Abstract
AbstractChromosome-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.
Publisher
Springer Science and Business Media LLC
Reference102 articles.
1. Schulte D, Close TJ, Graner A, Langridge P, Matsumoto T, Muehlbauer G, Sato K, Schulman AH, Waugh R, Wise RP, Stein N. The international barley sequencing consortium--at the threshold of efficient access to the barley genome. Plant Physiol. 2009;149:142–7.
2. Gill BS, Appels R, Botha-Oberholster AM, Buell CR, Bennetzen JL, Chalhoub B, Chumley F, Dvorak J, Iwanaga M, Keller B, et al. A workshop report on wheat genome sequencing: International Genome Research on Wheat Consortium. Genetics. 2004;168:1087–96.
3. Mascher M, Gundlach H, Himmelbach A, Beier S, Twardziok SO, Wicker T, Radchuk V, Dockter C, Hedley PE, Russell J, et al. A chromosome conformation capture ordered sequence of the barley genome. Nature. 2017;544:427–33.
4. The International Wheat Genome Sequencing Consortium (IWGSC): Shifting the limits in wheat research and breeding using a fully annotated reference genome. Science. 2018;361:eaar7191.
5. Maccaferri M, Harris NS, Twardziok SO, Pasam RK, Gundlach H, Spannagl M, Ormanbekova D, Lux T, Prade VM, Milner SG, et al. Durum wheat genome highlights past domestication signatures and future improvement targets. Nat Genet. 2019;51(5):885–95. https://doi.org/10.1038/s41588-019-0381-3.
Cited by
170 articles.
订阅此论文施引文献
订阅此论文施引文献，注册后可以免费订阅5篇论文的施引文献，订阅后可以查看论文全部施引文献