Table 2. Genomic consequences of experimental interspecific hybridization in plants and animals (Parisod et al., 2010a)

Genome Effect

References

Plants and Lower Eukaryotes

Animals

Alteration of epigenetic modifications to the genome

(Wang et al., 2013; Greaves et al., 2014; Greaves et al., 2015) (Shaked et al., 2001; Comai et al., 2003; Hegarty et al., 2006; Josefsson et al., 2006; Hegarty et al., 2008; Buggs et al., 2009a; Jones & Hegarty, 2009; Buggs et al., 2011) (Salmon et al., 2005; Josefsson et al., 2006; Nasrallah et al., 2007; Marfil et al., 2009; Martienssen, 2010; Parisod et al., 2010b; Groszmann et al., 2011; Hegarty et al., 2011; Moghaddam et al., 2011; Sanei et al., 2011; Greaves et al., 2012; Shivaprasad et al., 2012; Cara et al., 2013; He et al., 2013; Zhang et al., 2013; Sehrish et al., 2014; Senerchia et al., 2015; Senerchia et al., 2016; Ding & Chen, 2018).

(O'Neill et al., 1998; Vrana et al., 1998; Vrana et al., 2000; Schutt et al., 2003; Brown et al., 2008; Wiley et al., 2008; Brown et al., 2012; Kelleher et al., 2012; Xiao et al., 2013; Bamberger et al., 2018)

Alterations in expression patterns across the genome (“transcription shock”)

(Comai et al., 2000; Kunz et al., 2003; Hegarty et al., 2006; Josefsson et al., 2006; Albertin et al., 2007; Hegarty et al., 2008, 2009; Chelaifa et al., 2010; Buggs et al., 2011; Shivaprasad et al., 2012; He et al., 2013; Zhang et al., 2016)

(Hill-Burns & Clark, 2010; Renaut & Bernatchez, 2011; Wolf et al., 2014) (L'Hote et al., 2008; Czypionka et al., 2012; Kelleher et al., 2012; Erwin et al., 2015; Lopez-Maestre et al., 2017; Bamberger et al., 2018)

Activation and spread of mobile DNA elements

(Grandbastien et al., 2005; Madlung et al., 2005; Michalak, 2010; Parisod et al., 2010a) (Fontdevila, 2005; Michalak, 2009, 2010; Vela et al., 2014) (Ungerer et al., 2006; Ungerer et al., 2009; Kawakami et al., 2010; Kraitshtein et al., 2010; Scascitelli et al., 2010; Wang et al., 2010a; Wang et al., 2010b; Yaakov & Kashkush, 2011a, b, 2012; Ungerer & Kawakami, 2013; Yaakov et al., 2013; Zhang et al., 2013; Mixao & Gabaldon, 2017; Smukowski Heil et al., 2021) (Tayale & Parisod, 2013; Hénault et al., 2020)

(Fawcett et al., 1986; Yannopoulos et al., 1987; Bucheton, 1990; Scheinker et al., 1990; Petrov et al., 1995; Garcia Guerreiro, 1996; O'Neill et al., 1998; Labrador et al., 1999; Brown et al., 2012; Arkhipova & Rodriguez, 2013; Carnelossi et al., 2014; Guerreiro, 2014; Vela et al., 2014; Marburger et al., 2018)

Genome restructuring involving mobile DNA elements

(Ungerer et al., 2006; Parisod et al., 2009; Bento et al., 2013; Senerchia et al., 2015)

(Kidwell et al., 1977; Kidwell, 1985; Fawcett et al., 1986; Bucheton, 1990; Petrov et al., 1995; O'Neill et al., 1998; Vela et al., 2014; Romero-Soriano et al., 2016)

Changes in chromosome structure and karyotype

(Han et al., 2003; Lai et al., 2005; Madlung et al., 2005; Marfil et al., 2006; Li & Ge, 2007; Lim et al., 2008; Gao et al., 2010; Xie et al., 2010; Chester et al., 2012; Nicolas et al., 2012; Li et al., 2016; Danilova et al., 2017; Silkova et al., 2021; Wang et al., 2021; Zhao et al., 2021)

(Brown et al., 2002; Sakai et al., 2007; Ivanitskaya et al., 2010; Qin et al., 2014; Qin et al., 2016; Lo Bianco et al., 2017) (Deon et al., 2020) (Franchini et al., 2020); (Smalec et al., 2019)

 

Alteration of tandem repetitive DNA arrays and centromeres

(Guo et al., 2016)

(Metcalfe et al., 2007; Baicharoen et al., 2014)

Homeologous exchanges

(Wu et al., 2021)

 

Changes in ploidy (mostly whole genome duplications)

(Soltis et al., 2003; Baack et al., 2005; Hegarty et al., 2006; Hegarty & Hiscock, 2007; Doyle et al., 2008; Buggs et al., 2009b; Paun et al., 2009; Soltis, 2009; Muhlhausen & Kollmar, 2013; Tayale & Parisod, 2013; Alix et al., 2017; Fisher et al., 2018)

(Liu et al., 2007; Liu, 2010; Brieuc et al., 2014; Kodama et al., 2014; Nossa et al., 2014; Li et al., 2015; Marburger et al., 2018; Rodriguez & Arkhipova, 2018; Novikova et al., 2020)

 

 

REFERENCES

 

Albertin W, Alix K, Balliau T, Brabant P, Davanture M, Malosse C, Valot B & Thiellement H. (2007). Differential regulation of gene products in newly synthesized Brassica napus allotetraploids is not related to protein function nor subcellular localization. BMC Genomics 8, 56.

 

Alix K, Gerard PR, Schwarzacher T & Heslop-Harrison JSP. (2017). Polyploidy and interspecific hybridization: partners for adaptation, speciation and evolution in plants. Ann Bot 120, 183-194.

 

Arkhipova IR & Rodriguez F. (2013). Genetic and epigenetic changes involving (retro)transposons in animal hybrids and polyploids. Cytogenet Genome Res 140, 295-311.

 

Baack EJ, Whitney KD & Rieseberg LH. (2005). Hybridization and genome size evolution: timing and magnitude of nuclear DNA content increases in Helianthus homoploid hybrid species. New Phytol 167, 623-630.

 

Baicharoen S, Miyabe-Nishiwaki T, Arsaithamkul V, Hirai Y, Duangsa-ard K, Siriaroonrat B, Domae H, Srikulnath K, Koga A & Hirai H. (2014). Locational diversity of alpha satellite DNA and intergeneric hybridization aspects in the Nomascus and Hylobates genera of small apes. PLoS One 9, e109151.

 

Bamberger C, Martínez-Bartolomé S, Montgomery M, Lavallée-Adam M & Yates JR, 3rd. (2018). Increased proteomic complexity in Drosophila hybrids during development. Sci Adv 4, eaao3424.

 

Bento M, Tomas D, Viegas W & Silva M. (2013). Retrotransposons represent the most labile fraction for genomic rearrangements in polyploid plant species. Cytogenet Genome Res 140, 286-294.

 

Brieuc MS, Waters CD, Seeb JE & Naish KA. (2014). A dense linkage map for Chinook salmon (Oncorhynchus tshawytscha) reveals variable chromosomal divergence after an ancestral whole genome duplication event. G3 (Bethesda) 4, 447-460.

 

Brown JD, Golden D & O'Neill RJ. (2008). Methylation perturbations in retroelements within the genome of a Mus interspecific hybrid correlate with double minute chromosome formation. Genomics 91, 267-273.

 

Brown JD, Piccuillo V & O'Neill RJ. (2012). Retroelement demethylation associated with abnormal placentation in Mus musculus x Mus caroli hybrids. Biol Reprod 86, 88.

 

Brown JD, Strbuncelj M, Giardina C & O'Neill RJ. (2002). Interspecific hybridization induced amplification of Mdm2 on double minutes in a Mus hybrid. Cytogenet Genome Res 98, 184-188.

 

Bucheton A. (1990). I transposable elements and I-R hybrid dysgenesis in Drosophila. Trends Genet 6, 16-21.

 

Buggs RJ, Doust AN, Tate JA, Koh J, Soltis K, Feltus FA, Paterson AH, Soltis PS & Soltis DE. (2009a). Gene loss and silencing in Tragopogon miscellus (Asteraceae): comparison of natural and synthetic allotetraploids. Heredity 103, 73-81.

 

Buggs RJ, Soltis PS & Soltis DE. (2009b). Does hybridization between divergent progenitors drive whole-genome duplication? Mol Ecol 18, 3334-3339.

 

Buggs RJ, Zhang L, Miles N, Tate JA, Gao L, Wei W, Schnable PS, Barbazuk WB, Soltis PS & Soltis DE. (2011). Transcriptomic shock generates evolutionary novelty in a newly formed, natural allopolyploid plant. Curr Biol 21, 551-556.

 

Cara N, Marfil CF & Masuelli RW. (2013). Epigenetic patterns newly established after interspecific hybridization in natural populations of Solanum. Ecol Evol 3, 3764-3779.

 

Carnelossi EA, Lerat E, Henri H, Martinez S, Carareto CM & Vieira C. (2014). Specific activation of an I-like element in Drosophila interspecific hybrids. Genome Biol Evol 6, 1806-1817.

 

Chelaifa H, Monnier A & Ainouche M. (2010). Transcriptomic changes following recent natural hybridization and allopolyploidy in the salt marsh species Spartina x townsendii and Spartina anglica (Poaceae). New Phytol 186, 161-174.

 

Chester M, Gallagher JP, Symonds VV, Cruz da Silva AV, Mavrodiev EV, Leitch AR, Soltis PS & Soltis DE. (2012). Extensive chromosomal variation in a recently formed natural allopolyploid species, Tragopogon miscellus (Asteraceae). Proc Natl Acad Sci U S A 109, 1176-1181.

 

Comai L, Madlung A, Josefsson C & Tyagi A. (2003). Do the different parental 'heteromes' cause genomic shock in newly formed allopolyploids? Philos Trans R Soc Lond B Biol Sci 358, 1149-1155.

 

Comai L, Tyagi AP, Winter K, Holmes-Davis R, Reynolds SH, Stevens Y & Byers B. (2000). Phenotypic instability and rapid gene silencing in newly formed arabidopsis allotetraploids. Plant Cell 12, 1551-1568.

 

Czypionka T, Cheng J, Pozhitkov A & Nolte AW. (2012). Transcriptome changes after genome-wide admixture in invasive sculpins (Cottus). Mol Ecol 21, 4797-4810.

 

Danilova TV, Akhunova AR, Akhunov ED, Friebe B & Gill BS. (2017). Major structural genomic alterations can be associated with hybrid speciation in Aegilops markgrafii (Triticeae). Plant J 92, 317-330.

 

Deon GA, Glugoski L, Vicari MR, Nogaroto V, Sassi FMC, Cioffi MB, Liehr T, Bertollo LAC & Moreira-Filho O. (2020). Highly Rearranged Karyotypes and Multiple Sex Chromosome Systems in Armored Catfishes from the Genus Harttia (Teleostei, Siluriformes). Genes (Basel) 11.

 

Ding M & Chen ZJ. (2018). Epigenetic perspectives on the evolution and domestication of polyploid plant and crops. Curr Opin Plant Biol 42, 37-48.

 

Doyle JJ, Flagel LE, Paterson AH, Rapp RA, Soltis DE, Soltis PS & Wendel JF. (2008). Evolutionary genetics of genome merger and doubling in plants. Annu Rev Genet 42, 443-461.

 

Erwin AA, Galdos MA, Wickersheim ML, Harrison CC, Marr KD, Colicchio JM & Blumenstiel JP. (2015). piRNAs Are Associated with Diverse Transgenerational Effects on Gene and Transposon Expression in a Hybrid Dysgenic Syndrome of D. virilis. PLoS Genet 11, e1005332.

 

Fawcett DH, Lister CK, Kellett E & Finnegan DJ. (1986). Transposable elements controlling I-R hybrid dysgenesis in D. melanogaster are similar to mammalian LINEs. Cell 47, 1007-1015.

 

Fisher KJ, Buskirk SW, Vignogna RC, Marad DA & Lang GI. (2018). Adaptive genome duplication affects patterns of molecular evolution in Saccharomyces cerevisiae. PLoS Genet 14, e1007396.

 

Fontdevila A. (2005). Hybrid genome evolution by transposition. Cytogenet Genome Res 110, 49-55.

 

Franchini P, Kautt AF, Nater A, Antonini G, Castiglia R, Meyer A & Solano E. (2020). Reconstructing the Evolutionary History of Chromosomal Races on Islands: A Genome-Wide Analysis of Natural House Mouse Populations. Mol Biol Evol 37, 2825-2837.

 

Gao X, Liu SW, Sun Q & Xia GM. (2010). High frequency of HMW-GS sequence variation through somatic hybridization between Agropyron elongatum and common wheat. Planta 231, 245-250.

 

Garcia Guerreiro MP. (1996). Behaviour of the transposable elements copia and mdg1 in hybrids between the sibling species Drosophila melanogaster and D. simulans. Heredity (Edinb) 77 ( Pt 1), 40-46.

 

Grandbastien MA, Audeon C, Bonnivard E, Casacuberta JM, Chalhoub B, Costa AP, Le QH, Melayah D, Petit M, Poncet C, Tam SM, Van Sluys MA & Mhiri C. (2005). Stress activation and genomic impact of Tnt1 retrotransposons in Solanaceae. Cytogenet Genome Res 110, 229-241.

 

Greaves IK, Gonzalez-Bayon R, Wang L, Zhu A, Liu PC, Groszmann M, Peacock WJ & Dennis ES. (2015). Epigenetic Changes in Hybrids. Plant Physiol 168, 1197-1205.

 

Greaves IK, Groszmann M, Wang A, Peacock WJ & Dennis ES. (2014). Inheritance of Trans Chromosomal Methylation patterns from Arabidopsis F1 hybrids. Proc Natl Acad Sci U S A 111, 2017-2022.

 

Greaves IK, Groszmann M, Ying H, Taylor JM, Peacock WJ & Dennis ES. (2012). Trans chromosomal methylation in Arabidopsis hybrids. Proc Natl Acad Sci U S A 109, 3570-3575.

 

Groszmann M, Greaves IK, Albertyn ZI, Scofield GN, Peacock WJ & Dennis ES. (2011). Changes in 24-nt siRNA levels in Arabidopsis hybrids suggest an epigenetic contribution to hybrid vigor. Proc Natl Acad Sci U S A 108, 2617-2622.

 

Guerreiro MP. (2014). Interspecific hybridization as a genomic stressor inducing mobilization of transposable elements in Drosophila. Mob Genet Elements 4, e34394.

 

Guo X, Su H, Shi Q, Fu S, Wang J, Zhang X, Hu Z & Han F. (2016). De Novo Centromere Formation and Centromeric Sequence Expansion in Wheat and its Wide Hybrids. PLoS Genet 12, e1005997.

 

Han FP, Fedak G, Ouellet T & Liu B. (2003). Rapid genomic changes in interspecific and intergeneric hybrids and allopolyploids of Triticeae. Genome 46, 716-723.

 

He G, Chen B, Wang X, Li X, Li J, He H, Yang M, Lu L, Qi Y, Wang X & Wang Deng X. (2013). Conservation and divergence of transcriptomic and epigenomic variation in maize hybrids. Genome Biol 14, R57.

 

Hegarty M & Hiscock S. (2007). Polyploidy: doubling up for evolutionary success. Curr Biol 17, R927-R929.

 

Hegarty MJ, Barker GL, Brennan AC, Edwards KJ, Abbott RJ & Hiscock SJ. (2008). Changes to gene expression associated with hybrid speciation in plants: further insights from transcriptomic studies in Senecio. Philos Trans R Soc Lond B Biol Sci 363, 3055-3069.

 

Hegarty MJ, Barker GL, Brennan AC, Edwards KJ, Abbott RJ & Hiscock SJ. (2009). Extreme changes to gene expression associated with homoploid hybrid speciation. Mol Ecol 18, 877-889.

 

Hegarty MJ, Barker GL, Wilson ID, Abbott RJ, Edwards KJ & Hiscock SJ. (2006). Transcriptome shock after interspecific hybridization in senecio is ameliorated by genome duplication. Curr Biol 16, 1652-1659.

 

Hegarty MJ, Batstone T, Barker GL, Edwards KJ, Abbott RJ & Hiscock SJ. (2011). Nonadditive changes to cytosine methylation as a consequence of hybridization and genome duplication in Senecio (Asteraceae). Mol Ecol 20, 105-113.

 

Hénault M, Marsit S, Charron G & Landry CR. (2020). The effect of hybridization on transposable element accumulation in an undomesticated fungal species. Elife 9.

 

Hill-Burns EM & Clark AG. (2010). Functional regulatory divergence of the innate immune system in interspecific Drosophila hybrids. Mol Biol Evol 27, 2596-2605.

 

Ivanitskaya E, Rashkovetsky L & Nevo E. (2010). Chromosomes in a hybrid zone of Israeli mole rats (Spalax, Rodentia). Genetika 46, 1301-1304.

 

Jones RN & Hegarty M. (2009). Order out of chaos in the hybrid plant nucleus. Cytogenet Genome Res 126, 376-389.

 

Josefsson C, Dilkes B & Comai L. (2006). Parent-dependent loss of gene silencing during interspecies hybridization. Curr Biol 16, 1322-1328.

 

Kawakami T, Strakosh SC, Zhen Y & Ungerer MC. (2010). Different scales of Ty1/copia-like retrotransposon proliferation in the genomes of three diploid hybrid sunflower species. Heredity 104, 341-350.

 

Kelleher ES, Edelman NB & Barbash DA. (2012). Drosophila interspecific hybrids phenocopy piRNA-pathway mutants. PLoS Biol 10, e1001428.

 

Kidwell MG. (1985). Hybrid dysgenesis in Drosophila melanogaster: nature and inheritance of P element regulation. Genetics 111, 337-350.

 

Kidwell MG, Kidwell JF & Sved JA. (1977). Hybrid Dysgenesis in DROSOPHILA MELANOGASTER: A Syndrome of Aberrant Traits Including Mutation, Sterility and Male Recombination. Genetics 86, 813-833.

 

Kodama M, Brieuc MS, Devlin RH, Hard JJ & Naish KA. (2014). Comparative mapping between Coho Salmon (Oncorhynchus kisutch) and three other salmonids suggests a role for chromosomal rearrangements in the retention of duplicated regions following a whole genome duplication event. G3 (Bethesda) 4, 1717-1730.

 

Kraitshtein Z, Yaakov B, Khasdan V & Kashkush K. (2010). Genetic and epigenetic dynamics of a retrotransposon after allopolyploidization of wheat. Genetics 186, 801-812.

 

Kunz C, Narangajavana J, Jakowitsch J, Park YD, Delon TR, Kovarik A, Koukalova B, van der Winden J, Moscone E, Aufsatz W, Mette MF, Matzke M & Matzke AJ. (2003). Studies on the effects of a flanking repetitive sequence on the expression of single-copy transgenes in Nicotiana sylvestris and in N. sylvestris-N. tomentosiformis hybrids. Plant Mol Biol 52, 203-215.

 

L'Hote D, Serres C, Veitia RA, Montagutelli X, Oulmouden A & Vaiman D. (2008). Gene expression regulation in the context of mouse interspecific mosaic genomes. Genome Biol 9, R133.

 

Labrador M, Farre M, Utzet F & Fontdevila A. (1999). Interspecific hybridization increases transposition rates of Osvaldo. Mol Biol Evol 16, 931-937.

 

Lai Z, Nakazato T, Salmaso M, Burke JM, Tang S, Knapp SJ & Rieseberg LH. (2005). Extensive chromosomal repatterning and the evolution of sterility barriers in hybrid sunflower species. Genetics 171, 291-303.

 

Li JT, Hou GY, Kong XF, Li CY, Zeng JM, Li HD, Xiao GB, Li XM & Sun XW. (2015). The fate of recent duplicated genes following a fourth-round whole genome duplication in a tetraploid fish, common carp (Cyprinus carpio). Sci Rep 5, 8199.

 

Li W, Challa GS, Zhu H & Wei W. (2016). Recurrence of Chromosome Rearrangements and Reuse of DNA Breakpoints in the Evolution of the Triticeae Genomes. G3 (Bethesda) 6, 3837-3847.

 

Li ZY & Ge XH. (2007). Unique chromosome behavior and genetic control in Brassica x Orychophragmus wide hybrids: a review. Plant Cell Rep 26, 701-710.

 

Lim KY, Soltis DE, Soltis PS, Tate J, Matyasek R, Srubarova H, Kovarik A, Pires JC, Xiong Z & Leitch AR. (2008). Rapid chromosome evolution in recently formed polyploids in Tragopogon (Asteraceae). PLoS One 3, e3353.

 

Liu S. (2010). Distant hybridization leads to different ploidy fishes. Sci China Life Sci 53, 416-425.

 

Liu S, Qin Q, Xiao J, Lu W, Shen J, Li W, Liu J, Duan W, Zhang C, Tao M, Zhao R, Yan J & Liu Y. (2007). The formation of the polyploid hybrids from different subfamily fish crossings and its evolutionary significance. Genetics 176, 1023-1034.

 

Lo Bianco S, Masters JC & Sineo L. (2017). The evolution of the Cercopithecini: a (post)modern synthesis. Evol Anthropol 26, 336-349.

 

Lopez-Maestre H, Carnelossi EA, Lacroix V, Burlet N, Mugat B, Chambeyron S, Carareto CM & Vieira C. (2017). Identification of misexpressed genetic elements in hybrids between Drosophila-related species. Sci Rep 7, 40618.

 

Madlung A, Tyagi AP, Watson B, Jiang H, Kagochi T, Doerge RW, Martienssen R & Comai L. (2005). Genomic changes in synthetic Arabidopsis polyploids. Plant J 41, 221-230.

 

Marburger S, Alexandrou MA, Taggart JB, Creer S, Carvalho G, Oliveira C & Taylor MI. (2018). Whole genome duplication and transposable element proliferation drive genome expansion in Corydoradinae catfishes. Proc Biol Sci 285.

 

Marfil CF, Camadro EL & Masuelli RW. (2009). Phenotypic instability and epigenetic variability in a diploid potato of hybrid origin, Solanum ruiz-lealii. BMC Plant Biol 9, 21.

 

Marfil CF, Masuelli RW, Davison J & Comai L. (2006). Genomic instability in Solanum tuberosum x Solanum kurtzianum interspecific hybrids. Genome 49, 104-113.

 

Martienssen RA. (2010). Heterochromatin, small RNA and post-fertilization dysgenesis in allopolyploid and interploid hybrids of Arabidopsis. New Phytol 186, 46-53.

 

Metcalfe CJ, Bulazel KV, Ferreri GC, Schroeder-Reiter E, Wanner G, Rens W, Obergfell C, Eldridge MD & O'Neill RJ. (2007). Genomic instability within centromeres of interspecific marsupial hybrids. Genetics 177, 2507-2517.

 

Michalak P. (2009). Epigenetic, transposon and small RNA determinants of hybrid dysfunctions. Heredity 102, 45-50.

 

Michalak P. (2010). An eruption of mobile elements in genomes of hybrid sunflowers. Heredity (Edinb) 104, 329-330.

 

Mixao V & Gabaldon T. (2017). Hybridization and emergence of virulence in opportunistic human yeast pathogens. Yeast.

 

Moghaddam AM, Roudier F, Seifert M, Berard C, Magniette ML, Ashtiyani RK, Houben A, Colot V & Mette MF. (2011). Additive inheritance of histone modifications in Arabidopsis thaliana intra-specific hybrids. Plant J 67, 691-700.

 

Muhlhausen S & Kollmar M. (2013). Whole genome duplication events in plant evolution reconstructed and predicted using myosin motor proteins. BMC Evol Biol 13, 202.

 

Nasrallah JB, Liu P, Sherman-Broyles S, Schmidt R & Nasrallah ME. (2007). Epigenetic mechanisms for breakdown of self-incompatibility in interspecific hybrids. Genetics 175, 1965-1973.

 

Nicolas SD, Monod H, Eber F, Chevre AM & Jenczewski E. (2012). Non-random distribution of extensive chromosome rearrangements in Brassica napus depends on genome organization. Plant J.

 

Nossa CW, Havlak P, Yue JX, Lv J, Vincent KY, Brockmann HJ & Putnam NH. (2014). Joint assembly and genetic mapping of the Atlantic horseshoe crab genome reveals ancient whole genome duplication. Gigascience 3, 9.

 

Novikova PY, Brennan IG, Booker W, Mahony M, Doughty P, Lemmon AR, Moriarty Lemmon E, Roberts JD, Yant L, Van de Peer Y, Keogh JS & Donnellan SC. (2020). Polyploidy breaks speciation barriers in Australian burrowing frogs Neobatrachus. PLoS Genet 16, e1008769.

 

O'Neill RJ, O'Neill MJ & Graves JA. (1998). Undermethylation associated with retroelement activation and chromosome remodelling in an interspecific mammalian hybrid. Nature 393, 68-72.

 

Parisod C, Alix K, Just J, Petit M, Sarilar V, Mhiri C, Ainouche M, Chalhoub B & Grandbastien MA. (2010a). Impact of transposable elements on the organization and function of allopolyploid genomes. New Phytol 186, 37-45.

 

Parisod C, Holderegger R & Brochmann C. (2010b). Evolutionary consequences of autopolyploidy. New Phytol 186, 5-17.

 

Parisod C, Salmon A, Zerjal T, Tenaillon M, Grandbastien MA & Ainouche M. (2009). Rapid structural and epigenetic reorganization near transposable elements in hybrid and allopolyploid genomes in Spartina. New Phytol 184, 1003-1015.

 

Paun O, Forest F, Fay MF & Chase MW. (2009). Hybrid speciation in angiosperms: parental divergence drives ploidy. New Phytol 182, 507-518.

 

Petrov DA, Schutzman JL, Hartl DL & Lozovskaya ER. (1995). Diverse transposable elements are mobilized in hybrid dysgenesis in Drosophila virilis. Proceedings of the National Academy of Sciences of the United States of America 92, 8050-8054.

 

Qin Q, Lai Z, Cao L, Xiao Q, Wang Y & Liu S. (2016). Rapid genomic changes in allopolyploids of Carassius auratus red var. (female symbol) x Megalobrama amblycephala (male symbol). Sci Rep 6, 34417.

 

Qin Q, Wang Y, Wang J, Dai J, Liu Y & Liu S. (2014). Abnormal chromosome behavior during meiosis in the allotetraploid of Carassius auratus red var. (female symbol)xMegalobrama amblycephala (male symbol). BMC Genet 15, 95.

 

Renaut S & Bernatchez L. (2011). Transcriptome-wide signature of hybrid breakdown associated with intrinsic reproductive isolation in lake whitefish species pairs (Coregonus spp. Salmonidae). Heredity 106, 1003-1011.

 

Rodriguez F & Arkhipova IR. (2018). Transposable elements and polyploid evolution in animals. Curr Opin Genet Dev 49, 115-123.

 

Romero-Soriano V, Burlet N, Vela D, Fontdevila A, Vieira C & Garcia Guerreiro MP. (2016). Drosophila Females Undergo Genome Expansion after Interspecific Hybridization. Genome Biol Evol 8, 556-561.

 

Sakai C, Konno F, Nakano O, Iwai T, Yokota T, Lee J, Nishida-Umehara C, Kuroiwa A, Matsuda Y & Yamashita M. (2007). Chromosome elimination in the interspecific hybrid medaka between Oryzias latipes and O. hubbsi. Chromosome Res 15, 697-709.

 

Salmon A, Ainouche ML & Wendel JF. (2005). Genetic and epigenetic consequences of recent hybridization and polyploidy in Spartina (Poaceae). Mol Ecol 14, 1163-1175.

 

Sanei M, Pickering R, Kumke K, Nasuda S & Houben A. (2011). Loss of centromeric histone H3 (CENH3) from centromeres precedes uniparental chromosome elimination in interspecific barley hybrids. Proc Natl Acad Sci U S A 108, E498-505.

 

Scascitelli M, Cognet M & Adams KL. (2010). An interspecific plant hybrid shows novel changes in parental splice forms of genes for splicing factors. Genetics 184, 975-983.

 

Scheinker VS, Lozovskaya ER, Bishop JG, Corces VG & Evgen'ev MB. (1990). A long terminal repeat-containing retrotransposon is mobilized during hybrid dysgenesis in Drosophila virilis. Proc Natl Acad Sci U S A 87, 9615-9619.

 

Schutt S, Florl AR, Shi W, Hemberger M, Orth A, Otto S, Schulz WA & Fundele RH. (2003). DNA methylation in placentas of interspecies mouse hybrids. Genetics 165, 223-228.

 

Sehrish T, Symonds VV, Soltis DE, Soltis PS & Tate JA. (2014). Gene silencing via DNA methylation in naturally occurring Tragopogon miscellus (Asteraceae) allopolyploids. BMC Genomics 15, 701.

 

Senerchia N, Felber F, North B, Sarr A, Guadagnuolo R & Parisod C. (2016). Differential introgression and reorganization of retrotransposons in hybrid zones between wild wheats. Mol Ecol 25, 2518-2528.

 

Senerchia N, Felber F & Parisod C. (2015). Genome reorganization in F1 hybrids uncovers the role of retrotransposons in reproductive isolation. Proc Biol Sci 282, 20142874.

 

Shaked H, Kashkush K, Ozkan H, Feldman M & Levy AA. (2001). Sequence elimination and cytosine methylation are rapid and reproducible responses of the genome to wide hybridization and allopolyploidy in wheat. Plant Cell 13, 1749-1759.

 

Shivaprasad PV, Dunn RM, Santos BA, Bassett A & Baulcombe DC. (2012). Extraordinary transgressive phenotypes of hybrid tomato are influenced by epigenetics and small silencing RNAs. Embo J 31, 257-266.

 

Silkova OG, Ivanova YN, Loginova DB, Solovey LA, Sycheva EA & Dubovets NI. (2021). Karyotype Reorganization in Wheat-Rye Hybrids Obtained via Unreduced Gametes: Is There a Limit to the Chromosome Number in Triticale? Plants (Basel) 10.

 

Smalec BM, Heider TN, Flynn BL & O'Neill RJ. (2019). A centromere satellite concomitant with extensive karyotypic diversity across the Peromyscus genus defies predictions of molecular drive. Chromosome Res 27, 237-252.

 

Smukowski Heil C, Patterson K, Hickey AS, Alcantara E & Dunham MJ. (2021). Transposable Element Mobilization in Interspecific Yeast Hybrids. Genome Biol Evol 13.

 

Soltis DE. (2009). Polyploidy and angiosperm diversification. Am J Bot 96, 336-348.

 

Soltis DE, Soltis PS & Tate JA. (2003). Advances in the study of polyploidy since plant speciation. New Phytol 161, 173-191.

 

Tayale A & Parisod C. (2013). Natural pathways to polyploidy in plants and consequences for genome reorganization. Cytogenet Genome Res 140, 79-96.

 

Ungerer MC & Kawakami T. (2013). Transcriptional dynamics of LTR retrotransposons in early generation and ancient sunflower hybrids. Genome Biol Evol 5, 329-337.

 

Ungerer MC, Strakosh SC & Stimpson KM. (2009). Proliferation of Ty3/gypsy-like retrotransposons in hybrid sunflower taxa inferred from phylogenetic data. BMC Biol 7, 40.

 

Ungerer MC, Strakosh SC & Zhen Y. (2006). Genome expansion in three hybrid sunflower species is associated with retrotransposon proliferation. Curr Biol 16, R872-873.

 

Vela D, Fontdevila A, Vieira C & Garcia Guerreiro MP. (2014). A genome-wide survey of genetic instability by transposition in Drosophila hybrids. PLoS One 9, e88992.

 

Vrana PB, Fossella JA, Matteson P, del Rio T, O'Neill MJ & Tilghman SM. (2000). Genetic and epigenetic incompatibilities underlie hybrid dysgenesis in Peromyscus. Nat Genet 25, 120-124.

 

Vrana PB, Guan XJ, Ingram RS & Tilghman SM. (1998). Genomic imprinting is disrupted in interspecific Peromyscus hybrids. Nat Genet 20, 362-365.

 

Wang L, Jia G, Jiang X, Cao S, Chen ZJ & Song Q. (2021). Altered chromatin architecture and gene expression during polyploidization and domestication of soybean. Plant Cell 33, 1430-1446.

 

Wang N, Wang H, Wang H, Zhang D, Wu Y, Ou X, Liu S, Dong Z & Liu B. (2010a). Transpositional reactivation of the Dart transposon family in rice lines derived from introgressive hybridization with Zizania latifolia. BMC Plant Biol 10, 190.

 

Wang N, Wang H, Zhang D, Wu Y, Ou X, Liu S, Dong Z & Liu B. (2010b). Transpositional reactivation of the Dart transposon family in rice lines derived from introgressive hybridization with Zizania latifolia. BMC Plant Biol 10, 190.

 

Wang X, Wu R, Lin X, Bai Y, Song C, Yu X, Xu C, Zhao N, Dong Y & Liu B. (2013). Tissue culture-induced genetic and epigenetic alterations in rice pure-lines, F1 hybrids and polyploids. BMC Plant Biol 13, 77.

 

Wiley CD, Matundan HH, Duselis AR, Isaacs AT & Vrana PB. (2008). Patterns of hybrid loss of imprinting reveal tissue- and cluster-specific regulation. PLoS One 3, e3572.

 

Wolf JB, Oakey RJ & Feil R. (2014). Imprinted gene expression in hybrids: perturbed mechanisms and evolutionary implications. Heredity (Edinb).

 

Wu Y, Lin F, Zhou Y, Wang J, Sun S, Wang B, Zhang Z, Li G, Lin X, Wang X, Sun Y, Dong Q, Xu C, Gong L, Wendel JF, Zhang Z & Liu B. (2021). Genomic mosaicism due to homoeologous exchange generates extensive phenotypic diversity in nascent allopolyploids. Natl Sci Rev 8, nwaa277.

 

Xiao J, Song C, Liu S, Tao M, Hu J, Wang J, Liu W, Zeng M & Liu Y. (2013). DNA methylation analysis of allotetraploid hybrids of red crucian carp (Carassius auratus red var.) and common carp (Cyprinus carpio L.). PLoS One 8, e56409.

 

Xie S, Khan N, Ramanna MS, Niu L, Marasek-Ciolakowska A, Arens P & van Tuyl JM. (2010). An assessment of chromosomal rearrangements in neopolyploids of Lilium hybrids. Genome 53, 439-446.

 

Yaakov B & Kashkush K. (2011a). Massive alterations of the methylation patterns around DNA transposons in the first four generations of a newly formed wheat allohexaploid. Genome 54, 42-49.

 

Yaakov B & Kashkush K. (2011b). Methylation, transcription, and rearrangements of transposable elements in synthetic allopolyploids. Int J Plant Genomics 2011, 569826.

 

Yaakov B & Kashkush K. (2012). Mobilization of Stowaway-like MITEs in newly formed allohexaploid wheat species. Plant Mol Biol 80, 419-427.

 

Yaakov B, Meyer K, Ben-David S & Kashkush K. (2013). Copy number variation of transposable elements in Triticum-Aegilops genus suggests evolutionary and revolutionary dynamics following allopolyploidization. Plant Cell Rep 32, 1615-1624.

 

Yannopoulos G, Stamatis N, Monastirioti M, Hatzopoulos P & Louis C. (1987). hobo is responsible for the induction of hybrid dysgenesis by strains of Drosophila melanogaster bearing the male recombination factor 23.5MRF. Cell 49, 487-495.

 

Zhang H, Gou X, Zhang A, Wang X, Zhao N, Dong Y, Li L & Liu B. (2016). Transcriptome shock invokes disruption of parental expression-conserved genes in tetraploid wheat. Sci Rep 6, 26363.

 

Zhang X, Ge X, Shao Y, Sun G & Li Z. (2013). Genomic change, retrotransposon mobilization and extensive cytosine methylation alteration in Brassica napus introgressions from two intertribal hybridizations. PLoS One 8, e56346.

 

Zhao L, Xie D, Fan C, Zhang S, Huang L, Ning S, Jiang B, Zhang L, Yuan Z, Liu D & Hao M. (2021). Chromosome Stability of Synthetic-Natural Wheat Hybrids. Front Plant Sci 12, 654382.