Einkorn genomics sheds light on history of the oldest domesticated wheat.
Journal
Nature
ISSN: 1476-4687
Titre abrégé: Nature
Pays: England
ID NLM: 0410462
Informations de publication
Date de publication:
Aug 2023
Aug 2023
Historique:
received:
16
10
2022
accepted:
29
06
2023
medline:
25
8
2023
pubmed:
3
8
2023
entrez:
2
8
2023
Statut:
ppublish
Résumé
Einkorn (Triticum monococcum) was the first domesticated wheat species, and was central to the birth of agriculture and the Neolithic Revolution in the Fertile Crescent around 10,000 years ago
Identifiants
pubmed: 37532937
doi: 10.1038/s41586-023-06389-7
pii: 10.1038/s41586-023-06389-7
pmc: PMC10447253
doi:
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
830-838Informations de copyright
© 2023. The Author(s).
Références
Levy, A. A. & Feldman, M. Evolution and origin of bread wheat. Plant Cell 34, 2549–2567 (2022).
pubmed: 35512194
pmcid: 9252504
doi: 10.1093/plcell/koac130
Salamini, F., Ozkan, H., Brandolini, A., Schafer-Pregl, R. & Martin, W. Genetics and geography of wild cereal domestication in the Near East. Nat. Rev. Genet. 3, 429–441 (2002).
pubmed: 12042770
doi: 10.1038/nrg817
Arranz-Otaegui, A., Gonzalez Carretero, L., Ramsey, M. N., Fuller, D. Q. & Richter, T. Archaeobotanical evidence reveals the origins of bread 14,400 years ago in northeastern Jordan. Proc. Natl Acad. Sci. USA 115, 7925–7930 (2018).
pubmed: 30012614
pmcid: 6077754
doi: 10.1073/pnas.1801071115
Pourkheirandish, M. et al. On the origin of the non-brittle rachis trait of domesticated einkorn wheat. Front. Plant Sci. 8, 2031 (2018).
pubmed: 29354137
pmcid: 5758593
doi: 10.3389/fpls.2017.02031
Marcussen, T. et al. Ancient hybridizations among the ancestral genomes of bread wheat. Science 345, 1250092 (2014).
pubmed: 25035499
doi: 10.1126/science.1250092
Chen, S. et al. Stripe rust resistance gene Yr34 (synonym Yr48) is located within a distal translocation of Triticum monococcum chromosome 5A
pubmed: 33791822
pmcid: 8263425
doi: 10.1007/s00122-021-03816-z
Kerber, E. & Dyck, P. Inheritance of stem rust resistance transferred from diploid wheat (Triticum monococcum) to tetraploid and hexaploid wheat and chromosome location of the gene involved. Can. J. Genet. Cytol. 15, 397–409 (1973).
doi: 10.1139/g73-050
Saintenac, C. et al. Identification of wheat gene Sr35 that confers resistance to Ug99 stem rust race group. Science 341, 783–786 (2013).
pubmed: 23811222
pmcid: 4748951
doi: 10.1126/science.1239022
Kolmer, J., Anderson, J. & Flor, J. Chromosome location, linkage with simple sequence repeat markers, and leaf rust resistance conditioned by gene Lr63 in wheat. Crop Sci. 50, 2392–2395 (2010).
doi: 10.2135/cropsci2010.01.0005
The, T. Chromosome location of genes conditioning stem rust resistance transferred from diploid to hexaploid wheat. Nat. New Biol. 241, 256 (1973).
Heun, M. et al. Site of einkorn wheat domestication identified by DNA fingerprinting. Science 278, 1312–1314 (1997).
doi: 10.1126/science.278.5341.1312
Heun, M., Haldorsen, S. & Vollan, K. Reassessing domestication events in the Near East: einkorn and Triticum urartu. Genome 51, 444–451 (2008).
pubmed: 18521123
doi: 10.1139/G08-030
Kilian, B. et al. Molecular diversity at 18 loci in 321 wild and 92 domesticate lines reveal no reduction of nucleotide diversity during Triticum monococcum (einkorn) domestication: implications for the origin of agriculture. Mol. Biol. Evol. 24, 2657–2668 (2007).
pubmed: 17898361
doi: 10.1093/molbev/msm192
Brandolini, A., Volante, A. & Heun, M. Geographic differentiation of domesticated einkorn wheat and possible Neolithic migration routes. Heredity 117, 135–141 (2016).
pubmed: 27165766
pmcid: 4981680
doi: 10.1038/hdy.2016.32
Behre, K. E., Wasylikowa, K. & van Zeist, W. Progress in Old World Palaeoethnobotany (Taylor & Francis, 1991).
Harlan, J. R. & Zohary, D. Distribution of wild wheats and barley: the present distribution of wild forms may provide clues to the regions of early cereal domestication. Science 153, 1074–1080 (1966).
pubmed: 17737582
doi: 10.1126/science.153.3740.1074
Badr, A. et al. On the origin and domestication history of barley (Hordeum vulgare). Mol. Biol. Evol. 17, 499–510 (2000).
pubmed: 10742042
doi: 10.1093/oxfordjournals.molbev.a026330
Wenger, A. M. et al. Accurate circular consensus long-read sequencing improves variant detection and assembly of a human genome. Nat. Biotechnol. 37, 1155–1162 (2019).
pubmed: 31406327
pmcid: 6776680
doi: 10.1038/s41587-019-0217-9
Lam, E. T. et al. Genome mapping on nanochannel arrays for structural variation analysis and sequence assembly. Nat. Biotechnol. 30, 771–776 (2012).
pubmed: 22797562
doi: 10.1038/nbt.2303
Lieberman-Aiden, E. et al. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science 326, 289–293 (2009).
pubmed: 19815776
pmcid: 2858594
doi: 10.1126/science.1181369
Johnson, B. L. & Waines, J. G. Use of wild-wheat resources. Hilgardia 31, 8–9 (1977).
Dvorak, J. et al. Reassessment of the evolution of wheat chromosomes 4A, 5A, and 7B. Theor. Appl. Genet. 131, 2451–2462 (2018).
pubmed: 30141064
pmcid: 6208953
doi: 10.1007/s00122-018-3165-8
Walkowiak, S. et al. Multiple wheat genomes reveal global variation in modern breeding. Nature 588, 277–283 (2020).
pubmed: 33239791
pmcid: 7759465
doi: 10.1038/s41586-020-2961-x
International Wheat Genome Sequencing Consortium. Shifting the limits in wheat research and breeding using a fully annotated reference genome. Science 361, eaar7191 (2018).
doi: 10.1126/science.aar7191
Cossu, R. M. et al. LTR retrotransposons show low levels of unequal recombination and high rates of intraelement gene conversion in large plant genomes. Genome Biol. Evol. 9, 3449–3462 (2017).
pubmed: 29228262
pmcid: 5751070
doi: 10.1093/gbe/evx260
Backhaus, A. E. et al. High expression of the MADS-box gene VRT2 increases the number of rudimentary basal spikelets in wheat. Plant Physiol. 189, 1536–1552 (2022).
pubmed: 35377414
pmcid: 9237664
doi: 10.1093/plphys/kiac156
Li, K. et al. Interactions between SQUAMOSA and SHORT VEGETATIVE PHASE MADS-box proteins regulate meristem transitions during wheat spike development. Plant Cell 33, 3621–3644 (2021).
pubmed: 34726755
pmcid: 8643710
doi: 10.1093/plcell/koab243
Prasad, K., Parameswaran, S. & Vijayraghavan, U. OsMADS1, a rice MADS‐box factor, controls differentiation of specific cell types in the lemma and palea and is an early‐acting regulator of inner floral organs. Plant J. 43, 915–928 (2005).
pubmed: 16146529
doi: 10.1111/j.1365-313X.2005.02504.x
Huang, Y. et al. Wide Grain 7 increases grain width by enhancing H3K4me3 enrichment in the OsMADS1 promoter in rice (Oryza sativa L.). Plant J. 102, 517–528 (2020).
pubmed: 31830332
doi: 10.1111/tpj.14646
McKinley, K. L. & Cheeseman, I. M. The molecular basis for centromere identity and function. Nat. Rev. Mol. Cell Biol. 17, 16–29 (2016).
pubmed: 26601620
doi: 10.1038/nrm.2015.5
Earnshaw, W. C. Discovering centromere proteins: from cold white hands to the A, B, C of CENPs. Nat. Rev. Mol. Cell Biol. 16, 443–449 (2015).
pubmed: 25991376
doi: 10.1038/nrm4001
Liu, Z. et al. Structure and dynamics of retrotransposons at wheat centromeres and pericentromeres. Chromosoma 117, 445–456 (2008).
pubmed: 18496705
doi: 10.1007/s00412-008-0161-9
Li, B. C. et al. Wheat centromeric retrotransposons: the new ones take a major role in centromeric structure. Plant J. 73, 952–965 (2013).
pubmed: 23253213
doi: 10.1111/tpj.12086
Su, H. D. et al. Centromere satellite repeats have undergone rapid changes in polyploid wheat subgenomes. Plant Cell 31, 2035–2051 (2019).
pubmed: 31311836
pmcid: 6751130
doi: 10.1105/tpc.19.00133
Naish, M. et al. The genetic and epigenetic landscape of the Arabidopsis centromeres. Science 374, eabi7489 (2021).
pubmed: 34762468
pmcid: 10164409
doi: 10.1126/science.abi7489
International Brachypodium Initiative. Genome sequencing and analysis of the model grass Brachypodium distachyon. Nature 463, 763–768 (2010).
doi: 10.1038/nature08747
Schnable, P. S. et al. The B73 maize genome: complexity, diversity, and dynamics. Science 326, 1112–1115 (2009).
pubmed: 19965430
doi: 10.1126/science.1178534
Cheng, Z. et al. Functional rice centromeres are marked by a satellite repeat and a centromere-specific retrotransposon. Plant Cell 14, 1691–1704 (2002).
pubmed: 12172016
pmcid: 151459
doi: 10.1105/tpc.003079
Wicker, T. et al. Impact of transposable elements on genome structure and evolution in bread wheat. Genome Biol. 19, 103 (2018).
pubmed: 30115100
pmcid: 6097303
doi: 10.1186/s13059-018-1479-0
Neumann, P. et al. Plant centromeric retrotransposons: a structural and cytogenetic perspective. Mob. DNA 2, 4 (2011).
pubmed: 21371312
pmcid: 3059260
doi: 10.1186/1759-8753-2-4
Wolfgruber, T. K. et al. Maize centromere structure and evolution: sequence analysis of centromeres 2 and 5 reveals dynamic loci shaped primarily by retrotransposons. PLoS Genet. 5, e1000743 (2009).
pubmed: 19956743
pmcid: 2776974
doi: 10.1371/journal.pgen.1000743
Adhikari, L. et al. Genetic characterization and curation of diploid A-genome wheat species. Plant Physiol. 188, 2101–2114 (2022).
pubmed: 35134208
pmcid: 8968256
doi: 10.1093/plphys/kiac006
Zhao, X. et al. Population genomics unravels the Holocene history of bread wheat and its relatives. Nat. Plants 9, 403–419 (2023).
pubmed: 36928772
doi: 10.1038/s41477-023-01367-3
Zhou, Y. et al. Triticum population sequencing provides insights into wheat adaptation. Nat. Genet. 52, 1412–1422 (2020).
pubmed: 33106631
doi: 10.1038/s41588-020-00722-w
Ramu, P. et al. Cassava haplotype map highlights fixation of deleterious mutations during clonal propagation. Nat. Genet. 49, 959–963 (2017).
pubmed: 28416819
doi: 10.1038/ng.3845
Abrouk, M. et al. Fonio millet genome unlocks African orphan crop diversity for agriculture in a changing climate. Nat. Commun. 11, 4488 (2020).
pubmed: 32901040
pmcid: 7479619
doi: 10.1038/s41467-020-18329-4
Jordan, K. W. et al. The genetic architecture of genome‐wide recombination rate variation in allopolyploid wheat revealed by nested association mapping. Plant J. 95, 1039–1054 (2018).
pubmed: 29952048
pmcid: 6174997
doi: 10.1111/tpj.14009
Sidhu, D. & Gill, K. S. Distribution of genes and recombination in wheat and other eukaryotes. Plant Cell Tiss. Org. Cult. 79, 257–270 (2005).
doi: 10.1007/s11240-005-2487-9
Pickrell, J. & Pritchard, J. Inference of population splits and mixtures from genome-wide allele frequency data. PLoS Genet. 8, e1002967 (2012).
pubmed: 23166502
pmcid: 3499260
doi: 10.1371/journal.pgen.1002967
Narasimhan, V. M. et al. The formation of human populations in South and Central Asia. Science 365, eaat7487 (2019).
pubmed: 31488661
pmcid: 6822619
doi: 10.1126/science.aat7487
Keilwagen, J. et al. Detecting major introgressions in wheat and their putative origins using coverage analysis. Sci. Rep. 12, 1908 (2022).
pubmed: 35115645
pmcid: 8813953
doi: 10.1038/s41598-022-05865-w
Chhuneja, P. et al. Mapping of adult plant stripe rust resistance genes in diploid A genome wheat species and their transfer to bread wheat. Theor. Appl. Genet. 116, 313–324 (2008).
pubmed: 17989954
doi: 10.1007/s00122-007-0668-0
Shi, A., Leath, S. & Murphy, J. A major gene for powdery mildew resistance transferred to common wheat from wild einkorn wheat. Phytopathology 88, 144–147 (1998).
pubmed: 18944983
doi: 10.1094/PHYTO.1998.88.2.144
Bonafede, M., Kong, L., Tranquilli, G., Ohm, H. & Dubcovsky, J. Reduction of a Triticum monococcum chromosome segment carrying the softness genes Pina and Pinb translocated to bread wheat. Crop Sci. 47, 821–828 (2007).
doi: 10.2135/cropsci2006.07.0468
Kuraparthy, V., Sood, S., Dhaliwal, H. S., Chhuneja, P. & Gill, B. S. Identification and mapping of a tiller inhibition gene (tin3) in wheat. Theor. Appl. Genet. 114, 285–294 (2007).
pubmed: 17115129
doi: 10.1007/s00122-006-0431-y
Kuraparthy, V., Sood, S. & Gill, B. S. Genomic targeting and mapping of tiller inhibition gene (tin3) of wheat using ESTs and synteny with rice. Funct. Integr. Genom. 8, 33–42 (2008).
doi: 10.1007/s10142-007-0057-4
Abe, A. et al. Genome sequencing reveals agronomically important loci in rice using MutMap. Nat. Biotechnol. 30, 174–178 (2012).
pubmed: 22267009
doi: 10.1038/nbt.2095
Tavakol, E. et al. The barley Uniculme4 gene encodes a BLADE-ON-PETIOLE-like protein that controls tillering and leaf patterning. Plant Physiol. 168, 164–174 (2015).
pubmed: 25818702
pmcid: 4424007
doi: 10.1104/pp.114.252882
Rawat, N. et al. A TILLING resource for hard red winter wheat variety Jagger. Crop Sci. 59, 1666–1671 (2019).
doi: 10.2135/cropsci2019.01.0011
Mayjonade, B. et al. Extraction of high-molecular-weight genomic DNA for long-read sequencing of single molecules. Biotechniques 61, 203–205 (2016).
pubmed: 27712583
doi: 10.2144/000114460
Cheng, H., Concepcion, G. T., Feng, X., Zhang, H. & Li, H. Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm. Nat. Methods 18, 170–175 (2021).
pubmed: 33526886
pmcid: 7961889
doi: 10.1038/s41592-020-01056-5
Durand, N. C. et al. Juicer provides a one-click system for analyzing loop-resolution Hi-C experiments. Cell Syst. 3, 95–98 (2016).
pubmed: 27467249
pmcid: 5846465
doi: 10.1016/j.cels.2016.07.002
Dudchenko, O. et al. De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds. Science 356, 92–95 (2017).
pubmed: 28336562
pmcid: 5635820
doi: 10.1126/science.aal3327
Durand, N. C. et al. Juicebox provides a visualization system for Hi-C contact maps with unlimited zoom. Cell Syst. 3, 99–101 (2016).
pubmed: 27467250
pmcid: 5596920
doi: 10.1016/j.cels.2015.07.012
Simão, F. A., Waterhouse, R. M., Ioannidis, P., Kriventseva, E. V. & Zdobnov, E. M. BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics 31, 3210–3212 (2015).
pubmed: 26059717
doi: 10.1093/bioinformatics/btv351
Rhie, A., Walenz, B. P., Koren, S. & Phillippy, A. M. Merqury: reference-free quality, completeness, and phasing assessment for genome assemblies. Genome Biol. 21, 245 (2020).
pubmed: 32928274
pmcid: 7488777
doi: 10.1186/s13059-020-02134-9
Adhikari, L. et al. A high-throughput skim-sequencing approach for genotyping, dosage estimation and identifying translocations. Sci. Rep. 12, 17583 (2022).
pubmed: 36266371
pmcid: 9584886
doi: 10.1038/s41598-022-19858-2
Chen, S., Zhou, Y., Chen, Y. & Gu, J. fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics 34, i884–i890 (2018).
pubmed: 30423086
pmcid: 6129281
doi: 10.1093/bioinformatics/bty560
Li, H. et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25, 2078–2079 (2009).
pubmed: 19505943
pmcid: 2723002
doi: 10.1093/bioinformatics/btp352
Li, H. A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data. Bioinformatics 27, 2987–2993 (2011).
pubmed: 21903627
pmcid: 3198575
doi: 10.1093/bioinformatics/btr509
Agarwal, G. et al. A recombination bin-map identified a major QTL for resistance to Tomato Spotted Wilt Virus in peanut (Arachis hypogaea). Sci. Rep. 9, 18246 (2019).
pubmed: 31796847
pmcid: 6890646
doi: 10.1038/s41598-019-54747-1
Athiyannan, N. et al. Long-read genome sequencing of bread wheat facilitates disease resistance gene cloning. Nat. Genet. 54, 227–231 (2022).
pubmed: 35288708
pmcid: 8920886
doi: 10.1038/s41588-022-01022-1
Dobin, A. et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29, 15–21 (2013).
pubmed: 23104886
doi: 10.1093/bioinformatics/bts635
Pertea, M. et al. StringTie enables improved reconstruction of a transcriptome from RNA-seq reads. Nat. Biotechnol. 33, 290–295 (2015).
pubmed: 25690850
pmcid: 4643835
doi: 10.1038/nbt.3122
Li, H. Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics 34, 3094–3100 (2018).
pubmed: 29750242
pmcid: 6137996
doi: 10.1093/bioinformatics/bty191
Brůna, T., Hoff, K. J., Lomsadze, A., Stanke, M. & Borodovsky, M. BRAKER2: automatic eukaryotic genome annotation with GeneMark-EP+ and AUGUSTUS supported by a protein database. NAR Genom. Bioinformatics 3, lqaa108 (2021).
Ou, S. et al. Benchmarking transposable element annotation methods for creation of a streamlined, comprehensive pipeline. Genome Biol. 20, 275 (2019).
pubmed: 31843001
pmcid: 6913007
doi: 10.1186/s13059-019-1905-y
Wicker, T., Matthews, D. E. & Keller, B. TREP: a database for Triticeae repetitive elements. Trends Plant Sci. 7, 561–562 (2002).
doi: 10.1016/S1360-1385(02)02372-5
Ling, H.-Q. et al. Genome sequence of the progenitor of wheat A subgenome Triticum urartu. Nature 557, 424–428 (2018).
pubmed: 29743678
pmcid: 6784869
doi: 10.1038/s41586-018-0108-0
Luo, M.-C. et al. Genome sequence of the progenitor of the wheat D genome Aegilops tauschii. Nature 551, 498–502 (2017).
pubmed: 29143815
pmcid: 7416625
doi: 10.1038/nature24486
Avni, R. et al. Wild emmer genome architecture and diversity elucidate wheat evolution and domestication. Science 357, 93–97 (2017).
pubmed: 28684525
doi: 10.1126/science.aan0032
Mascher, M. et al. Long-read sequence assembly: a technical evaluation in barley. Plant Cell 33, 1888–1906 (2021).
pubmed: 33710295
pmcid: 8290290
doi: 10.1093/plcell/koab077
International Rice Genome Sequencing Project. The map-based sequence of the rice genome. Nature 436, 793–800 (2005).
doi: 10.1038/nature03895
Gremme, G., Brendel, V., Sparks, M. E. & Kurtz, S. Engineering a software tool for gene structure prediction in higher organisms. Inf. Softw. Technol. 47, 965–978 (2005).
doi: 10.1016/j.infsof.2005.09.005
Haas, B. J. et al. Automated eukaryotic gene structure annotation using EVidenceModeler and the program to assemble spliced alignments. Genome Biol. 9, R7 (2008).
pubmed: 18190707
pmcid: 2395244
doi: 10.1186/gb-2008-9-1-r7
Haas, B. J. et al. Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies. Nucleic Acids Res. 31, 5654–5666 (2003).
pubmed: 14500829
pmcid: 206470
doi: 10.1093/nar/gkg770
Buchfink, B., Xie, C. & Huson, D. H. Fast and sensitive protein alignment using DIAMOND. Nat. Methods 12, 59–60 (2015).
pubmed: 25402007
doi: 10.1038/nmeth.3176
Quevillon, E. et al. InterProScan: protein domains identifier. Nucleic Acids Res. 33, W116–W120 (2005).
pubmed: 15980438
pmcid: 1160203
doi: 10.1093/nar/gki442
Pérez-Wohlfeil, E., Diaz-del-Pino, S. & Trelles, O. Ultra-fast genome comparison for large-scale genomic experiments. Sci. Rep. 9, 10274 (2019).
pubmed: 31312019
pmcid: 6635410
doi: 10.1038/s41598-019-46773-w
Wang, Y. et al. MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity. Nucleic Acids Res. 40, e49 (2012).
pubmed: 22217600
pmcid: 3326336
doi: 10.1093/nar/gkr1293
Krzywinski, M. et al. Circos: an information aesthetic for comparative genomics. Genome Res. 19, 1639–1645 (2009).
pubmed: 19541911
pmcid: 2752132
doi: 10.1101/gr.092759.109
Krumsiek, J., Arnold, R. & Rattei, T. Gepard: a rapid and sensitive tool for creating dotplots on genome scale. Bioinformatics 23, 1026–1028 (2007).
pubmed: 17309896
doi: 10.1093/bioinformatics/btm039
Nagaki, K. et al. Chromatin immunoprecipitation reveals that the 180-bp satellite repeat is the key functional DNA element of Arabidopsis thaliana centromeres. Genetics 163, 1221–1225 (2003).
pubmed: 12663558
pmcid: 1462492
doi: 10.1093/genetics/163.3.1221
Koo, D.-H., Sehgal, S. K., Friebe, B. & Gill, B. S. Structure and stability of telocentric chromosomes in wheat. PLoS ONE 10, e0137747 (2015).
pubmed: 26381743
pmcid: 4575054
doi: 10.1371/journal.pone.0137747
Ni, P. et al. DNA 5-methylcytosine detection and methylation phasing using PacBio circular consensus sequencing. Nat. Commun. 14, 4054 (2023).
Li, H. & Durbin, R. Fast and accurate long-read alignment with Burrows–Wheeler transform. Bioinformatics 26, 589–595 (2010).
pubmed: 20080505
pmcid: 2828108
doi: 10.1093/bioinformatics/btp698
Kent, W. J., Zweig, A. S., Barber, G., Hinrichs, A. S. & Karolchik, D. BigWig and BigBed: enabling browsing of large distributed datasets. Bioinformatics 26, 2204–2207 (2010).
Ramirez, F. et al. deepTools2: a next generation web server for deep-sequencing data analysis. Nucleic Acids Res. 44, W160–W165 (2016).
pubmed: 27079975
pmcid: 4987876
doi: 10.1093/nar/gkw257
Bolger, A. M., Lohse, M. & Usadel, B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30, 2114–2120 (2014).
pubmed: 24695404
pmcid: 4103590
doi: 10.1093/bioinformatics/btu170
Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357–359 (2012).
pubmed: 22388286
pmcid: 3322381
doi: 10.1038/nmeth.1923
Stovner, E. B. & Saetrom, P. epic2 efficiently finds diffuse domains in ChIP-seq data. Bioinformatics 35, 4392–4393 (2019).
pubmed: 30923821
doi: 10.1093/bioinformatics/btz232
Marçais, G. et al. MUMmer4: a fast and versatile genome alignment system. PLoS Comput. Biol. 14, e1005944 (2018).
pubmed: 29373581
pmcid: 5802927
doi: 10.1371/journal.pcbi.1005944
Benson, G. Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res. 27, 573–580 (1999).
pubmed: 9862982
pmcid: 148217
doi: 10.1093/nar/27.2.573
Liao, Y., Smyth, G. K. & Shi, W. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics 30, 923–930 (2013).
pubmed: 24227677
doi: 10.1093/bioinformatics/btt656
Wicker, T. et al. Transposable element populations shed light on the evolutionary history of wheat and the complex co‐evolution of autonomous and non‐autonomous retrotransposons. Adv. Genet. 3, 2100022 (2021).
pubmed: 36619351
pmcid: 9744471
doi: 10.1002/ggn2.202100022
SanMiguel, P., Gaut, B. S., Tikhonov, A., Nakajima, Y. & Bennetzen, J. L. The paleontology of intergene retrotransposons of maize. Nat. Genet. 20, 43–45 (1998).
pubmed: 9731528
doi: 10.1038/1695
McKenna, A. et al. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 20, 1297–1303 (2010).
pubmed: 20644199
pmcid: 2928508
doi: 10.1101/gr.107524.110
Danecek, P. et al. The variant call format and VCFtools. Bioinformatics 27, 2156–2158 (2011).
pubmed: 21653522
pmcid: 3137218
doi: 10.1093/bioinformatics/btr330
Cingolani, P. et al. A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff. Fly 6, 80–92 (2012).
pubmed: 22728672
pmcid: 3679285
doi: 10.4161/fly.19695
Chang, C. C. et al. Second-generation PLINK: rising to the challenge of larger and richer datasets. Gigascience 4, 7 (2015).
pubmed: 25722852
pmcid: 4342193
doi: 10.1186/s13742-015-0047-8
Marçais, G. & Kingsford, C. A fast, lock-free approach for efficient parallel counting of occurrences of k-mers. Bioinformatics 27, 764–770 (2011).
pubmed: 21217122
pmcid: 3051319
doi: 10.1093/bioinformatics/btr011
Pedersen, B. S. & Quinlan, A. R. Mosdepth: quick coverage calculation for genomes and exomes. Bioinformatics 34, 867–868 (2018).
pubmed: 29096012
doi: 10.1093/bioinformatics/btx699
Kokot, M., Długosz, M. & Deorowicz, S. KMC 3: counting and manipulating k-mer statistics. Bioinformatics 33, 2759–2761 (2017).
pubmed: 28472236
doi: 10.1093/bioinformatics/btx304
Venglat, P. et al. Gene expression analysis of flax seed development. BMC Plant Biol. 11, 74 (2011).
pubmed: 21529361
pmcid: 3107784
doi: 10.1186/1471-2229-11-74
Venglat, S. P. et al. The homeobox gene BREVIPEDICELLUS is a key regulator of inflorescence architecture in Arabidopsis. Proc. Natl Acad. Sci. USA 99, 4730–4735 (2002).
pubmed: 11917137
pmcid: 123716
doi: 10.1073/pnas.072626099
Sugihara, Y. et al. High-performance pipeline for MutMap and QTL-seq. PeerJ 10, e13170 (2022).
pubmed: 35321412
pmcid: 8935991
doi: 10.7717/peerj.13170
Wickham, H. ggplot2—Elegant Graphics for Data Analysis (Springer, 2016).
Wang, Y. et al. GSP: a web-based platform for designing genome-specific primers in polyploids. Bioinformatics 32, 2382–2383 (2016).
pubmed: 27153733
doi: 10.1093/bioinformatics/btw134