Tim Close (University of California, Riverside) contributed funds from Hatch Project CA-R-BPS-5306-H to the Dovetail assembly. The Dovetail assembly was also supported by the Carlsberg Foundation.

PY - 2019/12/18

Y1 - 2019/12/18

N2 - 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.

AB - 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.

U2 - 10.1186/s13059-019-1899-5

DO - 10.1186/s13059-019-1899-5

M3 - Article

C2 - 31849336

SN - 1474-7596

VL - 20

SP - 1

EP - 18

JO - Genome Biology

JF - Genome Biology

IS - 1

M1 - 284

ER -

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

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A Reference Transcript Database for Improved Analysis of RNA-seq Data from Barley

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