vavilovВавиловский журнал генетики и селекцииVavilov Journal of Genetics and Breeding2500-3259Institute of Cytology and Genetics of Siberian Branch of the RAS10.18699/VJ19.459vavilov-1866Research ArticleАКТУАЛЬНЫЕ ТЕХНОЛОГИИ ГЕНЕТИКИ РАСТЕНИЙMAINSTREAM TECHNOLOGIES IN PLANT GENETICSПрогресс в секвенировании геномов растений – направления исследованийProgress in plant genome sequencing: research directionsБрагинаМ. К.BraginaM. K.

Новосибирск

Novosibirsk

koltunova@bionet.nsc.ruhttps://orcid.org/0000-0001-9738-1409АфонниковД. А.AfonnikovD. A.

Новосибирск

Novosibirsk

СалинаЕ. А.SalinaE. A.

Новосибирск

Novosibirsk

Федеральный исследовательский центр Институт цитологии и генетики Сибирского отделения Российской академии наукРоссияInstitute of Cytology and Genetics, SB RASRussian FederationФедеральный исследовательский центр Институт цитологии и генетики Сибирского отделения Российской академии наук; Новосибирский национальный исследовательский государственный университетРоссияInstitute of Cytology and Genetics, SB RAS; Novosibirsk State UniversityRussian Federation2019250220192313848Copyright © Брагина М.К., Афонников Д.А., Салина Е.А., 20192019Брагина М.К., Афонников Д.А., Салина Е.А.Bragina M.K., Afonnikov D.A., Salina E.A.This work is licensed under a Creative Commons Attribution 4.0 License.https://vavilov.elpub.ru/jour/article/view/1866

Геномные технологии претерпели значительные изменения с момента публикации первой последовательности генома растения Arabidopsis thaliana. Исследователи приняли на вооружение новые алгоритмы и технологии секвенирования и биоинформационные подходы для получения геномной последовательности, транскриптома и экзома для модельных и культурных видов растений, что позволило сделать глубокие выводы о биологии растений. В результате снижения затрат на секвенирование благодаря улучшению методов сборки и анализа геномов, количество и качество секвенированных геномов растений постоянно растет. В течение последних двадцати лет опубликовано более 300 геномных последовательностей растений. Хотя многие из опубликованных геномов считаются неполными, они, тем не менее, оказались ценным инструментом для идентификации генов-кандидатов, участвующих в формировании хозяйственно ценных признаков растений, для проведения работ по маркер-ориентированной и геномной селекции и сравнительного анализа геномов растений с целью установления основных закономерностей происхождения различных видов растений. В связи с тем, что высокого уровня покрытия и разрешения полногеномного секвенирования не хватает для обнаружения всех изменений в сложных образцах, стало развиваться целевое (таргетное) секвенирование, которое заключается в выделении и секвенировании определенной области генома. Основным преимуществом целевого секвенирования являются его высокая мощность обнаружения (способность идентифицировать новые варианты) и более высокое разрешение. Кроме того, активно развивается экзомное секвенирование (метод секвенирования только белок-кодирующих участков генов), позволяющее секвенировать участки генома, которые обогащены функциональными вариантами и демонстрируют низкий уровень содержания повторяющихся областей. В настоящем обзоре проведен анализ развития работ по секвенированию и построению «референсных» геномов растений. Сравниваются методы целевого секвенирования, базирующиеся на использовании референсной последовательности ДНК.

Since the first plant genome of Arabidopsis thaliana has been sequenced and published, genome sequencing technologies have undergone significant changes. New algorithms, sequencing technologies and bioinformatic approaches were adopted to obtain genome, transcriptome and exome sequences for model and crop species, which have permitted deep inferences into plant biology. As a result of an improved genome assembly and analysis methods, genome sequencing costs plummeted and the number of high-quality plant genome sequences is constantly growing. Consequently, more than 300 plant genome sequences have been published over the past twenty years. Although many of the published genomes are considered incomplete, they proved to be a valuable tool for identifying genes involved in the formation of economically valuable plant traits, for marker-assisted and genomic selection and for comparative analysis of plant genomes in order to determine the basic patterns of origin of various plant species. Since a high coverage and resolution of a genome sequence is not enough to detect all changes in complex samples, targeted sequencing, which consists in the isolation and sequencing of a specific region of the genome, has begun to develop. Targeted sequencing has a higher detection power (the ability to identify new differences/variants) and resolution (up to one basis). In addition, exome sequencing (the method of sequencing only protein-coding genes regions) is actively developed, which allows for the sequencing of non-expressed alleles and genes that cannot be found with RNA-seq. In this review, an analysis of sequencing technologies development and the construction of “reference” genomes of plants is performed. A comparison of the methods of targeted sequencing based on the use of the reference DNA sequence is accomplished.

растенияподходы к секвенированиюгеномэкзомное секвенированиецелевое секвенированиеplantssequencing approachesgenomeexome sequencingtargeted sequencingReferencesAird D., Ross M.G., Chen W.-S., Danielsson M., Fennell T., Russ C., Gnirke A. Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries. Genome Biol. 2011;12(2):R18. DOI 10.1186/gb-2011-12-2-r18.Aird D., Ross M.G., Chen W.-S., Danielsson M., Fennell T., Russ C., Gnirke A. Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries. Genome Biol. 2011;12(2):R18. DOI 10.1186/gb-2011-12-2-r18.Akpinar B.A., Biyiklioglu S., Alptekin B., Havránková M., Vrána J., Doležel J., Distelfeld A., Hernandez P., the IWGSC, Budak H. Chromosome-based survey sequencing reveals the genome organization of wild wheat progenitor Triticum dicoccoides. Plant Biotechnol. J. 2018;16:2077-2087. DOI 10.1111/pbi.12940.Akpinar B.A., Biyiklioglu S., Alptekin B., Havránková M., Vrána J., Doležel J., Distelfeld A., Hernandez P., the IWGSC, Budak H. Chromosome-based survey sequencing reveals the genome organization of wild wheat progenitor Triticum dicoccoides. Plant Biotechnol. J. 2018;16:2077-2087. DOI 10.1111/pbi.12940.Allen A.M., Barker G.L., Wilkinson P., Burridge A., Winfield M., Coghil J., Uauy C., Griffiths S., Jack P., Berry S., Werner P., Melichar J.P., McDougall J., Gwilliam R., Robinson P., Edwards K.J. Discovery and development of exome-based, co-dominant single nucleotide polymorphism markers in hexaploid wheat (Triticum aestivum L.). Plant Biotechnol. J. 2013;11:279-295. DOI 10.1111/pbi.12009.Allen A.M., Barker G.L., Wilkinson P., Burridge A., Winfield M., Coghil J., Uauy C., Griffiths S., Jack P., Berry S., Werner P., Melichar J.P., McDougall J., Gwilliam R., Robinson P., Edwards K.J. Discovery and development of exome-based, co-dominant single nucleotide polymorphism markers in hexaploid wheat (Triticum aestivum L.). Plant Biotechnol. J. 2013;11:279-295. DOI 10.1111/pbi.12009.Andolfo G., Jupe F., Witek K., Etherington G.J., Ercolano M.R., Jones J.D.G. Defining the full tomato NB-LRR resistance gene repertoire using genomic and cDNA RenSeq. BMC Plant Biol. 2014; 14(1):120. DOI 10.1186/1471-2229-14-120.Andolfo G., Jupe F., Witek K., Etherington G.J., Ercolano M.R., Jones J.D.G. Defining the full tomato NB-LRR resistance gene repertoire using genomic and cDNA RenSeq. BMC Plant Biol. 2014; 14(1):120. DOI 10.1186/1471-2229-14-120.Avni R., Nave M., Barad O., Baruch K., Twardziok S.O., Gundlach H., Distelfeld A. Wild emmer genome architecture and diversity elucidate wheat evolution and domestication. Science. 2017;357(6346): 93-97. DOI 10.1126/science.aan0032.Avni R., Nave M., Barad O., Baruch K., Twardziok S.O., Gundlach H., Distelfeld A. Wild emmer genome architecture and diversity elucidate wheat evolution and domestication. Science. 2017;357(6346): 93-97. DOI 10.1126/science.aan0032.Bai B., Wang L., Lee M., Zhang Y., Rahmadsyah, Alfiko Y., Ye B.Q., Wan Z.Y., Lim C.H., Suwanto A., Chua N.-H., Yue G.H. Genomewide identification of markers for selecting higher oil content in oil palm. BMC Plant Biol. 2017;17(1):93. DOI 10.1186/s12870-0171045-z.Bai B., Wang L., Lee M., Zhang Y., Rahmadsyah, Alfiko Y., Ye B.Q., Wan Z.Y., Lim C.H., Suwanto A., Chua N.-H., Yue G.H. Genomewide identification of markers for selecting higher oil content in oil palm. BMC Plant Biol. 2017;17(1):93. DOI 10.1186/s12870-0171045-z.Barabaschi D., TondelliA., Desiderio F., VolanteA., Vaccino P., Valè G., Cattivelli L. Next generation breeding. Plant Sci. 2016;242:3-13. DOI 10.1016/j.plantsci.2015.07.010.Barabaschi D., TondelliA., Desiderio F., VolanteA., Vaccino P., Valè G., Cattivelli L. Next generation breeding. Plant Sci. 2016;242:3-13. DOI 10.1016/j.plantsci.2015.07.010.Bassel G.W., Gaudinier A., Brady S.M., Hennig L., Rhee S.Y., De Smet I. Systems analysis of plant functional, transcriptional, physical interaction, and metabolic networks. Plant Cell. 2012;24(10):38593875. DOI 10.1105/tpc.112.100776.Bassel G.W., Gaudinier A., Brady S.M., Hennig L., Rhee S.Y., De Smet I. Systems analysis of plant functional, transcriptional, physical interaction, and metabolic networks. Plant Cell. 2012;24(10):38593875. DOI 10.1105/tpc.112.100776.Bennetzen J., Ma J., Devos K. Mechanisms of recent genome size variation in flowering plants. Ann. Bot. 2005;95(1):127-132. DOI 10.1093/aob/mci008.Bennetzen J., Ma J., Devos K. Mechanisms of recent genome size variation in flowering plants. Ann. Bot. 2005;95(1):127-132. DOI 10.1093/aob/mci008.Bennetzen J.L., Wang H. The contributions of transposable elements to the structure, function, and evolution of plant genomes. Annu. Rev. Plant Biol. 2014;65(1):505-530. DOI 10.1146/annurev-arplant050213-035811.Bennetzen J.L., Wang H. The contributions of transposable elements to the structure, function, and evolution of plant genomes. Annu. Rev. Plant Biol. 2014;65(1):505-530. DOI 10.1146/annurev-arplant050213-035811.Bolger M., Weisshaar B., Scholz U., Stein N., Usadel B., Mayer K. Plant genome sequencing – applications for crop improvement. Curr. Opin. Biotechnol. 2014;26:31-37. DOI 10.1016/j.copbio.2013.08.019.Bolger M., Weisshaar B., Scholz U., Stein N., Usadel B., Mayer K. Plant genome sequencing – applications for crop improvement. Curr. Opin. Biotechnol. 2014;26:31-37. DOI 10.1016/j.copbio.2013.08.019.Bolon Y.-T., Haun W.J., Xu W.W., Grant D., Stacey M.G., Nelson R.T., Gerhardt D.J., Jeddeloh J.A., Stacey G., Muehlbauer G.J., Orf J.H., Naeve S.L., Stupar R.M., Vance C.P. Phenotypic and genomic analyses of a fast neutron mutant population resource in soybean. Plant Physiol. 2011;156:240-253. DOI 10.1104/pp.110.170811.Bolon Y.-T., Haun W.J., Xu W.W., Grant D., Stacey M.G., Nelson R.T., Gerhardt D.J., Jeddeloh J.A., Stacey G., Muehlbauer G.J., Orf J.H., Naeve S.L., Stupar R.M., Vance C.P. Phenotypic and genomic analyses of a fast neutron mutant population resource in soybean. Plant Physiol. 2011;156:240-253. DOI 10.1104/pp.110.170811.Brenchley R., Spannagl M., Pfeifer M., Barker G.L.A., D’Amore R., Allen A.M., McKenzie N., Kramer M., Kerhornou A., Bolser D., Kay S., Waite D., Trick M., Bancroft I., Gu Y., Huo N., Luo M.-C., Sehgal S., Gill B., Kianian S., Anderson O., Kersey P., Dvorak J., McCombie W.R., HallA., Mayer K.F.X., Edwards K.J., Bevan M.W., Hall N. Analysis of the bread wheat genome using whole-genome shotgun sequencing. Nature. 2012;491:705-710. DOI 10.1038/nature11650.Brenchley R., Spannagl M., Pfeifer M., Barker G.L.A., D’Amore R., Allen A.M., McKenzie N., Kramer M., Kerhornou A., Bolser D., Kay S., Waite D., Trick M., Bancroft I., Gu Y., Huo N., Luo M.-C., Sehgal S., Gill B., Kianian S., Anderson O., Kersey P., Dvorak J., McCombie W.R., HallA., Mayer K.F.X., Edwards K.J., Bevan M.W., Hall N. Analysis of the bread wheat genome using whole-genome shotgun sequencing. Nature. 2012;491:705-710. DOI 10.1038/nature11650.Choulet F., Alberti A., Theil S., Glover N., Barbe V., Daron J., Pingault L., Sourdille P., Couloux A., Paux E., Leroy P., Mangenot S., Guilhot N., Le Gouis J., Balfourier F., Alaux M., Jamilloux V., Poulain J., Durand C., Bellec A., Gaspin C., Safar J., Dolezel J., Rogers J., Vandepoele K., Aury J.-M., Mayer K., Berges H., Quesneville H., Wincker P., Feuillet C. Structural and functional partitioning of bread wheat chromosome 3B. Science. 2014;345(6194):1249721. DOI 10.1126/science.1249721.Choulet F., Alberti A., Theil S., Glover N., Barbe V., Daron J., Pingault L., Sourdille P., Couloux A., Paux E., Leroy P., Mangenot S., Guilhot N., Le Gouis J., Balfourier F., Alaux M., Jamilloux V., Poulain J., Durand C., Bellec A., Gaspin C., Safar J., Dolezel J., Rogers J., Vandepoele K., Aury J.-M., Mayer K., Berges H., Quesneville H., Wincker P., Feuillet C. Structural and functional partitioning of bread wheat chromosome 3B. Science. 2014;345(6194):1249721. DOI 10.1126/science.1249721.Clarke W.E., Parkin I.A., Gajardo H.A., Gerhardt D.J., Higgins E. Genomic DNA enrichment using sequence capture microarrays: a novel approach to discover sequence nucleotide polymorphisms (SNP) in Brassica napus L. PLoS One. 2013;8(12):e81992. DOI 10.1371/journal.pone.0081992.Clarke W.E., Parkin I.A., Gajardo H.A., Gerhardt D.J., Higgins E. Genomic DNA enrichment using sequence capture microarrays: a novel approach to discover sequence nucleotide polymorphisms (SNP) in Brassica napus L. PLoS One. 2013;8(12):e81992. DOI 10.1371/journal.pone.0081992.Crain J., Mondal S., Rutkoski J., Singh R.P., Poland J. Combining high-throughput phenotyping and genomic information to increase prediction and selection accuracy in wheat breeding. Plant Genome. 2018;11(1). DOI 10.3835/plantgenome2017.05.0043.Crain J., Mondal S., Rutkoski J., Singh R.P., Poland J. Combining high-throughput phenotyping and genomic information to increase prediction and selection accuracy in wheat breeding. Plant Genome. 2018;11(1). DOI 10.3835/plantgenome2017.05.0043.Dasgupta M.G., Dharanishanthi V., Agarwal I., Krutovsky K.V. Development of genetic markers in Eucalyptus species by target enrichment and exome sequencing. PLoS One. 2015;10(1):e0116528. DOI 10.1371/journal.pone.0116528.Dasgupta M.G., Dharanishanthi V., Agarwal I., Krutovsky K.V. Development of genetic markers in Eucalyptus species by target enrichment and exome sequencing. PLoS One. 2015;10(1):e0116528. DOI 10.1371/journal.pone.0116528.Deschamps S., Llaca V., May G.D. Genotyping-by-sequencing in plants. Biology. 2012;1(3):460-483. DOI 10.3390/biology1030460.Deschamps S., Llaca V., May G.D. Genotyping-by-sequencing in plants. Biology. 2012;1(3):460-483. DOI 10.3390/biology1030460.Dohm J.C., Lottaz C., Borodina T., Himmelbauer H. Substantial biases in ultra-short read data sets from high-throughput DNA sequencing. Nucleic Acids Res. 2008;36(16):e105. DOI 10.1093/nar/gkn425.Dohm J.C., Lottaz C., Borodina T., Himmelbauer H. Substantial biases in ultra-short read data sets from high-throughput DNA sequencing. Nucleic Acids Res. 2008;36(16):e105. DOI 10.1093/nar/gkn425.Dohm J.C., Minoche A.E., Holtgräwe D., Capella-Gutiérrez S., Zakrzewski F., Tafer H., Rupp O., Sörensen T.R., Stracke R., Reinhardt R., Goesmann A., Kraft T., Schulz B., Stadler P.F., Schmidt T., Gabaldon T., Lehrach H., Weisshaar B., Himmelbauer H. The genome of the recently domesticated crop plant sugar beet (Beta vulgaris). Nature. 2014;505(7484):546-549. DOI 10.1038/nature12817.Dohm J.C., Minoche A.E., Holtgräwe D., Capella-Gutiérrez S., Zakrzewski F., Tafer H., Rupp O., Sörensen T.R., Stracke R., Reinhardt R., Goesmann A., Kraft T., Schulz B., Stadler P.F., Schmidt T., Gabaldon T., Lehrach H., Weisshaar B., Himmelbauer H. The genome of the recently domesticated crop plant sugar beet (Beta vulgaris). Nature. 2014;505(7484):546-549. DOI 10.1038/nature12817.DoleželJ., Kubaláková M., Paux E., BartošJ., Feuillet C. Chromosomebased genomics in the cereals. Chromosome Res. 2007;15(1):51-66. DOI 10.1007/s10577-006-1106-x.DoleželJ., Kubaláková M., Paux E., BartošJ., Feuillet C. Chromosomebased genomics in the cereals. Chromosome Res. 2007;15(1):51-66. DOI 10.1007/s10577-006-1106-x.Evans J., Kim J., Childs K.L., Vaillancourt B., Crisovan E., Nandety A., Gerhardt D.J., Richmond T.A., Jeddeloh J.A., Kaeppler S.M., Casler M.D., Buell C.R. Nucleotide polymorphism and copy number variant detection using exome capture and next-generation sequencing in the polyploid grass Panicum virgatum. Plant J. 2014;79(6): 993-1008. DOI 10.1111/tpj.12601.Evans J., Kim J., Childs K.L., Vaillancourt B., Crisovan E., Nandety A., Gerhardt D.J., Richmond T.A., Jeddeloh J.A., Kaeppler S.M., Casler M.D., Buell C.R. Nucleotide polymorphism and copy number variant detection using exome capture and next-generation sequencing in the polyploid grass Panicum virgatum. Plant J. 2014;79(6): 993-1008. DOI 10.1111/tpj.12601.Feuillet C., Leach J.E., Rogers J., Schnable P.S., Eversole K. Crop genome sequencing: lessons and rationales. Trends Plant Sci. 2011; 16(2):77-88. DOI 10.1016/j.tplants.2010.10.005.Feuillet C., Leach J.E., Rogers J., Schnable P.S., Eversole K. Crop genome sequencing: lessons and rationales. Trends Plant Sci. 2011; 16(2):77-88. DOI 10.1016/j.tplants.2010.10.005.Gardiner LJ., Gawroński P., Olohan L., Schnurbusch T., Hall N., HallA. Using genic sequence capture in combination with a syntenic pseudo genome to map a deletion mutant in a wheat species. Plant J. 2014; 80(5):895-904. DOI 10.1111/tpj.12660.Gardiner LJ., Gawroński P., Olohan L., Schnurbusch T., Hall N., HallA. Using genic sequence capture in combination with a syntenic pseudo genome to map a deletion mutant in a wheat species. Plant J. 2014; 80(5):895-904. DOI 10.1111/tpj.12660.Goff S.A., Ricke D., Lan T.-H., Presting G., Wang R., Dunn M., Glazebrook J., … Macalma T., Oliphant A., Briggs S. A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). Science. 2002; 296(5565):92-100. DOI 10.1126/science.1068275.Goff S.A., Ricke D., Lan T.-H., Presting G., Wang R., Dunn M., Glazebrook J., … Macalma T., Oliphant A., Briggs S. A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). Science. 2002; 296(5565):92-100. DOI 10.1126/science.1068275.Groenen M., Archibald A.L., Uenishi H., Tuggle C.K., Takeuchi Y., … Rogers J., Churcher C., Schook L.B. Analyses of pig genomes provide insight into porcine demography and evolution. Nature. 2012; 491:393-398. DOI 10.1038/nature11622.Groenen M., Archibald A.L., Uenishi H., Tuggle C.K., Takeuchi Y., … Rogers J., Churcher C., Schook L.B. Analyses of pig genomes provide insight into porcine demography and evolution. Nature. 2012; 491:393-398. DOI 10.1038/nature11622.Guo S., Zhang J., Sun H., Salse J., Lucas W.J., Zhang H., … LiY., Fei Z., Xu Y. The draft genome of watermelon (Citrullus lanatus) and resequencing of 20 diverse accessions. Nat. Genet. 2013;45(1):51-58. DOI 10.1038/ng.2470.Guo S., Zhang J., Sun H., Salse J., Lucas W.J., Zhang H., … LiY., Fei Z., Xu Y. The draft genome of watermelon (Citrullus lanatus) and resequencing of 20 diverse accessions. Nat. Genet. 2013;45(1):51-58. DOI 10.1038/ng.2470.Henry I.M., Nagalakshmi U., Lieberman M.C., Ngo K.J., Krasileva K.V., Vasquez-Gross H., Akhunova A., Akhunov E., Dubcovsky J., Tai T.H., Comai L. Efficient genome-wide detection and cataloging of EMS-induced mutations using exome capture and next-generation sequencing. Plant Cell. 2014;26:1382-1397. DOI 10.1105/tpc.113.121590.Henry I.M., Nagalakshmi U., Lieberman M.C., Ngo K.J., Krasileva K.V., Vasquez-Gross H., Akhunova A., Akhunov E., Dubcovsky J., Tai T.H., Comai L. Efficient genome-wide detection and cataloging of EMS-induced mutations using exome capture and next-generation sequencing. Plant Cell. 2014;26:1382-1397. DOI 10.1105/tpc.113.121590.Hernandez P., Martis M., Dorado G., Pfeifer M., Gálvez S., Schaaf S., Jouve N., Šimková H., Valárik M., Doležel J., Mayer K.F. Next-generation sequencing and syntenic integration of flow-sorted arms of wheat chromosome 4A exposes the chromosome structure and gene content. Plant J. 2012;69(3):377-386. DOI 10.1111/j.1365-313X.2011.04808.x.Hernandez P., Martis M., Dorado G., Pfeifer M., Gálvez S., Schaaf S., Jouve N., Šimková H., Valárik M., Doležel J., Mayer K.F. Next-generation sequencing and syntenic integration of flow-sorted arms of wheat chromosome 4A exposes the chromosome structure and gene content. Plant J. 2012;69(3):377-386. DOI 10.1111/j.1365-313X.2011.04808.x.Howe K., Clark M.D., Torroja C.F., Torrance J., Berthelot C., … Crollius H.R., Rogers J., Stemple D. The zebrafish reference genome sequence and its relationship to the human genome. Nature. 2013; 496:498-503. DOI 10.1038/nature12111.Howe K., Clark M.D., Torroja C.F., Torrance J., Berthelot C., … Crollius H.R., Rogers J., Stemple D. The zebrafish reference genome sequence and its relationship to the human genome. Nature. 2013; 496:498-503. DOI 10.1038/nature12111.Huang S., Li R., Zhang Z., Li L., Gu X., Fan W., … Wang J., Du Y., Li S. The genome of the cucumber, Cucumis sativus L. Nat. Genet. 2009;41:1275-1281. DOI 10.1038/ng.475.Huang S., Li R., Zhang Z., Li L., Gu X., Fan W., … Wang J., Du Y., Li S. The genome of the cucumber, Cucumis sativus L. Nat. Genet. 2009;41:1275-1281. DOI 10.1038/ng.475.International Wheat Genome Sequencing Consortium (IQGSC). Shifting the limits in wheat research and breeding using a fully annotated reference genome. Science. 2018;361(6403):eaar7191. DOI 10.1126/science.aar7191.International Wheat Genome Sequencing Consortium (IQGSC). Shifting the limits in wheat research and breeding using a fully annotated reference genome. Science. 2018;361(6403):eaar7191. DOI 10.1126/science.aar7191.Jaillon O., Aury J.M., Noel B., PolicritiA., Clepet C., CasagrandeA., … Weissenbach J., Quétier F., Wincker P. The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla. Nature. 2007;449(7161):463-467. DOI 10.1038/nature06148.Jaillon O., Aury J.M., Noel B., PolicritiA., Clepet C., CasagrandeA., … Weissenbach J., Quétier F., Wincker P. The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla. Nature. 2007;449(7161):463-467. DOI 10.1038/nature06148.Jiao Y., Peluso P., Shi J., Liang T., Stitzer M.C., Wang B., Campbell M.S., … Hastie A., Rank D.R., Ware D. Improved maize reference genome with single-molecule technologies. Nature. 2017;546: 524-527. DOI 10.1038/nature22971.Jiao Y., Peluso P., Shi J., Liang T., Stitzer M.C., Wang B., Campbell M.S., … Hastie A., Rank D.R., Ware D. Improved maize reference genome with single-molecule technologies. Nature. 2017;546: 524-527. DOI 10.1038/nature22971.Jupe F., Witek K., Verweij W., Sliwka J., Pritchard L., Etherington G.J., Maclean D., Cock P.J., Leggett R.M., Bryan G.J., Cardle L., Hein I., Jones J.D. Resistance gene enrichment sequencing (RenSeq) enables reannotation of the NB-LRR gene family from sequenced plant genomes and rapid mapping of resistance loci in segregating populations. Plant J. 2013;76(3):530-544. DOI 10.1111/tpj.12307.Jupe F., Witek K., Verweij W., Sliwka J., Pritchard L., Etherington G.J., Maclean D., Cock P.J., Leggett R.M., Bryan G.J., Cardle L., Hein I., Jones J.D. Resistance gene enrichment sequencing (RenSeq) enables reannotation of the NB-LRR gene family from sequenced plant genomes and rapid mapping of resistance loci in segregating populations. Plant J. 2013;76(3):530-544. DOI 10.1111/tpj.12307.Kol G. The next revolution in genomics: exploring complex genome assembly to pan-genome interconnection. Proc. of the Plant & Animal Genome Conference XXIV. 2016;W3289.Kol G. The next revolution in genomics: exploring complex genome assembly to pan-genome interconnection. Proc. of the Plant & Animal Genome Conference XXIV. 2016;W3289.Krasnov Y.M., Guseva N.P., Sharapova N.A., Cherkasov A.V. Modern methods of DNA sequencing (scientific review). Problemy Osobo Opasnykh Infektsiy = Problems of Particularly Dangerous Infections. 2014;2:73-79. DOI 10.21055/0370-1069-2014-2-73-79. (in Russian)Krasnov Y.M., Guseva N.P., Sharapova N.A., Cherkasov A.V. Modern methods of DNA sequencing (scientific review). Problemy Osobo Opasnykh Infektsiy = Problems of Particularly Dangerous Infections. 2014;2:73-79. DOI 10.21055/0370-1069-2014-2-73-79. (in Russian)Li F., Fan G., Lu C., Xiao G., Zou C., Kohel R.J., Ma Z., … Yu J.Z., Zhu Y., Yu S. Genome sequence of cultivated Upland cotton (Gossypium hirsutum TM-1) provides insights into genome evolution. Nat. Biotechnol. 2015;33:524-530. DOI 10.1038/nbt.3208.Li F., Fan G., Lu C., Xiao G., Zou C., Kohel R.J., Ma Z., … Yu J.Z., Zhu Y., Yu S. Genome sequence of cultivated Upland cotton (Gossypium hirsutum TM-1) provides insights into genome evolution. Nat. Biotechnol. 2015;33:524-530. DOI 10.1038/nbt.3208.Li Y., Ruperao P., Batley J., Edwards D., Khan T., Colmer T.D., Pang J., Siddique K.H.M., Sutton T. Investigating drought tolerance in chickpea using genome-wide association mapping and genomic selection based on whole-genome resequencing data. Front. Plant Sci. 2018;9:190. DOI 10.3389/fpls.2018.00190.Li Y., Ruperao P., Batley J., Edwards D., Khan T., Colmer T.D., Pang J., Siddique K.H.M., Sutton T. Investigating drought tolerance in chickpea using genome-wide association mapping and genomic selection based on whole-genome resequencing data. Front. Plant Sci. 2018;9:190. DOI 10.3389/fpls.2018.00190.Luo M.-C., Gu Y.Q., Puiu D., Wang H., Twardziok S.O., Deal K.R., Huo N., … Salzberg S.L., Devos K.M., Dvořák J. Genome sequence of the progenitor of the wheat D genome Aegilops tauschii. Nature. 2017;551:498-502. DOI 10.1038/nature24486.Luo M.-C., Gu Y.Q., Puiu D., Wang H., Twardziok S.O., Deal K.R., Huo N., … Salzberg S.L., Devos K.M., Dvořák J. Genome sequence of the progenitor of the wheat D genome Aegilops tauschii. Nature. 2017;551:498-502. DOI 10.1038/nature24486.Mardis E.R. DNA sequencing technologies: 2006–2016. Nat. Protoc. 2017;12(2):213-218. DOI 10.1038/nprot.2016.182.Mardis E.R. DNA sequencing technologies: 2006–2016. Nat. Protoc. 2017;12(2):213-218. DOI 10.1038/nprot.2016.182.Mascher M., Richmond T.A., Gerhardt D.J., Himmelbach A., Clissold L., Sampath D., Ayling S., Steuernagel B., Pfeifer M., D’Ascenzo M., Akhunov E.D., Hedley P.E., Gonzales A.M., Mor¬ rell P.L., Kilian B., Blattner F.R., Scholz U., Mayer K.F.X., Flavell A.J., Muehlbauer G.J., Waugh R., Jeddeloh J.A., Stein N. Barley whole exome capture: a tool for genomic research in the genus Hordeum and beyond. Plant J. 2013;76(3):494-505. DOI 10.1111/tpj.12294.Mascher M., Richmond T.A., Gerhardt D.J., Himmelbach A., Clissold L., Sampath D., Ayling S., Steuernagel B., Pfeifer M., D’Ascenzo M., Akhunov E.D., Hedley P.E., Gonzales A.M., Mor¬ rell P.L., Kilian B., Blattner F.R., Scholz U., Mayer K.F.X., Flavell A.J., Muehlbauer G.J., Waugh R., Jeddeloh J.A., Stein N. Barley whole exome capture: a tool for genomic research in the genus Hordeum and beyond. Plant J. 2013;76(3):494-505. DOI 10.1111/tpj.12294.Matasci N., Hung L.-H., Yan Z., Carpenter E.J., Wickett N.J., Mirarab S., Nguyen N., … Wang J., Leebens-Mack J., Wong G.K.-S. Data access for the 1,000 plants (1KP) project. GigaScience. 2014; 3(1):17. DOI 10.1186/2047-217X-3-17.Matasci N., Hung L.-H., Yan Z., Carpenter E.J., Wickett N.J., Mirarab S., Nguyen N., … Wang J., Leebens-Mack J., Wong G.K.-S. Data access for the 1,000 plants (1KP) project. GigaScience. 2014; 3(1):17. DOI 10.1186/2047-217X-3-17.Mayer K.F.X., Rogers J., Doležel J., Pozniak C., Eversole K., Feuillet C., Gill B., … Loaec M., Keller B., Praud S. A chromosomebased draft sequence of the hexaploid bread wheat (Triticum aestivum) genome. Nature. 2014;345(6194):1251788. DOI 10.1126/science.1251788.Mayer K.F.X., Rogers J., Doležel J., Pozniak C., Eversole K., Feuillet C., Gill B., … Loaec M., Keller B., Praud S. A chromosomebased draft sequence of the hexaploid bread wheat (Triticum aestivum) genome. Nature. 2014;345(6194):1251788. DOI 10.1126/science.1251788.Ming R., Hou S., Feng Y., Yu Q., Dionne-Laporte A., Saw J.H., Senin P., … Gonsalves D., Wang L., Alam M. The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus). Nature. 2008;452:991-996. DOI 10.1038/nature06856.Ming R., Hou S., Feng Y., Yu Q., Dionne-Laporte A., Saw J.H., Senin P., … Gonsalves D., Wang L., Alam M. The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus). Nature. 2008;452:991-996. DOI 10.1038/nature06856.Muraya M.M., Schmutzer T., Ulpinnis C., Scholz U., Altmann T. Targeted sequencing reveals large-scale sequence polymorphism in maize candidate genes for biomass production and composition. PLoS One. 2015;10(7):e0132120. DOI 0.1371/journal.pone.0132120.Muraya M.M., Schmutzer T., Ulpinnis C., Scholz U., Altmann T. Targeted sequencing reveals large-scale sequence polymorphism in maize candidate genes for biomass production and composition. PLoS One. 2015;10(7):e0132120. DOI 0.1371/journal.pone.0132120.Myburg A.A., Grattapaglia D., Tuskan G.A., Hellsten U., Hayes R.D., Grimwood J., JenkinsJ., … Van de Peer Y., Rokhsar D.S., Schmutz J. The genome of Eucalyptus grandis. Nature. 2014;510(7505):356362. DOI 10.1038/nature13308.Myburg A.A., Grattapaglia D., Tuskan G.A., Hellsten U., Hayes R.D., Grimwood J., JenkinsJ., … Van de Peer Y., Rokhsar D.S., Schmutz J. The genome of Eucalyptus grandis. Nature. 2014;510(7505):356362. DOI 10.1038/nature13308.Neves L.G., Davis J.M., Barbazuk W.B., Kirst M. Whole-exome targeted sequencing of the uncharacterized pine genome. Plant J. 2013; 75:146-156. DOI 10.1111/tpj.12193.Neves L.G., Davis J.M., Barbazuk W.B., Kirst M. Whole-exome targeted sequencing of the uncharacterized pine genome. Plant J. 2013; 75:146-156. DOI 10.1111/tpj.12193.Neves L.G., Davis J.M., Barbazuk W.B., Kirst M. A high-density gene map of loblolly pine (Pinus taeda L.) based on exome sequence capture genotyping. G3: Genes Genomes Genetics. 2014;4(1):29-37. DOI 10.1534/g3.113.008714.Neves L.G., Davis J.M., Barbazuk W.B., Kirst M. A high-density gene map of loblolly pine (Pinus taeda L.) based on exome sequence capture genotyping. G3: Genes Genomes Genetics. 2014;4(1):29-37. DOI 10.1534/g3.113.008714.Nystedt B., Street N.R., Wetterbom A., Zuccolo A., Lin Y.-C., Scofield D.G., Vezzi F., … Ingvarsson P.K., Lundeberg J., Jansson S. The Norway spruce genome sequence and conifer genome evolution. Nature. 2013;497(7451):579-584. DOI 10.1038/nature12211.Nystedt B., Street N.R., Wetterbom A., Zuccolo A., Lin Y.-C., Scofield D.G., Vezzi F., … Ingvarsson P.K., Lundeberg J., Jansson S. The Norway spruce genome sequence and conifer genome evolution. Nature. 2013;497(7451):579-584. DOI 10.1038/nature12211.O’Brien H.E., Thakur S., Guttman D.S. Evolution of plant pathogenesis in Pseudomonas syringae: A genomics perspective. Annu. Rev. Phytopathol. 2011;49(1):269-289. DOI 10.1146/annurev-phyto-072910-095242.O’Brien H.E., Thakur S., Guttman D.S. Evolution of plant pathogenesis in Pseudomonas syringae: A genomics perspective. Annu. Rev. Phytopathol. 2011;49(1):269-289. DOI 10.1146/annurev-phyto-072910-095242.PankinA., Campoli C., Dong X., Kilian B., Sharma R., HimmelbachA., Saini R., Davis S.J., Stein N., Schneeberger K., von Korff M. Mapping-by-sequencing identifies HvPHYTOCHROME C as a candidate gene for the early maturity 5 locus modulating the circadian clock and photoperiodic flowering in barley. Genetics. 2014;198(1):383396. DOI 10.1534/genetics.114.165613.PankinA., Campoli C., Dong X., Kilian B., Sharma R., HimmelbachA., Saini R., Davis S.J., Stein N., Schneeberger K., von Korff M. Mapping-by-sequencing identifies HvPHYTOCHROME C as a candidate gene for the early maturity 5 locus modulating the circadian clock and photoperiodic flowering in barley. Genetics. 2014;198(1):383396. DOI 10.1534/genetics.114.165613.Paux E., Sourdille P., Salse J., Saintenac C., Choulet F., Leroy P., Korol A., Michalak M., Kianian S., Spielmeyer W., Lagudah E., Somers D., Kilian A., Alaux M., Vautrin S., Bergès H., Eversole K., Appels R., Safar J., Simkova H., Dolezel J., Bernard M., Feuillet C. A physical map of the 1-gigabase bread wheat chromosome 3B. Science. 2008;322(5898):101-104. DOI 10.1126/science.1161847.Paux E., Sourdille P., Salse J., Saintenac C., Choulet F., Leroy P., Korol A., Michalak M., Kianian S., Spielmeyer W., Lagudah E., Somers D., Kilian A., Alaux M., Vautrin S., Bergès H., Eversole K., Appels R., Safar J., Simkova H., Dolezel J., Bernard M., Feuillet C. A physical map of the 1-gigabase bread wheat chromosome 3B. Science. 2008;322(5898):101-104. DOI 10.1126/science.1161847.Pootakham W., Shearman J.R., Ruang-areerate P., Sonthirod C., Sangsrakru D., Jomchai N., Yoocha T., Triwitayakorn K., Tragoonrung S., Tangphatsornruang S. Large-scale SNP discovery through RNA sequencing and SNP genotyping by targeted enrichment sequencing in cassava (Manihot esculenta Crantz). PLoS One. 2014; 9(12):e116028. DOI 10.1371/journal.pone.0116028.Pootakham W., Shearman J.R., Ruang-areerate P., Sonthirod C., Sangsrakru D., Jomchai N., Yoocha T., Triwitayakorn K., Tragoonrung S., Tangphatsornruang S. Large-scale SNP discovery through RNA sequencing and SNP genotyping by targeted enrichment sequencing in cassava (Manihot esculenta Crantz). PLoS One. 2014; 9(12):e116028. DOI 10.1371/journal.pone.0116028.Pucker B., Holtgräwe D., Rosleff Sörensen T., Stracke R., Viehöver P., Weisshaar B. A de novo genome sequence assembly of the Arabidopsis thaliana accession Niederzenz-1 displays presence/absence variation and strong synteny. PLoS One. 2016;11(10):e0164321. DOI 10.1371/journal.pone.0164321.Pucker B., Holtgräwe D., Rosleff Sörensen T., Stracke R., Viehöver P., Weisshaar B. A de novo genome sequence assembly of the Arabidopsis thaliana accession Niederzenz-1 displays presence/absence variation and strong synteny. PLoS One. 2016;11(10):e0164321. DOI 10.1371/journal.pone.0164321.Rensing S.A., Lang D., Zimmer A.D., Terry A., Salamov A., Shapiro H., Nishiyama T., … Grigoriev I.V., Quatrano R.S., Boore J.L. The Physcomitrella genome reveals evolutionary insights into the conquest of land by plants. Science. 2008;319(5859):64-69. DOI 10.1126/science.1150646.Rensing S.A., Lang D., Zimmer A.D., Terry A., Salamov A., Shapiro H., Nishiyama T., … Grigoriev I.V., Quatrano R.S., Boore J.L. The Physcomitrella genome reveals evolutionary insights into the conquest of land by plants. Science. 2008;319(5859):64-69. DOI 10.1126/science.1150646.Russell J., Mascher M., Dawson I.K., Kyriakidis S., Calixto C., Freund F., Bayer M., … Muehlbauer G.J., Stein N., Waugh R. Exome sequencing of geographically diverse barley landraces and wild relatives gives insights into environmental adaptation. Nat. Genet. 2016;48(9):1024-1030. DOI 10.1038/ng.3612.Russell J., Mascher M., Dawson I.K., Kyriakidis S., Calixto C., Freund F., Bayer M., … Muehlbauer G.J., Stein N., Waugh R. Exome sequencing of geographically diverse barley landraces and wild relatives gives insights into environmental adaptation. Nat. Genet. 2016;48(9):1024-1030. DOI 10.1038/ng.3612.Saintenac C., Jiang D., Akhunov E.D. Targeted analysis of nucleotide and copy number variation by exon capture in allotetraploid wheat genome. Genome Biol. 2011;12(9):R88. DOI 10.1186/gb-2011-129-r88.Saintenac C., Jiang D., Akhunov E.D. Targeted analysis of nucleotide and copy number variation by exon capture in allotetraploid wheat genome. Genome Biol. 2011;12(9):R88. DOI 10.1186/gb-2011-129-r88.Salmon A., Udall J., Jeddeloh J., Wendel J. Targeted capture of homoeologous coding and noncoding sequence in polyploid cotton. G3: Genes Genomes Genetics. 2012;2(8):921-930. DOI 10.1534/g3.112.003392.Salmon A., Udall J., Jeddeloh J., Wendel J. Targeted capture of homoeologous coding and noncoding sequence in polyploid cotton. G3: Genes Genomes Genetics. 2012;2(8):921-930. DOI 10.1534/g3.112.003392.Scheben A., Wolter F., Batley J., Puchta H., Edwards D. Towards CRISPR/Cas crops – bringing together genomics and genome editing. New Phytologist. 2017;216(3):682-698. DOI 10.1111/nph.14702.Scheben A., Wolter F., Batley J., Puchta H., Edwards D. Towards CRISPR/Cas crops – bringing together genomics and genome editing. New Phytologist. 2017;216(3):682-698. DOI 10.1111/nph.14702.Schiessl S., Samans B., Hüttel B., Reinhard R., Snowdon R.J. Capturing sequence variation among flowering-time regulatory gene homologs in the allopolyploid crop species Brassica napus. Front. Plant Sci. 2014;5:404. DOI 10.3389/fpls.2014.00404.Schiessl S., Samans B., Hüttel B., Reinhard R., Snowdon R.J. Capturing sequence variation among flowering-time regulatory gene homologs in the allopolyploid crop species Brassica napus. Front. Plant Sci. 2014;5:404. DOI 10.3389/fpls.2014.00404.Schmutz J., Cannon S.B., Schlueter J., Ma J., Mitros T., Nelson W., Hyten D.L., … Stacey G., Shoemaker R.C., Jackson S.A. Genome sequence of the palaeopolyploid soybean. Nature. 2010;463:178183. DOI 10.1038/nature08670.Schmutz J., Cannon S.B., Schlueter J., Ma J., Mitros T., Nelson W., Hyten D.L., … Stacey G., Shoemaker R.C., Jackson S.A. Genome sequence of the palaeopolyploid soybean. Nature. 2010;463:178183. DOI 10.1038/nature08670.Schnable P.S., Ware D., Fulton R.S., Stein J.C., Wei F., Pasternak S., Liang C., … McCombie W.R., Wing R.A., Wilson R.K. The B73 maize genome: complexity, diversity, and dynamics. Science. 2009; 326(5956):1112-1115. DOI 10.1126/science.1178534.Schnable P.S., Ware D., Fulton R.S., Stein J.C., Wei F., Pasternak S., Liang C., … McCombie W.R., Wing R.A., Wilson R.K. The B73 maize genome: complexity, diversity, and dynamics. Science. 2009; 326(5956):1112-1115. DOI 10.1126/science.1178534.Schneeberger K. Using next-generation sequencing to isolate mutant genes from forward genetic screens. Nat. Rev. Genet. 2014; 15(10):662-676. DOI 10.1038/nrg3745.Schneeberger K. Using next-generation sequencing to isolate mutant genes from forward genetic screens. Nat. Rev. Genet. 2014; 15(10):662-676. DOI 10.1038/nrg3745.Shendure J., Balasubramanian S., Church G.M., Gilbert W., Rogers J., Schloss J.A., Waterston R.H. DNA sequencing at 40: Past, present and future. Nature. 2017;550(7676):345-353. DOI 10.1038/nature24286.Shendure J., Balasubramanian S., Church G.M., Gilbert W., Rogers J., Schloss J.A., Waterston R.H. DNA sequencing at 40: Past, present and future. Nature. 2017;550(7676):345-353. DOI 10.1038/nature24286.Sierro N., Battey J.N.D., Ouadi S., Bakaher N., Bovet L., Willig A., Goepfert S., Peitsch M.C., Ivanov N.V. The tobacco genome sequence and its comparison with those of tomato and potato. Nat. Commun. 2014;5(1):3833. DOI 10.1038/ncomms4833.Sierro N., Battey J.N.D., Ouadi S., Bakaher N., Bovet L., Willig A., Goepfert S., Peitsch M.C., Ivanov N.V. The tobacco genome sequence and its comparison with those of tomato and potato. Nat. Commun. 2014;5(1):3833. DOI 10.1038/ncomms4833.Springer N.M., Anderson S.N., Andorf C.M., Ahern K.R., Bai F., Barad O., Barbazuk W.B., … Woodhouse M.R., Xiong W., Brutnell T.P. The maize W22 genome provides a foundation for functional genomics and transposon biology. Nat. Genet. 2018;50(9):12821288. DOI 10.1038/s41588-018-0158-0.Springer N.M., Anderson S.N., Andorf C.M., Ahern K.R., Bai F., Barad O., Barbazuk W.B., … Woodhouse M.R., Xiong W., Brutnell T.P. The maize W22 genome provides a foundation for functional genomics and transposon biology. Nat. Genet. 2018;50(9):12821288. DOI 10.1038/s41588-018-0158-0.Stull G.W., Moore M.J., Mandala V.S., Douglas N.A., Kates H.-R., Qi X., Brockington S.F., Soltis P.S., Soltis D.E., Gitzendanner M.A. A targeted enrichment strategy for massively parallel sequencing of angiosperm plastid genomes. Appl. Plant Sci. 2013;1(2):1200497. DOI 10.3732/apps.1200497.Stull G.W., Moore M.J., Mandala V.S., Douglas N.A., Kates H.-R., Qi X., Brockington S.F., Soltis P.S., Soltis D.E., Gitzendanner M.A. A targeted enrichment strategy for massively parallel sequencing of angiosperm plastid genomes. Appl. Plant Sci. 2013;1(2):1200497. DOI 10.3732/apps.1200497.Tennessen J.A., Govindarajulu R., Liston A., Ashman T.-L. Targeted sequence capture provides insight into genome structure and genetics of male sterility in a gynodioecious diploid strawberry, Fragaria vesca ssp. bracteata (Rosaceae). G3: Genes Genomes Genetics. 2013;3:1341-1351. DOI 10.1534/g3.113.006288.Tennessen J.A., Govindarajulu R., Liston A., Ashman T.-L. Targeted sequence capture provides insight into genome structure and genetics of male sterility in a gynodioecious diploid strawberry, Fragaria vesca ssp. bracteata (Rosaceae). G3: Genes Genomes Genetics. 2013;3:1341-1351. DOI 10.1534/g3.113.006288.Terracciano I., Cantarella C., D’Agostino N. Hybridization-Based Enrichment and Next Generation Sequencing to Explore Genetic Diversity in Plants. In: Rogato A., Zazzu V., Guarracino M. (Eds.). Dynamics of Mathematical Models in Biology. Springer, Cham., 2016. DOI 10.1007/978-3-319-45723-9_10.Terracciano I., Cantarella C., D’Agostino N. Hybridization-Based Enrichment and Next Generation Sequencing to Explore Genetic Diversity in Plants. In: Rogato A., Zazzu V., Guarracino M. (Eds.). Dynamics of Mathematical Models in Biology. Springer, Cham., 2016. DOI 10.1007/978-3-319-45723-9_10.The 1001 Genomes Consortium. 1,135 genomes reveal the global pattern of polymorphism in Arabidopsis thaliana. Cell. 2016;166(2):481491. DOI 10.1016/j.cell.2016.05.063.The 1001 Genomes Consortium. 1,135 genomes reveal the global pattern of polymorphism in Arabidopsis thaliana. Cell. 2016;166(2):481491. DOI 10.1016/j.cell.2016.05.063.The 3,000 rice genomes project. The 3,000 Rice Genomes Project. GigaScience. 2014;3(1):7. DOI 10.1186/2047-217X-3-7.The 3,000 rice genomes project. The 3,000 Rice Genomes Project. GigaScience. 2014;3(1):7. DOI 10.1186/2047-217X-3-7.The Arabidopsis Genome Initiative. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature. 2000;408:796815. DOI 10.1038/35048692.The Arabidopsis Genome Initiative. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature. 2000;408:796815. DOI 10.1038/35048692.The International Barley Genome Sequencing Consortium. A physical, genetic and functional sequence assembly of the barley genome. Nature. 2012;491(7426):711-716. DOI 10.1038/nature11543.The International Barley Genome Sequencing Consortium. A physical, genetic and functional sequence assembly of the barley genome. Nature. 2012;491(7426):711-716. DOI 10.1038/nature11543.The International Brachypodium Initiative. Genome sequencing and analysis of the model grass Brachypodium distachyon. Nature. 2010; 463(7282):763-768. DOI 10.1038/nature08747.The International Brachypodium Initiative. Genome sequencing and analysis of the model grass Brachypodium distachyon. Nature. 2010; 463(7282):763-768. DOI 10.1038/nature08747.The Potato Genome Sequencing Consortium. Genome sequence and analysis of the tuber crop potato. Nature. 2011;475:189-195. DOI 10.1038/nature10158.The Potato Genome Sequencing Consortium. Genome sequence and analysis of the tuber crop potato. Nature. 2011;475:189-195. DOI 10.1038/nature10158.The Tomato Genome Consortium. The tomato genome sequence provides insights into fleshy fruit evolution. Nature. 2012;485:635-641. DOI 10.1038/nature11119.The Tomato Genome Consortium. The tomato genome sequence provides insights into fleshy fruit evolution. Nature. 2012;485:635-641. DOI 10.1038/nature11119.Tuskan G.A., DiFazio S., Jansson S., Bohlmann J., Grigoriev I., Hellsten U., Putnam N., … Sandberg G., Van de Peer Y., Rokhsar D. The genome of black cottonwood, Populus trichocarpa (Torr. & Gray). Science. 2006;313(5793):1596-1604. DOI 10.1126/science.1128691.Tuskan G.A., DiFazio S., Jansson S., Bohlmann J., Grigoriev I., Hellsten U., Putnam N., … Sandberg G., Van de Peer Y., Rokhsar D. The genome of black cottonwood, Populus trichocarpa (Torr. & Gray). Science. 2006;313(5793):1596-1604. DOI 10.1126/science.1128691.Uitdewilligen J.G.A.M.L., WoltersA.-M.A., D’hoop B.B., Borm T.J.A., Visser R.G.F., van Eck H.J. A next-generation sequencing method for genotyping-by-sequencing of highly heterozygous autotetraploid potato. PLoS One. 2013;8(5):e62355. DOI 10.1371/journal.pone.0062355.Uitdewilligen J.G.A.M.L., WoltersA.-M.A., D’hoop B.B., Borm T.J.A., Visser R.G.F., van Eck H.J. A next-generation sequencing method for genotyping-by-sequencing of highly heterozygous autotetraploid potato. PLoS One. 2013;8(5):e62355. DOI 10.1371/journal.pone.0062355.Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., Kalyanaraman A., Fontana P., … Van de Peer Y., Salamini F., Viola R. The genome of the domesticated apple (Malus×domestica Borkh.). Nat. Genet. 2010;42:833-839. DOI 10.1038/ng.654.Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., Kalyanaraman A., Fontana P., … Van de Peer Y., Salamini F., Viola R. The genome of the domesticated apple (Malus×domestica Borkh.). Nat. Genet. 2010;42:833-839. DOI 10.1038/ng.654.Venu R.C., Zhang Y., Weaver B., Carswell P., Mitchell T.K., Meyers B.C., Boehm M.J., Wang G.-L. Large Scale Identification of Genes Involved in Plant–Fungal Interactions Using Illumina’s Sequencing-by-Synthesis Technology. In: Xu J.-R., Bluhm B.H. (Eds.). Fungal Genomics: Methods and Protocols. Springer, 2011;167-178. DOI 10.1007/978-1-61779-040-9_12.Venu R.C., Zhang Y., Weaver B., Carswell P., Mitchell T.K., Meyers B.C., Boehm M.J., Wang G.-L. Large Scale Identification of Genes Involved in Plant–Fungal Interactions Using Illumina’s Sequencing-by-Synthesis Technology. In: Xu J.-R., Bluhm B.H. (Eds.). Fungal Genomics: Methods and Protocols. Springer, 2011;167-178. DOI 10.1007/978-1-61779-040-9_12.WarrA., Robert C., Hume D., ArchibaldA., Deeb N., Watson M. Exome sequencing: Current and future perspectives. G3: Genes Genomes Genetics. 2013;5(8):1543-1550. DOI 10.1534/g3.115.018564.WarrA., Robert C., Hume D., ArchibaldA., Deeb N., Watson M. Exome sequencing: Current and future perspectives. G3: Genes Genomes Genetics. 2013;5(8):1543-1550. DOI 10.1534/g3.115.018564.Wendler N., Mascher M., Nöh C., Himmelbach A., Scholz U., RugeWehling B., Stein N. Unlocking the secondary gene-pool of barley with next-generation sequencing. Plant Biotechnol. J. 2014;12:11221131. DOI 10.1111/pbi.12219.Wendler N., Mascher M., Nöh C., Himmelbach A., Scholz U., RugeWehling B., Stein N. Unlocking the secondary gene-pool of barley with next-generation sequencing. Plant Biotechnol. J. 2014;12:11221131. DOI 10.1111/pbi.12219.Westwood J.H., dePamphilis C.W., Das M., Fernández-Aparicio M., Honaas L.A., Timko M.P., Wafula E.K., Wickett N.J., Yoder J.I. The Parasitic Plant Genome Project: New tools for understanding the biology of Orobanche and Striga. Weed Sci. 2012;60(02):295-306. DOI 10.1614/WS-D-11-00113.1.Westwood J.H., dePamphilis C.W., Das M., Fernández-Aparicio M., Honaas L.A., Timko M.P., Wafula E.K., Wickett N.J., Yoder J.I. The Parasitic Plant Genome Project: New tools for understanding the biology of Orobanche and Striga. Weed Sci. 2012;60(02):295-306. DOI 10.1614/WS-D-11-00113.1.Winfield M.O., Wilkinson P.A., Allen A.M., Barker G.L., Coghill J.A., Burridge A., Hall A., Brenchley R.C., D’Amore R., Hall N., Bevan M.W., Richmond T., Gerhardt D.J., Jeddeloh J.A., Edwards K.J. Plant Biotechnol. J. 2012;10(6):733-742. DOI 10.1111/j.1467-7652.2012.00713.x.Winfield M.O., Wilkinson P.A., Allen A.M., Barker G.L., Coghill J.A., Burridge A., Hall A., Brenchley R.C., D’Amore R., Hall N., Bevan M.W., Richmond T., Gerhardt D.J., Jeddeloh J.A., Edwards K.J. Plant Biotechnol. J. 2012;10(6):733-742. DOI 10.1111/j.1467-7652.2012.00713.x.Xu X., Pan S., Cheng S., Zhang B., Mu D., Ni P., Zhang G., … Goverse A., van Ham R.C.H.J., Visser R.G.F. (The Potato Genome Sequencing Consortium). Genome sequence and analysis of the tuber crop potato. Nature. 2011;475(7355):189-195. DOI 10.1038/nature 10158.Xu X., Pan S., Cheng S., Zhang B., Mu D., Ni P., Zhang G., … Goverse A., van Ham R.C.H.J., Visser R.G.F. (The Potato Genome Sequencing Consortium). Genome sequence and analysis of the tuber crop potato. Nature. 2011;475(7355):189-195. DOI 10.1038/nature 10158.Yu J., Hu S., Wang J., Wong G.K.-S., Li S., Liu B., Deng Y., … Zhu L., Yuan L., Yang H. A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science. 2002;296(5565):79-92. DOI 10.1126/science.1068037.Yu J., Hu S., Wang J., Wong G.K.-S., Li S., Liu B., Deng Y., … Zhu L., Yuan L., Yang H. A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science. 2002;296(5565):79-92. DOI 10.1126/science.1068037.Zhang H., Scheuring C., Zhang M., Zhang Y., Wu C., Dong J., Li Y. Construction of BIBAC and BAC libraries from a variety of organisms for advanced genomics research. Nat. Protoc. 2012;7(3):479499. DOI 10.1038/nprot.2011.456.Zhang H., Scheuring C., Zhang M., Zhang Y., Wu C., Dong J., Li Y. Construction of BIBAC and BAC libraries from a variety of organisms for advanced genomics research. Nat. Protoc. 2012;7(3):479499. DOI 10.1038/nprot.2011.456.Zhang J., Zhang Y., Du Y., Chen S., Tang H. Dynamic metabonomic responses of tobacco (Nicotiana tabacum) plants to salt stress. J. Proteome Res. 2011;10(4):1904-1914. DOI 10.1021/pr101140n.Zhang J., Zhang Y., Du Y., Chen S., Tang H. Dynamic metabonomic responses of tobacco (Nicotiana tabacum) plants to salt stress. J. Proteome Res. 2011;10(4):1904-1914. DOI 10.1021/pr101140n.Zhou G., Chen Y., Yao W., Zhang C., Xie W., Hua J., Xing Y., Xiao J., Zhang Q. Genetic composition of yield heterosis in an elite rice hybrid. Proc. Natl. Acad. Sci. USA. 2012; 109(39):15847-15852. DOI 10.1073/pnas.1214141109.Zhou G., Chen Y., Yao W., Zhang C., Xie W., Hua J., Xing Y., Xiao J., Zhang Q. Genetic composition of yield heterosis in an elite rice hybrid. Proc. Natl. Acad. Sci. USA. 2012; 109(39):15847-15852. DOI 10.1073/pnas.1214141109.Zhu C., Bortesi L., Baysal C., Twyman R. M., Fischer R., Capell T., Schillberg S., Christou P. Characteristics of genome editing mutations in cereal crops. Trends Plant Sci. 2017; 22(1):38-52. DOI 10.1016/j.tplants.2016.08.009.Zhu C., Bortesi L., Baysal C., Twyman R. M., Fischer R., Capell T., Schillberg S., Christou P. Characteristics of genome editing mutations in cereal crops. Trends Plant Sci. 2017; 22(1):38-52. DOI 10.1016/j.tplants.2016.08.009.

The authors declare that there are no conflicts of interest present.