The Genomic Shock Hypothesis: Genetic and Epigenetic Alterations of Transposable Elements after Interspecific Hybridization in Plants
Abstract
:1. Transposable Elements
2. Epigenetic Control of Transposable Elements
2.1. Epigenetic Silencing of TEs: Initiation
2.2. Epigenetic Silencing of TEs: Maintenance
2.3. Epigenetic Silencing of TEs: Loss
3. Changes in the Epigenetic Silencing of the TEs in Plant Interspecific Hybrids
3.1. Zea
3.2. Helianthus
3.3. Capsella
3.4. Aegilops
3.5. Arabidopsis
3.6. Arachis
3.7. Brassica
3.8. Camellia
3.9. Dactylorhiza
3.10. Gossypium
3.11. Lotus
3.12. Nicotiana
3.13. Oryza
3.14. Poa
3.15. Populus
3.16. Solanum
3.17. Triticum
3.18. Vitis
3.19. Yucca
3.20. Cajanus
3.21. Hieracium
3.22. Mimulus
3.23. Prunus
3.24. Spartina
3.25. Sorghum
Species | Hybrid Type |
Genomic
Shock |
Transcription
Alterations |
DNA
Methylation 1 Alterations | Description | References |
---|---|---|---|---|---|---|
Capsella bursa-pastoris (C. grandiflora × C. orientalis) | Allotetraploid | Yes | - | - | Higher number of TEs only in gene-rich chromosome arms with no important global differences. | [65,66] |
Helianthus spp. | Hybrid Natural & synthetic | Yes | Yes | - | Ancient hybrids have more DNA than parents due to the expansion of certain TE families that are transcriptionally active. Synthetic hybrids do not show increases in genome size. | [8,50,59,60,61,62,63,64] |
Zea mays | Hybrid | Yes | - | - | Alterations in siRNAs and DNA methylation. | [56,57] |
Hybrid | Yes | - | - | Differences in TE protein accumulation. | [55] | |
Hybrid | Yes | Both | - | Most TE families do not show transcriptional differences in the hybrid, but some yes. | [54] | |
Aegilops spp. | Hybrid | Limited | - | Higher | Increase in copy number of some families and increase in DNA methylation in the hybrid. | [67] |
Aegilops geniculata × A. triuncialis | Hybrid | Limited | - | - | Activation of some retrotransposon families. | [68] |
Aegilops markgrafii | Allotetraploid | Limited | - | - | Activation of some TE families. | [69] |
Aegilops sharonensis × Triticum monococcum | Allohexaploid | Limited | Yes | - | Transcriptional activation of some retrotransposon families. | [114,115] |
Aegilops speltoides | Hybrid | Limited | - | - | Activation of some TE families. | [70] |
Arabidopsis suecica (A.thaliana × A. arenosa) | Allotetraploid Natural & synthetic | Limited | Yes | - | Limited higher transpositional activity of TEs in the hybrid. Changes in siRNA population. | [33,71,72,73] |
Arachis duranensis × A. ipaensis | Allotetraploid | Limited | - | - | Mobilization of AhMITE1. | [82] |
Brassica napus | Allotetraploid synthetic | Limited | Yes | Higher | Activation of some families is associated with changes in DNA methylation and siRNA contents in some cases and no activation in others. | [86,87,88,89,90,91,92,93,94] |
Camellia azalea × C. amplexicaulis | Hybrid | Limited | Higher | - | Increase in TE transcription. | [95] |
Dactylorhiza | Allotetraploids | Limited | - | - | Increase in genome size due to the activity of an MITE family. | [96] |
Gossypium arboreum × G. raimondi | Hybrid | Undeter-mined | - | - | Many lncRNAs are activated in the hybrid corresponding to LINEs. | [97] |
Lotus | RIL population | Limited | - | Lower | Mobilization of some retrotransposons associated with demethylation, but does not seem to affect all TE families. | [98] |
Nicotiana arentsii, N. rustica, N. tabacum | Allotetraploid | Limited | - | - | Increase in copy number of some retrotransposon families. | [99,100] |
Oryza sativa × Oenothera biennis | Hybrid | Limited | - | Altered | Mobilization of some TEs and changes in DNA methylation. | [105] |
Oryza sativa × Zizania latifolia | Hybrid | Limited | Yes | Altered | Increase in some TEs copy numbers and transcription. Changes in DNA methylation. | [101,102,103,104] |
Poa annua (P. infirma × P. supina) | Allotetraploid | Limited | - | - | Differences in TE content and distribution between subgenomes and between individuals. | [106] |
Populus canadiensis (P. deltoides × P. nigra) | Allotetraploid | Limited | Higher | - | Differences in the presence of new copies and the transcription of certain retrotransposon families, but not a generalized activation of the TEs. | [107] |
Solanum kurtzianum × S. microdontum | Hybrid | Limited | - | Lower | Tnt1 and Tto1 retrotransposons have moderate mobility and demethylation in the hybrid. | [112] |
Solanum tuberosum × S. kurtzianum | Hybrid Allotetraploid | Limited | - | - | Activation of certain TE families. | [110] |
Triticum aestivum × Secale cereale | Allohexaploid | Limited | - | - | DNA sequence rearrangements associated with TEs. | [122] |
Triticum turgidum × Aegilops tauschii | Hybrid Allohexaploid | Limited | Yes | Altered | Changes in transcriptional activity and DNA methylation in some TE families. | [116,117,118,119,120,121] |
Vitis | Hybrids | Limited | - | - | Increase in Gret1 LTR-retrotransposon copy number in hybrids. | [123] |
Yucca aloifolia × Yucca filamentosa | Hybrid | Limited | Similar | - | No significant changes in TE abundance or transcription. Only one LTR retrotransposon family has more abundance in the hybrid. | [124] |
Arabidopsis thaliana × Arabidopsis lyrata | Allotetraploid | No | - | Yes | No increases in TE mobility. | [34,74,75] |
Arabidopsis thaliana Col-0 × Ler | Hybrid | No | - | Higher | No differences in small RNAs. | [76,77,78,79,80] |
Arabidopsis thaliana Col-0 × met-1 mutant | Hybrid | No | Lower | Higher | Lower transcription and higher DNA methylation compared to mut1. | [81] |
Brassica napus | Allotetraploid natural | No | - | - | No differences. | [83,84,85] |
Cajanus cajan | Hybrid | No | - | Higher | DMRs. | [125] |
Hieracium intybaceum × H. prenanthoides | Hybrid Triploid hybrid | No | - | - | No increase in the TE copy number. Overabundance of endogenous pararetrovirus in triploid hybrids. | [126] |
Mimulus guttatus × Mimulus luteus | Allopolyploid Triploid hybrid | No | - | Lower | Lower DNA methylation in the F1 hybrid returns to the parental levels in few generations, but shows differences between subgenomes. | [127] |
Prunus persica × P. dulcis | Hybrid | No | Similar | Similar | DMRs. | [128,129,135] |
Spartina spp | Hybrid Allotetraploid | No | Some | Some | Few new insertions were detected, a limited TE transcriptional increase, and limited DNA methylation changes. Differential expression of TE-related small RNAs. | [130,131,132,133] |
Solanum lycopersicum × S. pimpinellifolium | Hybrid | No | - | Lower | DNA methylation is lower in the hybrid. | [109] |
Sorghum halepense (S. bicolor × S. ropinquum) | Allotetraploid | No | - | - | No differences in TE content. | [134] |
4. Conclusions: Genomic Shock?
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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de Tomás, C.; Vicient, C.M. The Genomic Shock Hypothesis: Genetic and Epigenetic Alterations of Transposable Elements after Interspecific Hybridization in Plants. Epigenomes 2024, 8, 2. https://doi.org/10.3390/epigenomes8010002
de Tomás C, Vicient CM. The Genomic Shock Hypothesis: Genetic and Epigenetic Alterations of Transposable Elements after Interspecific Hybridization in Plants. Epigenomes. 2024; 8(1):2. https://doi.org/10.3390/epigenomes8010002
Chicago/Turabian Stylede Tomás, Carlos, and Carlos M. Vicient. 2024. "The Genomic Shock Hypothesis: Genetic and Epigenetic Alterations of Transposable Elements after Interspecific Hybridization in Plants" Epigenomes 8, no. 1: 2. https://doi.org/10.3390/epigenomes8010002