TRITEX: chromosome-scale sequence assembly of Triticeae genomes with open-source tools
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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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Genome annotation and assembly were subsequently improved.
“Genome annotation and assembly were subsequently improved (Mascher et al., 2017;Monat et al., 2019).”
From Genetic resources and precise gene editing for targeted improvement of barley abiotic stress tolerance (2023) · cites this paper as Monat et al., 2019
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Cites
R: A Language and Environment for Statistical Computing
R Core Team (2000) · doi:10.32614/r.manuals · Cited by 355,706 · see citing works
Basic local alignment search tool
Altschul, S. F., Gish, W., Miller, W., Myers, E. W., & Lipman, D. J. (1990) · Journal of Molecular Biology · doi:10.1006/jmbi.1990.9999 · Cited by 98,669 · see citing works
Trimmomatic: a flexible trimmer for Illumina sequence data
Bolger, A. M., Lohse, M., & Usadel, B. (2014) · Bioinformatics · doi:10.1093/bioinformatics/btu170 · Cited by 65,548 · see citing works
The Sequence Alignment/Map format and SAMtools
Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., Durbin, R., & 1000 Genome Project Data Processing Subgroup (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp352 · Cited by 62,041 · see citing works
Cutadapt removes adapter sequences from high-throughput sequencing reads
Martin, M. (2011) · EMBnet.journal · doi:10.14806/ej.17.1.200 · Cited by 33,889 · see citing works
BEDTools: a flexible suite of utilities for comparing genomic features
Quinlan, A. R., & Hall, I. M. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btq033 · Cited by 27,437 · see citing works
HISAT: a fast spliced aligner with low memory requirements
Kim, D., Langmead, B., & Salzberg, S. L. (2015) · Nature Methods · doi:10.1038/nmeth.3317 · Cited by 24,112 · see citing works
Minimap2: Pairwise alignment for nucleotide sequences
Li, H. (2018) · Bioinformatics · doi:10.1093/bioinformatics/bty191 · Cited by 14,807 · see citing works
StringTie enables improved reconstruction of a transcriptome from RNA-seq reads
Pertea, M., Pertea, G. M., Antonescu, C. M., Chang, T.-C., Mendell, J. T., & Salzberg, S. L. (2015) · Nature Biotechnology · doi:10.1038/nbt.3122 · Cited by 14,118 · see citing works
BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs
Simão, F. A., Waterhouse, R. M., Ioannidis, P., Kriventseva, E. V., & Zdobnov, E. M. (2015) · Bioinformatics · doi:10.1093/bioinformatics/btv351 · Cited by 13,344 · see citing works
The igraph software package for complex network research
Csárdi, G., & Nepusz, T. (2006) · Medical Entomology and Zoology · Cited by 10,078 · see citing works
EMBOSS: the European molecular biology open software suite.
Rice, P., Longden, I., & Bleasby, A. (2000) · Trends in Genetics · doi:10.1016/s0168-9525(00)02024-2 · Cited by 9,466 · see citing works
Tandem repeats finder: a program to analyze DNA sequences
Benson, G. (1999) · Nucleic Acids Research · doi:10.1093/nar/27.2.573 · Cited by 9,374 · see citing works
Accelerated Profile HMM Searches
Eddy, S. R. (2011) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1002195 · Cited by 6,975 · see citing works
SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler
Luo, R., Liu, B., Xie, Y., Li, Z., Huang, W., Yuan, J., He, G., Chen, Y., Pan, Q., Liu, Y., et al. (2012) · GigaScience · doi:10.1186/2047-217x-1-18 · Cited by 5,274 · see citing works
Aligning sequence reads, clone sequences and assembly con*gs with BWA-MEMPreprint
Li, H. (2014) · arXiv (Cornell University) · doi:10.6084/m9.figshare.963153.v1 · Cited by 5,150 · see citing works
PEAR: a fast and accurate Illumina Paired-End reAd mergeR
Zhang, J., Kobert, K., Flouri, T., & Stamatakis, A. (2014) · Bioinformatics · doi:10.1093/bioinformatics/btt593 · Cited by 4,497 · see citing works
Haas, B. J., Salzberg, S. L., Zhu, W., Pertea, M., Allen, J., Orvis, J., White, O. R., Buell, C. R., & Wortman, J. R. (2008) · Genome biology · doi:10.1186/gb-2008-9-1-r7 · Cited by 4,051 · see citing works
The B73 Maize Genome: Complexity, Diversity, and Dynamics
Schnable, P., Ware, D., Fulton, R., Stein, J., Wei, F., Pasternak, S., Liang, C.-Z., Zhang, J.-W., Fulton, L., Graves, T., et al. (2009) · Science · doi:10.1126/science.1178534 · Cited by 3,985 · see citing works
Shifting the limits in wheat research and breeding using a fully annotated reference genome
Appels, R., Eversole, K., Stein, N., Feuillet, C., Keller, B., Rogers, J., Pozniak, C. J., Choulet, F., Distelfeld, A., Poland, J., et al. (2018) · Science · doi:10.1126/science.aar7191 · Cited by 3,107 · see citing works
Self-citationA unified classification system for eukaryotic transposable elements
Wicker, T., Sabot, F., Hua‐Van, A., Bennetzen, J. L., Capy, P., Chalhoub, B., Flavell, A. J., Leroy, P., Morgante, M., Panaud, O., et al. (2007) · Nature Reviews Genetics · doi:10.1038/nrg2165 · Cited by 3,021 · see citing works
Self-citationGMAP: A genomic mapping and alignment program for mRNA and EST sequences
Wu, T. D., & Watanabe, C. K. (2005) · Bioinformatics · doi:10.1093/bioinformatics/bti310 · Cited by 2,354 · see citing works
Wenger, A. M., Peluso, P., Rowell, W. J., Chang, P.-C., Hall, R. J., Concepcion, G. T., Ebler, J., Fungtammasan, A., Kolesnikov, A., Olson, N. D., et al. (2019) · Nature Biotechnology · doi:10.1038/s41587-019-0217-9 · Cited by 1,841 · see citing works
LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons
Ellinghaus, D., Kurtz, S., & Willhoeft, U. (2008) · BMC Bioinformatics · doi:10.1186/1471-2105-9-18 · Cited by 1,623 · see citing works
Challenges in homology search: HMMER3 and convergent evolution of coiled-coil regions
Mistry, J., Finn, R. D., Eddy, S. R., Bateman, A. G., & Punta, M. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt263 · Cited by 1,622 · see citing works
BBMerge – Accurate paired shotgun read merging via overlap
Bushnell, B., Rood, J., & Singer, E. (2017) · PLoS ONE · doi:10.1371/journal.pone.0185056 · Cited by 1,495 · see citing works
Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions
Burton, J. N., Adey, A., Patwardhan, R. P., Qiu, R., Kitzman, J. O., & Shendure, J. (2013) · Nature Biotechnology · doi:10.1038/nbt.2727 · Cited by 1,470 · see citing works
A physical, genetic and functional sequence assembly of the barley genome
The International Barley Genome Sequencing Consortium (2012) · Nature · doi:10.1038/nature11543 · Cited by 1,456 · see citing works
A chromosome conformation capture ordered sequence of the barley genome
Mascher, M., Gundlach, H., Himmelbach, A., Beier, S., Twardziok, S. O., Wicker, T., Radchuk, V., Dockter, C., Hedley, P. E., Russell, J., et al. (2017) · Nature · doi:10.1038/nature22043 · Cited by 1,450 · see citing works
Self-citationZimin, A. V., Marçais, G., Puiu, D., Roberts, M., Salzberg, S. L., & Yorke, J. A. (2013) · Bioinformatics · doi:10.1093/bioinformatics/btt476 · Cited by 1,421 · see citing works
Stanke, M., Schöffmann, O., Morgenstern, B., & Waack, S. (2006) · BMC Bioinformatics · doi:10.1186/1471-2105-7-62 · Cited by 1,304 · see citing works
Improved maize reference genome with single-molecule technologies
Jiao, Y., Peluso, P. S., Shi, J., Liang, T. Y., Stitzer, M. C., Wang, B., Campbell, M. S., Stein, J. C., Wei, X., Chin, C.-S., et al. (2017) · Nature · doi:10.1038/nature22971 · Cited by 1,197 · see citing works
The paleontology of intergene retrotransposons of maize
SanMiguel, P. J., Gaut, B. S., Tikhonov, A. P., Nakajima, Y., & Bennetzen, J. L. (1998) · Nature Genetics · doi:10.1038/1695 · Cited by 1,001 · see citing works
GNU Parallel: The Command-Line Power Tool.
Tange, O. (2011) · Cited by 934 · see citing works
A physical map of the human genome
McPherson, J. D., Marra, M. A., Hillier, L., Waterston, R., Chinwalla, A., Wallis, J. W., Sekhon, M., Wylie, K. M., Mardis, E. R., Wilson, R. K., et al. (2001) · Nature · doi:10.1038/35057157 · Cited by 925 · see citing works
Wild emmer genome architecture and diversity elucidate wheat evolution and domestication
Avni, R., Nave, M., Barad, O., Baruch, K., Twardziok, S. O., Gundlach, H., Hale, I. L., Mascher, M., Spannagl, M., Wiebe, K., et al. (2017) · Science · doi:10.1126/science.aan0032 · Cited by 824 · see citing works
Self-citationDurum wheat genome highlights past domestication signatures and future improvement targets
Maccaferri, M., Harris, N. S., Twardziok, S. O., Pasam, R., Gundlach, H., Spannagl, M., Ormanbekova, D., Lux, T. M., Prade, V. M., Milner, S. G., et al. (2019) · Nature Genetics · doi:10.1038/s41588-019-0381-3 · Cited by 770 · see citing works
Self-citationChromosome-scale shotgun assembly using an in vitro method for long-range linkage
Putnam, N. H., O'Connell, B. L., Stites, J. C., Rice, B. J., Blanchette, M., Calef, R., Troll, C. J., Fields, A., Hartley, P. D., Sugnet, C. W., et al. (2016) · Genome Research · doi:10.1101/gr.193474.115 · Cited by 732 · see citing works
Genome mapping on nanochannel arrays for structural variation analysis and sequence assembly
Lam, E. T., Hastie, A. R., Lin, C. J., Ehrlich, D., Das, S. K., Austin, M. D., Deshpande, P., Cao, H., Nagarajan, N., Xiao, M., et al. (2012) · Nature Biotechnology · doi:10.1038/nbt.2303 · Cited by 650 · see citing works
Wang, M.-J., Tu, L., Yuan, D., Zhu, D., Shen, C., Li, J.-Y., Liu, F.-Y., Pei, L., Wang, P.-C., Zhao, G., et al. (2018) · Nature Genetics · doi:10.1038/s41588-018-0282-x · Cited by 617 · see citing works
Genome sequence of the progenitor of the wheat D genome Aegilops tauschii
Luo, M., Gu, Y., Puiu, D., Wang, H., Twardziok, S. O., Deal, K. R., Huo, N., Zhu, T., Wang, L., Wang, Y., et al. (2017) · Nature · doi:10.1038/nature24486 · Cited by 614 · see citing works
Self-citationAnalysis of RNA-Seq Data Using TopHat and Cufflinks
Ghosh, S., & Chan, C. K. (2015) · Methods in molecular biology · doi:10.1007/978-1-4939-3167-5_18 · Cited by 596 · see citing works
Structural and functional partitioning of bread wheat chromosome 3B
Choulet, F., Alberti, A., Theil, S., Glover, N., Barbe, V., Daron, J., Pingault, L., Sourdille, P., Couloux, A., Paux, E., et al. (2014) · Science · doi:10.1126/science.1249721 · Cited by 586 · see citing works
Self-citationGenome sequence of the progenitor of wheat A subgenome Triticum urartu
Ling, H., Ma, B., Shi, X., Liu, H., Dong, L., Sun, H., Cao, Y., Gao, Q., Zheng, S., Li, Y., et al. (2018) · Nature · doi:10.1038/s41586-018-0108-0 · Cited by 444 · see citing works
Clavijo, B., Venturini, L., Schudoma, C., Accinelli, G. G., Kaithakottil, G., Wright, J., Borrill, P., Kettleborough, G., Heavens, D., Chapman, H., et al. (2017) · Genome Research · doi:10.1101/gr.217117.116 · Cited by 413 · see citing works
Self-citationZimin, A. V., Puiu, D., Luo, M., Zhu, T., Koren, S., Marçais, G., Yorke, J. A., Dvořák, J., & Salzberg, S. L. (2017) · Genome Research · doi:10.1101/gr.213405.116 · Cited by 412 · see citing works
Engineering a software tool for gene structure prediction in higher organisms
Gremme, G., Brendel, V., Sparks, M. E., & Kurtz, S. (2005) · Information and Software Technology · doi:10.1016/j.infsof.2005.09.005 · Cited by 377 · see citing works
Space-efficient and exact de Bruijn graph representation based on a Bloom filter
Chikhi, R., & Rizk, G. (2013) · Algorithms for Molecular Biology · doi:10.1186/1748-7188-8-22 · Cited by 365 · see citing works
A Workshop Report on Wheat Genome Sequencing
Gill, B. S., Appels, R., Botha, A., Buell, C. R., Bennetzen, J. L., Chalhoub, B., Chumley, F. G., Dvořák, J., Iwanaga, M., Keller, B., et al. (2004) · Genetics · doi:10.1534/genetics.104.034769 · Cited by 332 · see citing works
Scaffolding of long read assemblies using long range contact information
Ghurye, J., Pop, M., Koren, S., Bickhart, D. M., & Chin, C.-S. (2017) · BMC Genomics · doi:10.1186/s12864-017-3879-z · Cited by 293 · see citing works
The first near-complete assembly of the hexaploid bread wheat genome, Triticum aestivum
Zimin, A. V., Puiu, D., Hall, R. J., Kingan, S. B., Clavijo, B., & Salzberg, S. L. (2017) · GigaScience · doi:10.1093/gigascience/gix097 · Cited by 292 · see citing works
Kurtz, S., Narechania, A., Stein, J. C., & Ware, D. (2008) · BMC Genomics · doi:10.1186/1471-2164-9-517 · Cited by 264 · see citing works
Anchoring and ordering NGS contig assemblies by population sequencing ( POPSEQ )
Mascher, M., Muehlbauer, G. J., Rokhsar, D. S., Chapman, J., Schmutz, J., Barry, K., Muñoz‐Amatriaín, M., Close, T. J., Wise, R. P., Schulman, A. H., et al. (2013) · The Plant Journal · doi:10.1111/tpj.12319 · Cited by 260 · see citing works
Self-citationHiCNorm: removing biases in Hi-C data via Poisson regression
Hu, M., Deng, K., Selvaraj, S., Qin, Z., Ren, B., & Liu, J. S. (2012) · Bioinform. · doi:10.1093/bioinformatics/bts570 · Cited by 250 · see citing works
Compacting de Bruijn graphs from sequencing data quickly and in low memory
Chikhi, R., Limasset, A., & Medvedev, P. (2016) · Bioinformatics · doi:10.1093/bioinformatics/btw279 · Cited by 243 · see citing works
A whole-genome shotgun approach for assembling and anchoring the hexaploid bread wheat genome
Chapman, J., Mascher, M., Buluç, A., Barry, K., Georganas, E., Session, A. M., Strnadová-Neeley, V., Jenkins, J. W., Sehgal, S. K., Oliker, L., et al. (2015) · Genome biology · doi:10.1186/s13059-015-0582-8 · Cited by 241 · see citing works
Self-citationSchulte, D., Close, T. J., Graner, A., et al. (2009) · PLANT PHYSIOLOGY · doi:10.1104/pp.108.128967 · Cited by 235 · see citing works
The maize W22 genome provides a foundation for functional genomics and transposon biology
Springer, N. M., Anderson, S. N., Andorf, C. M., Ahern, K. R., Bai, F., Barad, O., Barbazuk, W. B., Bass, H. W., Baruch, K., Ben-Zvi, G., et al. (2018) · Nature Genetics · doi:10.1038/s41588-018-0158-0 · Cited by 226 · see citing works
BFC: correcting Illumina sequencing errors
Li, H. (2015) · Bioinformatics · doi:10.1093/bioinformatics/btv290 · Cited by 217 · see citing works
Rapid cloning of genes in hexaploid wheat using cultivar-specific long-range chromosome assembly
Thind, A. K., Wicker, T., Šimková, H., Fossati, D., Moullet, O., Brabant, C., Vrána, J., Doležel, J., & Krattinger, S. G. (2017) · Nature Biotechnology · doi:10.1038/nbt.3877 · Cited by 215 · see citing works
Self-citationTowards a whole‐genome sequence for rye ( Secale cereale L.)
Bauer, E., Schmutzer, T., Barilar, I., Mascher, M., Gundlach, H., Martis, M. M., Twardziok, S. O., Hackauf, B., Gordillo, A., Wilde, P., et al. (2016) · The Plant Journal · doi:10.1111/tpj.13436 · Cited by 214 · see citing works
Self-citationDe Novo Assembly of a New Solanum pennellii Accession Using Nanopore Sequencing
Schmidt, M., Vogel, A., Denton, A. K., Istace, B., Wormit, A., van de Geest, H., Bolger, M., Alseekh, S., Maß, J., Pfaff, C., et al. (2017) · The Plant Cell · doi:10.1105/tpc.17.00521 · Cited by 202 · see citing works
Hirsch, C. N., Hirsch, C. D., Brohammer, A. B., Bowman, M. J., Soifer, I., Barad, O., Shem‐Tov, D., Baruch, K., Lü, F., Hernandez, A. G., et al. (2016) · The Plant Cell · doi:10.1105/tpc.16.00353 · Cited by 197 · see citing works
Comprehensive Sequence Analysis of 24,783 Barley Full-Length cDNAs Derived from 12 Clone Libraries
Matsumoto, T., Tanaka, T., Sakai, H., Amano, N., Kanamori, H., Kurita, K., Kikuta, A., Kamiya, K., Yamamoto, M., Ikawa, H., et al. (2011) · PLANT PHYSIOLOGY · doi:10.1104/pp.110.171579 · Cited by 195 · see citing works
High-throughput genome scaffolding from in vivo DNA interaction frequency
Kaplan, N., & Dekker, J. (2013) · Nature Biotechnology · doi:10.1038/nbt.2768 · Cited by 177 · see citing works
NxTrim: optimized trimming of Illumina mate pair reads
O’Connell, J., Schulz-Trieglaff, O. B., Carlson, E., Hims, M. M., Gormley, N. A., & Cox, A. J. (2015) · Bioinformatics · doi:10.1093/bioinformatics/btv057 · Cited by 166 · see citing works
BESST - Efficient scaffolding of large fragmented assemblies
Sahlin, K., Vezzi, F., Nystedt, B., Lundeberg, J., & Arvestad, L. (2014) · BMC Bioinformatics · doi:10.1186/1471-2105-15-281 · Cited by 155 · see citing works
Construction of a map-based reference genome sequence for barley, Hordeum vulgare L.
Beier, S., Himmelbach, A., Colmsee, C., Zhang, X., Barrero, R. A., Zhang, Q., Li, L., Bayer, M., Bolser, D. M., Taudien, S., et al. (2017) · Scientific Data · doi:10.1038/sdata.2017.44 · Cited by 150 · see citing works
Self-citationGeiger, H. H., & Miedaner, T. (2009) · Springer eBooks · doi:10.1007/978-0-387-72297-9_4 · Cited by 117 · see citing works
PGSB PlantsDB: updates to the database framework for comparative plant genome research
Spannagl, M., Nußbaumer, T., Bader, K. C., Martis, M. M., Seidel, M. A., Kugler, K., Gundlach, H., & Mayer, K. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv1130 · Cited by 106 · see citing works
Self-citationPGP repository: a plant phenomics and genomics data publication infrastructure
Arend, D., Junker, A., Scholz, U., Schüler, D., Wylie, J., & Lange, M. (2016) · Database · doi:10.1093/database/baw033 · Cited by 106 · see citing works
Self-citatione!DAL - a framework to store, share and publish research data
Arend, D., Lange, M., Chen, J., Colmsee, C., Flemming, S., Hecht, D., & Scholz, U. (2014) · BMC Bioinformatics · doi:10.1186/1471-2105-15-214 · Cited by 103 · see citing works
Self-citationMochida, K., Yoshida, T., Sakurai, T., Ogihara, Y., & Shinozaki, K. (2009) · PLANT PHYSIOLOGY · doi:10.1104/pp.109.138214 · Cited by 101 · see citing works
Improved Genome Sequence of Wild Emmer Wheat Zavitan with the Aid of Optical Maps
Zhu, T., Wang, L., Rodriguez, J., Deal, K. R., Avni, R., Distelfeld, A., McGuire, P. E., Dvořák, J., & Luo, M. (2019) · G3 Genes Genomes Genetics · doi:10.1534/g3.118.200902 · Cited by 97 · see citing works
ntCard: a streaming algorithm for cardinality estimation in genomics data
Mohamadi, H., Khan, H., & Birol, I. (2017) · Bioinform. · doi:10.1093/bioinformatics/btw832 · Cited by 76 · see citing works
KmerStream: streaming algorithms for k -mer abundance estimation
Melsted, P., & Halldórsson, B. V. (2014) · Bioinformatics · doi:10.1093/bioinformatics/btu713 · Cited by 72 · see citing works
Gao, S., Bertrand, D., Chia, B. K. H., & Nagarajan, N. (2016) · Genome biology · doi:10.1186/s13059-016-0951-y · Cited by 65 · see citing works
In Situ Hi-C for Plants: An Improved Method to Detect Long-Range Chromatin Interactions
Padmarasu, S., Himmelbach, A., Mascher, M., & Stein, N. (2019) · Methods in molecular biology · doi:10.1007/978-1-4939-9045-0_28 · Cited by 65 · see citing works
Self-citationBulbosum to Go: A Toolbox to Utilize Hordeum vulgare/bulbosum Introgressions for Breeding and Beyond
Wendler, N., Mascher, M., Himmelbach, A., Johnston, P. A., Pickering, R. A., & Stein, N. (2015) · Molecular Plant · doi:10.1016/j.molp.2015.05.004 · Cited by 56 · see citing works
Self-citationWicker, T., Yu, Y., Haberer, G., Mayer, K. F. X., Marri, P. R., Rounsley, S., Chen, M., Zuccolo, A., Panaud, O., Wing, R. A., et al. (2016) · Nature Communications · doi:10.1038/ncomms12790 · Cited by 55 · see citing works
Self-citationProspects of pan-genomics in barley
Monat, C., Schreiber, M., Stein, N., & Mascher, M. (2018) · Theoretical and Applied Genetics · doi:10.1007/s00122-018-3234-z · Cited by 53 · see citing works
Self-citationAssembly scaffolding with PE-contaminated mate-pair libraries
Sahlin, K., Chikhi, R., & Arvestad, L. (2016) · Bioinformatics · doi:10.1093/bioinformatics/btw064 · Cited by 51 · see citing works
An Alternate Algorithm for (3x3) Median Filtering of Digital Images
Singh, S. (2012) · INTERNATIONAL JOURNAL OF COMPUTERS & TECHNOLOGY · doi:10.24297/ijct.v1i1.6732 · Cited by 40 · see citing works
Discovery and characterization of two new stem rust resistance genes in Aegilops sharonensis
Yu, G., Champouret, N., Steuernagel, B., Olivera, P. D., Simmons, J., Williams, C., Johnson, R., Moscou, M., Hernández‐Pinzón, I., Green, P., et al. (2017) · Theoretical and Applied Genetics · doi:10.1007/s00122-017-2882-8 · Cited by 35 · see citing works
SNIC Science Cloud (SSC): A National-Scale Cloud Infrastructure for Swedish Academia
Salman Zubair, T. O. O. R., Lindberg, M., Falman, I., et al. (2017) · IEEE International Conference on eScience · doi:10.1109/escience.2017.35 · Cited by 34 · see citing works
Himmelbach, A., Ruban, A. S., Walde, I., Šimková, H., Doležel, J., Hastie, A. R., Stein, N., & Mascher, M. (2018) · The Plant Journal · doi:10.1111/tpj.14109 · Cited by 34 · see citing works
Self-citationResistance of Aegilops longissima to the Rusts of Wheat
Huang, S., Steffenson, B. J., Sela, H., et al. (2017) · Plant Disease · doi:10.1094/pdis-06-17-0880-re · Cited by 30 · see citing works
Xue, S., KOLMER, J. A., Wang, S., et al. (2018) · G3 Genes Genomes Genetics · doi:10.1534/g3.118.200058 · Cited by 28 · see citing works
European Flint reference sequences complement the maize pan-genomePreprint
Unterseer, S., Seidel, M. A., Bauer, E., et al. (2017) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/103747 · Cited by 26 · see citing works
Multiplex sequencing of bacterial artificial chromosomes for assembling complex plant genomes
Beier, S., Himmelbach, A., Schmutzer, T., Felder, M., Taudien, S., Mayer, K., Platzer, M., Stein, N., Scholz, U., & Mascher, M. (2016) · Plant Biotechnology Journal · doi:10.1111/pbi.12511 · Cited by 23 · see citing works
Self-citationHimmelbach, A., Walde, I., Mascher, M., & Stein, N. (2018) · BIO-PROTOCOL · doi:10.21769/bioprotoc.2955 · Cited by 17 · see citing works
Self-citationSchmutzer, T., Bolger, M., Rudd, S. A., Chen, J., Gundlach, H., Arend, D., Oppermann, M., Weise, S. F., Lange, M., Spannagl, M., et al. (2017) · Journal of Biotechnology · doi:10.1016/j.jbiotec.2017.07.006 · Cited by 16 · see citing works
Self-citationLu, F.-H., McKenzie, N., Kettleborough, G., Heavens, D., Clark, M. D., & Bevan, M. W. (2018) · GigaScience · doi:10.1093/gigascience/giy053 · Cited by 14 · see citing works
Joyce, B. L., Haug-Baltzell, A. K., Hulvey, J. P., et al. (2017) · Journal of Visualized Experiments · doi:10.3791/55009 · Cited by 7 · see citing works
Bloocoo, a memory efficient read corrector
Benoit, G., Lavenier, D. D., Lemaitre, C., et al. (2014) · HAL (Le Centre pour la Communication Scientifique Directe) · Cited by 5 · see citing works
Small group scoops international effort to sequence huge wheat genome
Callaway, E. (2017) · Nature · doi:10.1038/nature.2017.22924 · Cited by 4 · see citing works
Flagged first, then by citations
Research works printed but not linked: 2
- [94]Mascher M: Source of the TRITEX assembly pipeline. e!DAL - Plant Genomics & Phenomics Research Data Repository 2019, doi: 10.5447/IPK/2019/19. Accessed 10 Dec 2019. · DOI
- [99]Monat C, Padmarasu S, Lux T, Wicker T, Gundlach H, Himmelbach A, Ens J, Li C, Muehlbauer GJ, Schulman AH, et al: TRITEX assembly of bread wheat cv. Chinese Spring. EMBL ENA 2019, https://www.ebi.ac.uk/ena/data/view/CACRSF010000000. PMC6918601 31849336
Cited by
Sorted by citations
The barley pan-genome reveals the hidden legacy of mutation breeding
Jayakodi, M., Padmarasu, S., Haberer, G., Bonthala, V. S., Gundlach, H., Monat, C., Lux, T., Kamal, N., Lang, D., Himmelbach, A., et al. (2020) · Nature · doi:10.1038/s41586-020-2947-8 · Cited by 565 · see citing works
Self-citationA Genome Assembly of the Barley ‘Transformation Reference’ Cultivar Golden Promise
Schreiber, M., Mascher, M., Wright, J., Padmarasu, S., Himmelbach, A., Heavens, D., Milne, L., Clavijo, B. J., Stein, N., & Waugh, R. (2020) · G3 Genes|Genomes|Genetics · doi:10.1534/g3.119.401010 · Cited by 94 · see citing works
Self-citationKarunarathne, S., Walker, E., Sharma, D., Li, C., & Han, Y. (2023) · Journal of Zhejiang University-SCIENCE B · doi:10.1631/jzus.b2200552 · Cited by 18 · see citing works
“Genome annotation and assembly were sub‐ sequently improved (Mascher et al., 2017; Monat et al., 2019).”
Self-citation
- Authors
- 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.
- Affiliations
- Leibniz-Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK) (DE)
- Helmholtz Munich (DE)
- University of Zurich (CH)
- University of Saskatchewan (CA)
- Murdoch University (AU)
- University of Minnesota (US)
- University of Helsinki (FI)
- James Hutton Institute (GB)
- Carlsberg Laboratory (DK)
- German Centre for Integrative Biodiversity Research (DE)
- Corresponding author
- Stein, Nils
- Mascher, Martin
- ORCID
- Venue
- Genome Biology
- Published
- 2019-12
- Volume
- 20
- Issue
- 1
- Pages
- 284-284
- ISSN
- 1465-6906 (ISSN-L)
- 1474-760X
- PMC
- PMC6918601
- OpenAlex
- W2995585781
- Cited by
- 251
- References
- 96
- Citations by year
- 2026: 15 · 2025: 17 · 2024: 35 · 2023: 30 · 2022: 59 · 2021: 69 · 2020: 22 · 2019: 3 · 2018: 1
- FWCI
- 29.13
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Genome biology (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Discovery Research Portal (University of Dundee) (publishedVersion, cc-by)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion)
- GoeScholar The Publication Server of the Georg-August-Universität Göttingen (Georg-August-Universität Göttingen) (submittedVersion, cc-by)
- Työväentutkimus Vuosikirja (submittedVersion)
- mediaTUM – the media and publications repository of the Technical University Munich (Technical University Munich) (submittedVersion, other-oa)
- Site cant be reached (submittedVersion, cc-by)
- PuSH - Publication Server of Helmholtz Zentrum München (submittedVersion)
- Zurich Open Repository and Archive (University of Zurich) (submittedVersion, cc-by)
- Funders
- BMBF (FKZ 031B0190, FKZ 031A536)
- BMEL (2819103915)
- Topics
- Life Sciences › Agricultural and Biological Sciences › Plant Science › Wheat and Barley Genetics and Pathology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Agricultural and Biological Sciences › Plant Science › Chromosomal and Genetic Variations
- Keywords
- chromosome-level genome assembly, Triticeae, wheat, barley, chromosome conformation capture, chromosomal pseudomolecules, pangenomics, wild emmer wheat
- MeSH terms
- Hordeum, Genetic Techniques, Software, Triticum, Genome, Plant, Chromosomes, Plant
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Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
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