Effects of genome structure variation, homeologous genes and repetitive DNA on polyploid crop research in the age of genomics

Plant Science

Volumn 242, Issue , 2016, Pages 37-46

  Fu, Donghui ^a   Mason, Annaliese S ^b   Xiao, Meili ^a   Yan, Hui ^a  

^a JIANGXI AGRICULTURAL UNIVERSITY   (China)

^b JUSTUS LIEBIG UNIVERSITY   (Germany)

Author keywords

Genomic variations; Homoeologous sequences; Polyploids; Repetitive DNA sequences; Transposons

Indexed keywords

CHROMOSOMAL MAPPING; CLASSIFICATION; CROP; GENE EXPRESSION REGULATION; GENETIC VARIATION; GENETICS; GENOMICS; HIGH THROUGHPUT SEQUENCING; NUCLEOTIDE REPEAT; PLANT GENOME; POLYPLOIDY; PROCEDURES; QUANTITATIVE TRAIT LOCUS;

CHROMOSOME MAPPING; CROPS, AGRICULTURAL; GENE EXPRESSION REGULATION, PLANT; GENETIC VARIATION; GENOME, PLANT; GENOMICS; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; POLYPLOIDY; QUANTITATIVE TRAIT LOCI; REPETITIVE SEQUENCES, NUCLEIC ACID;

EID: 84947029258     PISSN: 01689452     EISSN: 18732259     Source Type: Journal    
DOI: 10.1016/j.plantsci.2015.09.017     Document Type: Article

References (107)

1. Jiao Y.N., Wickett N.J., Ayyampalayam S., Chanderbali A.S., Landherr L., Ralph P.E., Tomsho L.P., Hu Y., Liang H.Y., Soltis P.S., Soltis D.E., Clifton S.W., Schlarbaum S.E., Schuster S.C., Ma H., Leebens-Mack J., dePamphilis C.W. Ancestral polyploidy in seed plants and angiosperms. Nature 2011, 473:97-100.
2. Chalhoub B., Denoeud F., Liu S., Parkin I.A., Tang H., Wang X., Chiquet J., Belcram H., Tong C., Samans B., Correa M., Da Silva C., Just J., Falentin C., Koh C.S., Le Clainche I., Bernard M., Bento P., Noel B., Labadie K., Alberti A., Charles M., Arnaud D., Guo H., Daviaud C., Alamery S., Jabbari K., Zhao M., Edger P.P., Chelaifa H., Tack D., Lassalle G., Mestiri I., Schnel N., Le Paslier M.C., Fan G., Renault V., Bayer P.E., Golicz A.A., Manoli S., Lee T.H., Thi V.H., Chalabi S., Hu Q., Fan C., Tollenaere R., Lu Y., Battail C., Shen J., Sidebottom C.H., Wang X., Canaguier A., Chauveau A., Berard A., Deniot G., Guan M., Liu Z., Sun F., Lim Y.P., Lyons E., Town C.D., Bancroft I., Wang X., Meng J., Ma J., Pires J.C., King G.J., Brunel D., Delourme R., Renard M., Aury J.M., Adams K.L., Batley J., Snowdon R.J., Tost J., Edwards D., Zhou Y., Hua W., Sharpe A.G., Paterson A.H., Guan C., Wincker P. Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome. Science 2014, 345:950-953.
3. Nagaharu U. Genome analysis in Brassica with special reference to the experimental formation of B. napus and peculiar mode of fertilization. Japan J. Bot. 1935, 7:389-452.
4. Xu X., Pan S., Cheng S., Zhang B., Mu D., Ni P., Zhang G., Yang S., Li R., Wang J., Orjeda G., Guzman F., Torres M., Lozano R., Ponce O., Martinez D., De la Cruz G., Chakrabarti S.K., Patil V.U., Skryabin K.G., Kuznetsov B.B., Ravin N.V., Kolganova T.V., Beletsky A.V., Mardanov A.V., Di Genova A., Bolser D.M., Martin D.M., Li G., Yang Y., Kuang H., Hu Q., Xiong X., Bishop G.J., Sagredo B., Mejia N., Zagorski W., Gromadka R., Gawor J., Szczesny P., Huang S., Zhang Z., Liang C., He J., Li Y., He Y., Xu J., Zhang Y., Xie B., Du Y., Qu D., Bonierbale M., Ghislain M., Herrera Mdel R., Giuliano G., Pietrella M., Perrotta G., Facella P., O'Brien K., Feingold S.E., Barreiro L.E., Massa G.A., Diambra L., Whitty B.R., Vaillancourt B., Lin H., Massa A.N., Geoffroy M., Lundback S., DellaPenna D., Buell C.R., Sharma S.K., Marshall D.F., Waugh R., Bryan G.J., Destefanis M., Nagy I., Milbourne D., Thomson S.J., Fiers M., Jacobs J.M., Nielsen K.L., Sonderkaer M., Iovene M., Torres G.A., Jiang J., Veilleux R.E., Bachem C.W., de Boer J., Borm T., Kloosterman B., van Eck H., Datema E., Hekkert B., Goverse A., van Ham R.C., Visser R.G. Genome sequence and analysis of the tuber crop potato. Nature 2011, 475:189-195.
5. Tayale A., Parisod C. Natural pathways to polyploidy in plants and consequences for genome reorganization. Cytogenet. Genome Res. 2013, 140:79-96.
6. Soltis D.E., Albert V.A., Leebens-Mack J., Bell C.D., Paterson A.H., Zheng C., Sankoff D., dePamphilis C.W., Wall P.K., Soltis P.S. Polyploidy and angiosperm diversification. Am. J. Bot. 2009, 96:336-348.
7. Mandakova T.S., Joly M., Krzywinski K., Mummenhoff Lysak M.A. Fast diploidization in close mesopolyploid relatives of Arabidopsis. Plant Cell 2010, 22:2277-2290.
8. Parkin I.A., Koh C., Tang H., Robinson S.J., Kagale S., Clarke W.E., Town C.D., Nixon J., Krishnakumar V., Bidwell S.L., Denoeud F., Belcram H., Links M.G., Just J., Clarke C., Bender T., Huebert T., Mason A.S., Pires J.C., Barker G., Moore J., Walley P.G., Manoli S., Batley J., Edwards D., Nelson M.N., Wang X., Paterson A.H., King G., Bancroft I., Chalhoub B., Sharpe A.G. Transcriptome and methylome profiling reveals relics of genome dominance in the mesopolyploid Brassica oleracea. Genome Biol. 2014, 15:R77.
9. Wang X.W., Wang H.Z., Wang J., Sun R.F., Wu J., Liu S.Y., Bai Y.Q., Mun J.H., Bancroft I., Cheng F., Huang S.W., Li X.X., Hua W., Wang J.Y., Wang X.Y., Freeling M., Pires J.C., Paterson A.H., Chalhoub B., Wang B., Hayward A., Sharpe A.G., Park B.S., Weisshaar B., Liu B.H., Li B., Liu B., Tong C.B., Song C., Duran C., Peng C.F., Geng C.Y., Koh C.S., Lin C.Y., Edwards D., Mu D.S., Shen D., Soumpourou E., Li F., Fraser F., Conant G., Lassalle G., King G.J., Bonnema G., Tang H.B., Wang H.P., Belcram H., Zhou H.L., Hirakawa H., Abe H., Guo H., Wang H., Jin H.Z., Parkin I.A.P., Batley J., Kim J.S., Just J., Li J.W., Xu J.H., Deng J., Kim J.A., Li J.P., Yu J.Y., Meng J.L., Wang J.P., Min J.M., Poulain J., Wang J., Hatakeyama K., Wu K., Wang L., Fang L., Trick M., Links M.G., Zhao M.X., Jin M.N., Ramchiary N., Drou N., Berkman P.J., Cai Q.L., Huang Q.F., Li R.Q., Tabata S., Cheng S.F., Zhang S., Zhang S.J., Huang S.M., Sato S., Sun S.L., Kwon S.J., Choi S.R., Lee T.H., Fan W., Zhao X., Tan X., Xu X., Wang Y., Qiu Y., Yin Y., Li Y.R., Li Y.R., Du Y.C., Liao Y., Lim Y., Narusaka Y., Wang Y.P., Wang Z.Y., Li Z.Y., Wang Z.W., Xiong Z.Y., Zhang Z.H. The genome of the mesopolyploid crop species Brassica rapa. Nat. Genet. 2011, 43:1035-1039.
10. Paterson A.H., Wendel J.F., Gundlach H., Guo H., Jenkins J., Jin D.C., Llewellyn D., Showmaker K.C., Shu S.Q., Udall J., Yoo M.J., Byers R., Chen W., Doron-Faigenboim A., Duke M.V., Gong L., Grimwood J., Grover C., Grupp K., Hu G.J., Lee T.H., Li J.P., Lin L.F., Liu T., Marler B.S., Page J.T., Roberts A.W., Romanel E., Sanders W.S., Szadkowski E., Tan X., Tang H.B., Xu C.M., Wang J.P., Wang Z.N., Zhang D., Zhang L., Ashrafi H., Bedon F., Bowers J.E., Brubaker C.L., Chee P.W., Das S., Gingle A.R., Haigler C.H., Harker D., Hoffmann L.V., Hovav R., Jones D.C., Lemke C., Mansoor S., Rahman M.U., Rainville L.N., Rambani A., Reddy U.K., Rong J.K., Saranga Y., Scheffler B.E., Scheffler J.A., Stelly D.M., Triplett B.A., Van Deynze A., Vaslin M.F.S., Waghmare V.N., Walford S.A., Wright R.J., Zaki E.A., Zhang T.Z., Dennis E.S., Mayer K.F.X., Peterson D.G., Rokhsar D.S., Wang X.Y., Schmutz J. Repeated polyploidization of Gossypium genomes and the evolution of spinnable cotton fibres. Nature 2012, 492:423-427.
11. Yang C.W., Zhao L., Zhang H.K., Yang Z.Z., Wang H., Wen S.S., Zhang C.Y., Rustgi S., von Wettstein D., Liu B. Evolution of physiological responses to salt stress in hexaploid wheat. Proc. Natl. Acad. Sci. U. S. A. 2014, 111:11882-11887.
12. Kagale S., Robinson S.J., Nixon J., Xiao R., Huebert T., Condie J., Kessler D., Clarke W.E., Edger P.P., Links M.G., Sharpe A.G., Parkin I.A.P. Polyploid evolution of the Brassicaceae during the Cenozoic Era. Plant Cell 2014, 26:2777-2791.
13. Edwards D., Batley J., Snowdon R.J. Accessing complex crop genomes with next-generation sequencing. Theor. Appl. Genet. 2013, 126:1-11.
14. Metzker M.L. Sequencing technologies-the next generation. Nat. Rev. Genet. 2010, 11:31-46.
15. Mayer K.F.X., Rogers J., Dolezel J., Pozniak C., Eversole K., Feuillet C., Gill B., Friebe B., Lukaszewski A.J., Sourdille P., Endo T.R., Dolezel J., Kubalakova M., Cihalikova J., Dubska Z., Vrana J., Sperkova R., Simkova H., Rogers J., Febrer M., Clissold L., McLay K., Singh K., Chhuneja P., Singh N.K., Khurana J., Akhunov E., Choulet F., Sourdille P., Feuillet C., Alberti A., Barbe V., Wincker P., Kanamori H., Kobayashi F., Itoh T., Matsumoto T., Sakai H., Tanaka T., Wu J.Z., Ogihara Y., Handa H., Pozniak C., Maclachlan P.R., Sharpe A., Klassen D., Edwards D., Batley J., Olsen O.A., Sandve S.R., Lien S., Steuernagel B., Wulff B., Caccamo M., Ayling S., Ramirez-Gonzalez R.H., Clavijo B.J., Steuernagel B., Wright J., Pfeifer M., Spannagl M., Mayer K.F.X., Martis M.M., Akhunov E., Choulet F., Mayer K.F.X., Mascher M., Chapman J., Poland J.A., Scholz U., Barry K., Waugh R., Rokhsar D.S., Muehlbauer G.J., Stein N., Gundlach H., Zytnicki M., Jamilloux V., Quesneville H., Wicker T., Mayer K.F.X., Faccioli P., Colaiacovo M., Pfeifer M., Stanca A.M., Budak H., Cattivelli L., Glover N., Martis M.M., Choulet F., Feuillet C., Mayer K.F.X., Pfeifer M., Pingault L., Mayer K.F.X., Paux E., Spannagl M., Sharma S., Mayer K.F.X., Pozniak C., Appels R., Bellgard M., Chapman B., Pfeifer M., Pfeifer M., Sandve S.R., Nussbaumer T., Bader K.C., Choulet F., Feuillet C., Mayer K.F.X., Akhunov E., Paux E., Rimbert H., Wang S.C., Poland J.A., Knox R., Kilian A., Pozniak C., Alaux M., Alfama F., Couderc L., Jamilloux V., Guilhot N., Viseux C., Loaec M., Quesneville H., Rogers J., Dolezel J., Eversole K., Feuillet C., Keller B., Mayer K.F.X., Olsen O.A., Praud S. A chromosome-based draft sequence of the hexaploid bread wheat (Triticum aestivum) genome. Science 2014, 345:1251788.
16. 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, 5:3833.
17. Xu X., Pan S.K., Cheng S.F., Zhang B., Mu D.S., Ni P.X., Zhang G.Y., Yang S., Li R.Q., Wang J., Orjeda G., Guzman F., Torres M., Lozano R., Ponce O., Martinez D., De la Cruz G., Chakrabarti S.K., Patil V.U., Skryabin K.G., Kuznetsov B.B., Ravin N.V., Kolganova T.V., Beletsky A.V., Mardanov A.V., Di Genova A., Bolser D.M., Martin D.M.A., Li G.C., Yang Y., Kuang H.H., Hu Q., Xiong X.Y., Bishop G.J., Sagredo B., Mejia N., Zagorski W., Gromadka R., Gawor J., Szczesny P., Huang S.W., Zhang Z.H., Liang C.B., He J., Li Y., He Y., Xu J.F., Zhang Y.J., Xie B.Y., Du Y.C., Qu D.Y., Bonierbale M., Ghislain M., Herrera M.D., Giuliano G., Pietrella M., Perrotta G., Facella P., O'Brien K., Feingold S.E., Barreiro L.E., Massa G.A., Diambra L., Whitty B.R., Vaillancourt B., Lin H.N., Massa A., Geoffroy M., Lundback S., DellaPenna D., Buell C.R., Sharma S.K., Marshall D.F., Waugh R., Bryan G.J., Destefanis M., Nagy I., Milbourne D., Thomson S.J., Fiers M., Jacobs J.M.E., Nielsen K.L., Sonderkaer M., Iovene M., Torres G.A., Jiang J.M., Veilleux R.E., Bachem C.W.B., de Boer J., Borm T., Kloosterman B., van Eck H., Datema E., Hekkert B.T.L., Goverse A., van Ham R.C.H.J., Visser R.G.F., Consortium P.G.S. Genome sequence and analysis of the tuber crop potato. Nature 2011, 475:189-U194.
18. Chalhoub B., Denoeud F., Liu S.Y., Parkin I.A.P., Tang H.B., Wang X.Y., Chiquet J., Belcram H., Tong C.B., Samans B., Correa M., Da Silva C., Just J., Falentin C., Koh C.S., Le Clainche I., Bernard M., Bento B., Labadie K., Alberti A., Charles M., Arnaud D., Guo H., Daviaud C., Alamery S., Jabbari K., Zhao M.X., Edger P.P., Chelaifa H., Tack D., Lassalle G., Mestiri I., Schnel N., Le Paslier M.C., Fan G.Y., Renault V., Bayer P.E., Golicz A.A., Manoli S., Lee T.H., Thi V.H.D., Chalabi S., Hu Q., Fan C.C., Tollenaere R., Lu Y.H., Battail C., Shen J.X., Sidebottom C.H.D., Wang X.F., Canaguier A., Chauveau A., Berard A., Deniot G., Guan M., Liu Z.S., Sun F.M., Lim Y.P., Lyons E., Town C.D., Bancroft I., Wang X.W., Meng J.L., Ma J.X., Pires J.C., King G.J., Brunel D., Delourme R., Renard M., Aury J.M., Adams K.L., Batley J., Snowdon R.J., Tost J., Edwards D., Zhou Y.M., Hua W., Sharpe A.G., Paterson A.H., Guan C.Y., Wincker P. Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome. Science 2014, 345:950-953.
19. Leitch A.R., Leitch I.J. Genomic plasticity and the diversity of polyploid plants. Science 2008, 320:481-483.
20. McClintock B. The significance of responses of the genome to challenge. Science 1984, 226:792-801.
21. Comai L., Madlung A., Josefsson C., Tyagi A. Do the different parental 'heteromes' cause genomic shock in newly formed allopolyploids?. Philos. Trans. R. Soc. B 2003, 358:1149-1155.
22. Renny-Byfield S., Wendel J.F. Doubling down on genomes: polyploidy and crop plants American. J. Bot. 2014, 101:1711-1725.
23. Hegarty M.J., Barker G.L., Wilson I.D., Abbott R.J., Edwards K.J., Hiscock S.J. Transcriptome shock after interspecific hybridization in Senecio is ameliorated by genome duplication. Curr. Biol. 2006, 16:1652-1659.
24. Ma X.F., Gustafson J.P. Allopolyploidization-accommodated genomic sequence changes in triticale. Ann. Bot. 2008, 101:825-832.
25. Henry I.M., Dilkes B.P., Tyagi A., Gao J., Christensen B., Comai L. The BOY NAMED SUE quantitative trait locus confers increased meiotic stability to an adapted natural allopolyploid of Arabidopsis. Plant Cell 2014, 26. 10.1105/tpc.113.120626.
26. Song K.M., Lu P., Tang K.L., Osborn T.C. Rapid genome change in synthetic polyploids of Brassica and its implications for polyploid evolution. Proc. Natl. Acad. Sci. U. S. A. 1995, 92:7719-7723.
27. Szadkowski E., Eber F., Huteau V., Lodé M., Huneau C., Belcram H., Coriton O., Manzanares-Dauleux M.J., Delourme R., King G.J., Chalhoub B., Jenczewski E., Chèvre A.M. The first meiosis of resynthesized Brassica napus, a genome blender. New Phytol. 2010, 186:102-112.
28. Udall J.A., Quijada P., Osborn T.C. Detection of chromosomal rearrangements derived from homeologous recombination in four mapping populations of Brassica napus L. Genetics 2005, 169:967-979.
29. Gao C., Yin J., Mason A.S., Tang Z., Ren X., Li C., An Z., Fu D., Li J. Regularities in simple sequence repeat variations induced by a cross of resynthesized 'Brassica napus' and natural 'Brassica napus'. Plant Omics J. 2014, 7:35-46.
30. Gaeta R.T., Pires J.C. Homoelogous recombination in allopolyploids: the polyploid ratchet. New Phytol. 2010, 186:18-28.
31. Nicolas S.D., Monod H., Eber F., Chèvre A.M., Jenczewski E. Non-random distribution of extensive chromosome rearrangements in Brassica napus depends on genome organization. Plant J. 2012, 70:691-703.
32. Guo H., Wang X.Y., Gundlach H., Mayer K.F.X., Peterson D.G., Scheffler B.E., Chee P.W., Paterson A.H. Extensive and biased intergenomic nonreciprocal DNA exchanges shaped a nascent polyploid genome, Gossypium (cotton). Genetics 2014, 197:1153-U1163.
33. Madlung A., Tyagi A.P., Watson B., Jiang H.M., Kagochi T., Doerge R.W., Martienssen R., Comai L. Genomic changes in synthetic Arabidopsis polyploids. Plant J. 2005, 41:221-230.
34. Petit M., Lim K.Y., Julio E., Poncet C., de Borne F.D., Kovarik A., Leitch A.R., Grandbastien M.A., Mhiri C. Differential impact of retrotransposon populations on the genome of allotetraploid tobacco (Nicotiana tabacum). Mol. Genet. Genomics 2007, 278:1-15.
35. Kraitshtein Z., Yaakov B., Khasdan V., Kashkush K. Genetic and epigenetic dynamics of a retrotransposon after allopolyploidization of wheat. Genetics 2010, 186:801-U889.
36. Stephan W. Tandem-repetitive noncoding DNA-forms and forces. Mol. Biol. Evol. 1989, 6:198-212.
37. Mehrotra S., Goyal V. Repetitive sequences in plant nuclear DNA: types, distribution, evolution and function. Genomics Proteom. Bioinf. 2014, 12:164-171.
38. Bento M., Pereira H.S., Rocheta M., Gustafson P., Viegas W., Silva M. Polyploidization as a retraction force in plant genome evolution: sequence rearrangements in triticale. PLoS One 2008, 3.
39. Tang Z.X., Fu S.L., Ren Z.L., Zou Y.T. Rapid evolution of simple sequence repeat induced by allopolyploidization. J. Mol. Evol. 2009, 69:217-228.
40. De Storme N., Mason A.S. Plant speciation through chromosome instability and ploidy change: cellular mechanisms, molecular factors and evolutionary relevance. Curr. Plant Biol. 2014, 1:10-33.
41. Ramsey J., Schemske D.W. Neopolyploidy in flowering plants. Annu. Rev. Ecol. Syst. 2002, 33:589-639.
42. Schranz M.E., Osborn T.C. De novo variation in life-history traits and responses to growth conditions of resynthesized polyploid Brassica napus (Brassicaceae). Am. J. Bot. 2004, 91:174-183.
43. Anssour S., Krugel T., Sharbel T.F., Saluz H.P., Bonaventure G., Baldwin I.T. Phenotypic, genetic and genomic consequences of natural and synthetic polyploidization of Nicotiana attenuata and Nicotiana obtusifolia. Ann. Bot. 2009, 103:1207-1217.
44. Snowdon R. Cytogenetics and genome analysis in Brassica crops. Chromosome Res. 2007, 15:85-95.
45. Kato A., Vega J.M., Han F.P., Lamb J.C., Birchler J.A. Advances in plant chromosome identification and cytogenetic techniques. Curr. Opin. Plant Biol. 2005, 8:148-154.
46. Xiong Z.Y., Gaeta R.T., Pires J.C. Homoeologous shuffling and chromosome compensation maintain genome balance in resynthesized allopolyploid Brassica napus. Proc. Natl. Acad. Sci. U. S. A. 2011, 108:7908-7913.
47. Nagy E.D., Molnar-Lang M., Linc G., Lang L. Identification of wheat-barley translocations by sequential GISH and two-colour FISH in combination with the use of genetically mapped barley SSR markers. Genome 2002, 45:1238-1247.
48. Branton D., Deamer D.W., Marziali A., Bayley H., Benner S.A., Butler T., Di Ventra M., Garaj S., Hibbs A., Huang X.H., Jovanovich S.B., Krstic P.S., Lindsay S., Ling X.S.S., Mastrangelo C.H., Meller A., Oliver J.S., Pershin Y.V., Ramsey J.M., Riehn R., Soni G.V., Tabard-Cossa V., Wanunu M., Wiggin M., Schloss J.A. The potential and challenges of nanopore sequencing. Nat. Biotechnol. 2008, 26:1146-1153.
49. Neely R.K., Deen J., Hofkens J. Optical mapping of DNA: single-molecule-based methods for mapping genomes. Biopolymers 2011, 95:298-311.
50. S. Goodwin, J. Gurtowski, S. Ethe-Sayers, P. Deshpande, M.C. Schatz, W.R. McCombie, Oxford Nanopore sequencing and de novo assembly of a eukaryotic genome bioRxiv, Preprint; doi: (2015). http://dx.doi.org/10.1101/013490.
51. Madoui S., Engelen C., Cruaud C., Belser L., Bertrand A., Alberti A., Lemainque P. Genome assembly using nanopore-guided long and error-free DNA reads. BMC Genomics 2015, 16:237.
52. Shearer L.A., Anderson L.K., de Jong H., Smit S., Goicoechea J.L., Roe B.A., Hua A., Giovannoni J.J., Stack S.M. Fluorescence in situ hybridization and optical mapping to correct scaffold arrangement in the tomato genome. G3-Genes Genomes Genet. 2014, 4:1395-1405.
53. Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., Kalyanaraman A., Fontana P., Bhatnagar S.K., Troggio M., Pruss D., Salvi S., Pindo M., Baldi P., Castelletti S., Cavaiuolo M., Coppola G., Costa F., Cova V., Dal Ri A., Goremykin V., Komjanc M., Longhi S., Magnago P., Malacarne G., Malnoy M., Micheletti D., Moretto M., Perazzolli M., Si-Ammour A., Vezzulli S., Zini E., Eldredge G., Fitzgerald L.M., Gutin N., Lanchbury J., Macalma T., Mitchell J.T., Reid J., Wardell B., Kodira C., Chen Z., Desany B., Niazi F., Palmer M., Koepke T., Jiwan D., Schaeffer S., Krishnan V., Wu C., Chu V.T., King S.T., Vick J., Tao Q., Mraz A., Stormo A., Stormo K., Bogden R., Ederle D., Stella A., Vecchietti A., Kater M.M., Masiero S., Lasserre P., Lespinasse Y., Allan A.C., Bus V., Chagne D., Crowhurst R.N., Gleave A.P., Lavezzo E., Fawcett J.A., Proost S., Rouze P., Sterck L., Toppo S., Lazzari B., Hellens R.P., Durel C.E., Gutin A., Bumgarner R.E., Gardiner S.E., Skolnick M., Egholm M., Van de Peer Y., Salamini F., Viola R. The genome of the domesticated apple (Malus×domestica Borkh.). Nat. Genet. 2010, 42:833.
54. Schmutz J., Cannon S.B., Schlueter J., Ma J.X., Mitros T., Nelson W., Hyten D.L., Song Q.J., Thelen J.J., Cheng J.L., Xu D., Hellsten U., May G.D., Yu Y., Sakurai T., Umezawa T., Bhattacharyya M.K., Sandhu D., Valliyodan B., Lindquist E., Peto M., Grant D., Shu S.Q., Goodstein D., Barry K., Futrell-Griggs M., Abernathy B., Du J.C., Tian Z.X., Zhu L.C., Gill N., Joshi T., Libault M., Sethuraman A., Zhang X.C., Shinozaki K., Nguyen H.T., Wing R.A., Cregan P., Specht J., Grimwood J., Rokhsar D., Stacey G., Shoemaker R.C., Jackson S.A. Genome sequence of the palaeopolyploid soybean. Nature 2010, 463:178-183.
55. Jenczewski E., Alix K. From diploids to allopolyploids: the emergence of efficient pairing control genes in plants. Crit. Rev. Plant Sci. 2004, 23:21-45.
56. Doyle J.J., Flagel L.E., Paterson A.H., Rapp R.A., Soltis D.E., Soltis P.S., Wendel J.F. Evolutionary genetics of genome merger and doubling in plants. Annu. Rev. Genet. 2008, 42:443-461.
57. Hollister J.D., Arnold B.J., Svedin E., Xue K.S., Dilkes B.P., Bomblies K. Genetic adaptation associated with genome-doubling in autotetraploid Arabidopsis arenosa. PLoS Genet. 2012, 8:e1003093.
58. Schnable J.C., Springer N.M., Freeling M. Differentiation of the maize subgenomes by genome dominance and both ancient and ongoing gene loss. Proc. Natl. Acad. Sci. U. S. A. 2011, 108:4069-4074.
59. Cheng F., Wu J., Fang L., Sun S.L., Liu B., Lin K., Bonnema G., Wang X.W. Biased gene fractionation and dominant gene expression among the subgenomes of Brassica rapa. PLoS One 2012, 7:e36442.
60. Li W.H., Gojobori T., Nei M. Pseudogenes as a paradigm of neutral evolution. Nature 1981, 292:237-239.
61. Sato S., Tabata S., Hirakawa H., Asamizu E., Shirasawa K., Isobe S., Kaneko T., Nakamura Y., Shibata D., Aoki K., Egholm M., Knight J., Bogden R., Li C.B., Shuang Y., Xu X., Pan S.K., Cheng S.F., Liu X., Ren Y.Y., Wang J., Albiero A., Dal Pero F., Todesco S., Van Eck J., Buels R.M., Bombarely A., Gosselin J.R., Huang M.Y., Leto J.A., Menda N., Strickler S., Mao L.Y., Gao S., Tecle I.Y., York T., Zheng Y., Vrebalov J.T., Lee J., Zhong S.L., Mueller L.A., Stiekema W.J., Ribeca P., Alioto T., Yang W.C., Huang S.W., Du Y.C., Zhang Z.H., Gao J.C., Guo Y.M., Wang X.X., Li Y., He J., Li C.Y., Cheng Z.K., Zuo J.R., Ren J.F., Zhao J.H., Yan L.H., Jiang H.L., Wang B., Li H.S., Li Z.J., Fu F.Y., Chen B.T., Han B., Feng Q., Fan D.L., Wang Y., Ling H.Q., Xue Y.B.A., Ware D., McCombie W.R., Lippman Z.B., Chia J.M., Jiang K., Pasternak S., Gelley L., Kramer M., Anderson L.K., Chang S.B., Royer S.M., Shearer L.A., Stack S.M., Rose J.K.C., Xu Y.M., Eannetta N., Matas A.J., McQuinn R., Tanksley S.D., Camara F., Guigo R., Rombauts S., Fawcett J., Van de Peer Y., Zamir D., Liang C.B., Spannagl M., Gundlach H., Bruggmann R., Mayer K., Jia Z.Q., Zhang J.H., Ye Z.B.A., Bishop G.J., Butcher S., Lopez-Cobollo R., Buchan D., Filippis I., Abbott J., Dixit R., Singh M., Singh A., Pal J.K., Pandit A., Singh P.K., Mahato A.K., Dogra V., Gaikwad K., Sharma T.R., Mohapatra T., Singh N.K., Causse M., Rothan C., Schiex T., Noirot C., Bellec A., Klopp C., Delalande C., Berges H., Mariette J., Frasse P., Vautrin S., Zouine M., Latche A., Rousseau C., Regad F., Pech J.C., Philippot M., Bouzayen M., Pericard P., Osorio S., del Carmen A.F., Monforte A., Granell A., Fernandez-Munoz R., Conte M., Lichtenstein G., Carrari F., De Bellis G., Fuligni F., Peano C., Grandillo S., Termolino P., Pietrella M., Fantini E., Falcone G., Fiore A., Giuliano G., Lopez L., Facella P., Perrotta G., Daddiego L., Bryan G., Orozco M., Pastor X., Torrents D., van Schriek K.N.V.M.G.M., Feron R.M.C., van Oeveren J., de Heer P., daPonte L., Jacobs-Oomen S., Cariaso M., Prins M., van Eijk M.J.T., Janssen A., van Haaren M.J.J., Jo S.H., Kim J., Kwon S.Y., Kim S., Koo D.H., Lee S., Hur C.G., Clouser C., Rico A., Hallab A., Gebhardt C., Klee K., Jocker A., Warfsmann J., Gobel U., Kawamura S., Yano K., Sherman J.D., Fukuoka H., Negoro S., Bhutty S., Chowdhury P., Chattopadhyay D., Datema E., Smit S., Schijlen E.W.M., van de Belt J., van Haarst J.C., Peters S.A., van Staveren M.J., Henkens M.H.C., Mooyman P.J.W., Hesselink T., van Ham R.C.H.J., Jiang G.Y., Droege M., Choi D., Kang B.C., Kim B.D., Park M., Kim S., Yeom S.I., Lee Y.H., Choi Y.D., Li G.C., Gao J.W., Liu Y.S., Huang S.X., Fernandez-Pedrosa V., Collado C., Zuniga S., Wang G.P., Cade R., Dietrich R.A., Rogers J., Knapp S., Fei Z.J., White R.A., Thannhauser T.W., Giovannoni J.J., Botella M.A., Gilbert L., Gonzalez R., Goicoechea J.L., Yu Y., Kudrna D., Collura K., Wissotski M., Wing R., Schoof H., Meyers B.C., Gurazada A.B., Green P.J., Mathur S., Vyas S., Solanke A.U., Kumar R., Gupta V., Sharma A.K., Khurana P., Khurana J.P., Tyagi A.K., Dalmay T., Mohorianu I., Walts B., Chamala S., Barbazuk W.B., Li J.P., Guo H., Lee T.H., Wang Y.P., Zhang D., Paterson A.H., Wang X.Y., Tang H.B., Barone A., Chiusano M.L., Ercolano M.R., D'Agostino N., Di Filippo M., Traini A., Sanseverino W., Frusciante L., Seymour G.B., Elharam M., Fu Y., Hua A., Kenton S., Lewis J., Lin S.P., Najar F., Lai H.S., Qin B.F., Qu C.M., Shi R.H., White D., White J., Xing Y.B., Yang K.Q., Yi J., Yao Z.Y., Zhou L.P., Roe B.A., Vezzi A., D'Angelo M., Zimbello R., Schiavon R., Caniato E., Rigobello C., Campagna D., Vitulo N., Valle G., Nelson D.R., De Paoli E., Szinay D., de Jong H.H., Bai Y.L., Visser R.G.F., Lankhorst R.M.K., Beasley H., McLaren K., Nicholson C., Riddle C., Gianese G., Consortium T.G. The tomato genome sequence provides insights into fleshy fruit evolution. Nature 2012, 485:635-641.
62. Chelaifa H., Chague V., Chalabi S., Mestiri I., Arnaud D., Deffains D., Lu Y.H., Belcram H., Huteau V., Chiquet J., Coriton O., Just J., Jahier J., Chalhoub B. Prevalence of gene expression additivity in genetically stable wheat allohexaploids. New Phytol. 2013, 197:730-736.
63. Roulin A., Auer P.L., Libault M., Schlueter J., Farmer A., May G., Stacey G., Doerge R.W., Jackson S.A. The fate of duplicated genes in a polyploid plant genome. Plant J. 2013, 73:143-153.
64. Pumphrey M., Bai J.F., Laudencia-Chingcuanco D., Anderson O., Gill B.S. Nonadditive expression of homoeologous genes is established upon polyploidization in hexaploid wheat. Genetics 2009, 181:1147-1157.
65. Adams K.L., Cronn R., Percifield R., Wendel J.F. Genes duplicated by polyploidy show unequal contributions to the transcriptome and organ-specific reciprocal silencing. Proc. Natl. Acad. Sci. U. S. A. 2003, 100:4649-4654.
66. Chaudhary B., Flagel L., Stupar R.M., Udall J.A., Verma N., Springer N.M., Wendel J.F. Reciprocal silencing, transcriptional bias and functional divergence of homeologs in polyploid cotton (Gossypium). Genetics 2009, 182:503-517.
67. Combes M.C., Cenci A., Baraille H., Bertrand B., Lashermes P. Homeologous gene expression in response to growing temperature in a recent allopolyploid (Coffea arabica L.). J. Hered. 2012, 103:36-46.
68. Liu Z.L., Adams K.L. Expression partitioning between genes duplicated by polyploidy under abiotic stress and during organ development. Curr. Biol. 2007, 17:1669-1674.
69. Reddy A.S.N. Alternative splicing of pre-messenger RNAs in plants in the genomic era. Annu. Rev. Plant Biol. 2007, 58:267-294.
70. Zhou R.C., Moshgabadi N., Adams K.L. Extensive changes to alternative splicing patterns following allopolyploidy in natural and resynthesized polyploids. Proc. Natl. Acad. Sci. U. S. A. 2011, 108:16122-16127.
71. Clevenger J., Chavarro C., Pearl S.A., Ozias-Akins P., Jackson S.A. Single nucleotide polymorphism identification in polyploids: a review, example, and recommendations. Mol. Plant 2015, 8:831-846.
72. Lai K., Duran C., Berkman P.J., Lorenc M.T., Stiller J., Manoli S., Hayden M.J., Forrest K.L., Fleury D., Baumann U., Zander M., Mason A.S., Batley J., Edwards D. Single nucleotide polymorphism discovery from wheat next-generation sequence data. Plant Biotechnol. J. 2012, 10:743-749.
73. Oliver R.E., Lazo G.R., Lutz J.D., Rubenfield M.J., Tinker N.A., Anderson J.M., Morehead N.H.W., Adhikary D., Jellen E.N., Maughan P.J., Guedira G.L.B., Chao S.M., Beattie A.D., Carson M.L., Rines H.W., Obert D.E., Bonman J.M., Jackson E.W. Model SNP development for complex genomes based on hexaploid oat using high-throughput 454 sequencing technology. BMC Genomics 2011, 12.
74. Imelfort M., Duran C., Batley J., Edwards D. Discovering genetic polymorphisms in next-generation sequencing data. Plant Biotechnol. J. 2009, 7:312-317.
75. Akama S., Shimizu-Inatsugi R., Shimizu K.K., Sese J. Genome-wide quantification of homeolog expression ratio revealed nonstochastic gene regulation in synthetic allopolyploid Arabidopsis. Nucleic Acids Res. 2014, 42:e46.
76. Lynch M., Force A. The probability of duplicate gene preservation by subfunctionalization. Genetics 2000, 154:459-473.
77. Collard B.C.Y., Jahufer M.Z.Z., Brouwer J.B., Pang E.C.K. An introduction to markers, quantitative trait loci (QTL) mapping and marker-assisted selection for crop improvement: the basic concepts. Euphytica 2005, 142:169-196.
78. Jiang G.L. Molecular markers and marker-assisted breeding in plants. Plant Breeding from Laboratories to Fields 2013, 45-84. InTech. S.B. Anderson (Ed.).
79. Carroll D. Genome engineering with zinc-finger nucleases. Genetics 2011, 188:773-782.
80. Durai S., Mani M., Kandavelou K., Wu J., Porteus M.H., Chandrasegaran S. Zinc finger nucleases: custom-designed molecular scissors for genome engineering of plant and mammalian cells. Nucleic Acids Res. 2005, 33:5978-5990.
81. Carroll D. A CRISPR approach to gene targeting. Mol. Ther. 2012, 20:1658-1660.
82. Cong L., Ran F.A., Cox D., Lin S.L., Barretto R., Habib N., Hsu P.D., Wu X.B., Jiang W.Y., Marraffini L.A., Zhang F. Multiplex genome engineering using CRISPR/Cas systems. Science 2013, 339:819-823.
83. Christian M., Cermak T., Doyle E.L., Schmidt C., Zhang F., Hummel A., Bogdanove A.J., Voytas D.F. Targeting DNA double-strand breaks with TAL effector nucleases. Genetics 2010, 186:U476-757.
84. Cermak T., Doyle E.L., Christian M., Wang L., Zhang Y., Schmidt C., Baller J.A., Somia N.V., Bogdanove A.J., Voytas D.F. Efficient design and assembly of custom TALEN and other TAL effector-based constructs for DNA targeting. Nucleic Acids Res. 2011, 39:e82.
85. Gaj T., Gersbach C.A., Barbas C.F. ZFN, TALEN, and CRISPR/Cas-based methods for genome engineering. Trends Biotechnol. 2013, 31:397-405.
86. Jackson S.A., Iwata A., Lee S.H., Schmutz J., Shoemaker R. Sequencing crop genomes: approaches and applications. New Phytol. 2011, 191:915-925.
87. Lapitan N.L.V. Organization and evolution of higher-plant nuclear genomes. Genome 1992, 35:171-181.
88. Claros M.G., Bautista R., Guerrero-Fernández D., Benzerki H., Seoane P., Fernández-Pozo N. Why assembling plant genome sequences is so challenging. Biology (Basel) 2012, 1:439-459.
89. van Oeveren J., de Ruiter M., Jesse T., van der Poel H., Tang J.F., Yalcin F., Janssen A., Volpin H., Stormo K.E., Bogden R., van Eijk M.J.T., Prins M. Sequence-based physical mapping of complex genomes by whole genome profiling. Genome Res. 2011, 21:618-625.
90. Wicker T., Sabot F., Hua-Van A., Bennetzen J.L., Capy P., Chalhoub B., Flavell A., Leroy P., Morgante M., Panaud O., Paux E., SanMiguel P., Schulman A.H. A unified classification system for eukaryotic transposable elements. Nat. Rev. Genet. 2007, 8:973-982.
91. Munoz-Lopez M., Garcia-Perez J.L. DNA transposons: nature and applications in genomics. Curr. Genom. 2010, 11:115-128.
92. Parisod C., Alix K., Just J., Petit M., Sarilar V., Mhiri C., Ainouche M., Chalhoub B., Grandbastien M.A. Impact of transposable elements on the organization and function of allopolyploid genomes. New Phytol. 2010, 186:37-45.
93. Janicki M., Rooke R., Yang G.J. Bioinformatics and genomic analysis of transposable elements in eukaryotic genomes. Chromosome Res. 2011, 19:787-808.
94. Bennetzen J.L. Transposable elements, gene creation and genome rearrangement in flowering plants. Curr. Opin. Genet. Dev. 2005, 15:621-627.
95. Parisod C., Salmon A., Zerjal T., Tenaillon M., Grandbastien M.A., Ainouche M. Rapid structural and epigenetic reorganization near transposable elements in hybrid and allopolyploid genomes in Spartina. New Phytol. 2009, 184:1003-1015.
96. Petit M., Guidat C., Daniel J., Denis E., Montoriol E., Bui Q.T., Lim K.Y., Kovarik A., Leitch A.R., Grandbastien M.A., Mhiri C. Mobilization of retrotransposons in synthetic allotetraploid tobacco. New Phytol. 2010, 186:135-147.
97. Feschotte C., Jiang N., Wessler S.R. Plant transposable elements: where genetics meets genomics. Nat. Rev. Genet. 2002, 3:329-341.
98. Chen M., Ha M., Lackey E., Wang J.L., Chen Z.J. RNAi of met1 reduces DNA methylation and induces genome-specific changes in gene expression and centromeric small RNA accumulation in Arabidopsis allopolyploids. Genetics 2008, 178:1845-1858.
99. Bologna N.G., Voinnet O. The diversity, biogenesis, and activities of endogenous silencing small RNAs in Arabidopsis. Annu. Rev. Plant Biol. 2014, 65:473-503.
100. Sun J., Zhou M., Mao Z.T., Li C.X. Characterization and evolution of microRNA genes derived from repetitive elements and duplication events in plants. PLoS One 2012, 7:e34092.
101. Kuang H.H., Padmanabhan C., Li F., Kamei A., Bhaskar P.B., Shu O.Y., Jiang J.M., Buell C.R., Baker B. Identification of miniature inverted-repeat transposable elements (MITEs) and biogenesis of their siRNAs in the Solanaceae: new functional implications for MITEs. Genome Res. 2009, 19:42-56.
102. Gent J.I., Ellis N.A., Guo L., Harkess A.E., Yao Y.Y., Zhang X.Y., Dawe R.K. CHH islands: de novo DNA methylation in near-gene chromatin regulation in maize. Genome Res. 2013, 23:628-637.
103. Girard A., Hannon G.J. Conserved themes in small-RNA-mediated transposon control. Trends Cell Biol. 2008, 18:136-148.
104. Hirakawa H., Shirasawa K., Kosugi S., Tashiro K., Nakayama S., Yamada M., Kohara M., Watanabe Y., Fujishiro T., Tsuruoka H., Minami C., Sasamoto S., Kato M., Nanri K., Komaki A., Yanagi T., Qin G.X., Maeda F., Ishikawa M., Kuhara S., Sato S., Tabata S., Isobe S.N. Dissection of the octoploid strawberry genome by deep sequencing of the genomes of Fragaria species. DNA Res. 2014, 21:169-181.
105. Njuguna W., Liston A., Cronn R., Ashman T.L., Bassil N. Insights into phylogeny, sex function and age of Fragaria based on whole chloroplast genome sequencing. Mol. Phylogen. Evol. 2013, 66:17-29.
106. D'Hont A., Denoeud F., Aury J.M., Baurens F.C., Carreel F., Garsmeur O., Noel B., Bocs S., Droc G., Rouard M., Da Silva C., Jabbari K., Cardi C., Poulain J., Souquet M., Labadie K., Jourda C., Lengelle J., Rodier-Goud M., Alberti A., Bernard M., Correa M., Ayyampalayam S., Mckain M.R., Leebens-Mack J., Burgess D., Freeling M., Mbeguie-A-Mbeguie D., Chabannes M., Wicker T., Panaud O., Barbosa J., Hribova E., Heslop-Harrison P., Habas R., Rivallan R., Francois P., Poiron C., Kilian A., Burthia D., Jenny C., Bakry F., Brown S., Guignon V., Kema G., Dita M., Waalwijk C., Joseph S., Dievart A., Jaillon O., Leclercq J., Argout X., Lyons E., Almeida A., Jeridi M., Dolezel J., Roux N., Risterucci A.M., Weissenbach J., Ruiz M., Glaszmann J.C., Quetier F., Yahiaoui N., Wincker P. The banana (Musa acuminata) genome and the evolution of monocotyledonous plants. Nature 2012, 488:213-217.
107. Paterson A.H., Bowers J.E., Bruggmann R., Dubchak I., Grimwood J., Gundlach H., Haberer G., Hellsten U., Mitros T., Poliakov A., Schmutz J., Spannagl M., Tang H.B., Wang X.Y., Wicker T., Bharti A.K., Chapman J., Feltus F.A., Gowik U., Grigoriev I.V., Lyons E., Maher C.A., Martis M., Narechania A., Otillar R.P., Penning B.W., Salamov A.A., Wang Y., Zhang L.F., Carpita N.C., Freeling M., Gingle A.R., Hash C.T., Keller B., Klein P., Kresovich S., McCann M.C., Ming R., Peterson D.G., Mehboob-ur-Rahman, Ware D., Westhoff P., Mayer K.F.X., Messing J., Rokhsar D.S. The Sorghum bicolor genome and the diversification of grasses. Nature 2009, 457:551-556.