- PII
- S3034510325100064-1
- DOI
- 10.7868/S3034510325100064
- Publication type
- Article
- Status
- Published
- Authors
- Volume/ Edition
- Volume 61 / Issue number 10
- Pages
- 62-77
- Abstract
- The DNA transposon superfamily is one of the most widespread among eukaryotes. This study investigates the evolutionary dynamics and transcriptional activity of elements in different individuals of the Pacific oyster (Thunberg, 1793). Transcriptional analysis revealed that the transposase gene of more than half of transposons is expressed, sometimes at high levels. Cases of gene activity dependence on environmental conditions, developmental stages, and tissues were also identified. Data on evolutionary dynamics demonstrate that despite the presence of potentially functional copies in over half of transposons, only a few elements have shown transpositional activity in the recent past. The following scenarios are considered: 1) transposon activity in oysters is strongly suppressed by RNA interference, requiring more extreme and/or prolonged stress exposure to overcome this repression; 2) During evolution, oyster transposons accumulated mutations that did not visibly alter the protein sequence but impaired or inactivated DNA-binding and/or catalytic domains, leaving promoters active (transcription occurs) while rendering the transposase incapable of catalyzing transposition. Since some elements remain transcriptionally active, it is plausible that a combination of favorable factors could trigger transposition events. Studying the evolutionary dynamics of transposable elements (TEs) at the intraspecific level enhances our understanding of evolutionary mechanisms and population genetic structure.
- Keywords
- мобильные генетические элементы ДНК-транспозоны Te1/mariner тихоокеанская устрица Crassostrea gigas Magallana gigas генетическое разнообразие эволюционная динамика
- Date of publication
- 01.10.2025
- Year of publication
- 2025
- Number of purchasers
- 0
- Views
- 20
References
- 1. Frost L.S., Leplae R., Summers A.O., Toussaint A. Mobile genetic elements: The agents of open source evolution // Nat. Rev. Microbiol. 2005. V. 3. № 9. P. 722–732. https://doi.org/10.1038/nrmicro1235
- 2. Kidwell M.G., Lisch D.R. Perspective: Transposable elements, parasitic DNA, and genome evolution // Evolution. 2001. V. 55. № 1. P. 1–24. https://doi.org/10.1111/j.0014-3820.2001.tb01268.x
- 3. Gao B., Wang Y., Diaby M. et al. Evolution of pogo, a separate superfamily of IS630-Tc1-mariner transposons, revealing recurrent domestication events in vertebrates // Mobile DNA. 2020. V. 11. P. 25. https://doi.org/10.1186/s13100-020-00220-0
- 4. Kidwell M.G. Transposable elements and the evolution of genome size in eukaryotes // Genetica. 2002. V. 115. № 1. P. 49–63. https://doi.org/10.1023/a:1016072014259
- 5. Guo B., Zou M., Gan X., He S. Genome size evolution in pufferfish: An insight from BAC clone-based Diodon holocanthus genome sequencing // BMC Genomics. 2010. V. 11. https://doi.org/10.1186/1471-2164-11-396
- 6. De Koning A.P., Gu W., Castoe T.A. et al. Repetitive elements may comprise over two-thirds of the human genome // PLoS Genet. 2011. V. 7. № 12. https://doi.org/10.1371/journal.pgen.1002384
- 7. Bourque G., Burns K.H., Gehring M. et al. Ten things you should know about transposable elements // Genome Biology. 2018. V. 19. № 1. P. 199. https://doi.org/10.1186/s13059-018-1577-z
- 8. Piacentini L., Fanti L., Speechia V. et al. Transposons, environmental changes, and heritable induced phenotypic variability // Chromosoma. 2014. V. 123. № 4. P. 345–354. https://doi.org/10.1007/s00412-014-0464-y
- 9. Koga A., Iida A., Hori H. et al. Vertebrate DNA transposon as a natural mutator: The medaka fish Tol2 element contributes to genetic variation without recognizable traces // Mol. Biol. Evol. 2006. V. 23. № 7. P. 1414–1419. https://doi.org/10.1093/molbev/msl003
- 10. Timmons C.M., Shazib S.U.A., Katz L.A. Epigenetic influences of mobile genetic elements on ciliate genome architecture and evolution // J. Eukaryot. Microbiol. 2022. V. 69. № 5. https://doi.org/10.1111/jeu.12891
- 11. Sinzelle L., Izsvák Z., Ivics Z. Molecular domestication of transposable elements: From detrimental parasites to useful host genes // Cell. Mol. Life Sci. 2009. V. 66. № 6. P. 1073–1093. https://doi.org/10.1007/s00018-009-8376-3
- 12. Kojima K.K. Structural and sequence diversity of eukaryotic transposable elements // Genes Genet. Syst. 2020. V. 94. P. 233–252. https://doi.org/10.1266/ggs.18-00024
- 13. Hotopp J.C.D., Clark M.E. Mобильные элементы как потенциальные векторы горизонтального переноса генетической информации в системах паразит–хозяин // Труды ЗИН. 2009. V. 313. № 3. P. 283–296. https://doi.org/10.31610/trudyzin/2009.313.3.283
- 14. Feschotte C., Pritham E.J. DNA transposons and the evolution of eukaryotic genomes // Annu. Rev. Genet. 2007. V. 41. P. 331–368. https://doi.org/10.1146/annurev.genet.40.110405.090448
- 15. Diaby M., Guan Z., Shi S. et al. Revisiting the Tigger transposon evolution revealing extensive involvement in the shaping of mammal genomes // Biology. 2022. V. 11. № 6. https://doi.org/10.3390/biology11060921
- 16. Tellier M., Bouuaert C.C., Chalmers R. Mariner and the ITm superfamily of transposons // Microbiol. Spectr. 2015. V. 3. № 2. https://doi.org/10.1128/microbiolspec.MDNA3-0033-2014
- 17. Shi S., Puzakov M., Guan Z. et al. Prokaryotic and eukaryotic horizontal transfer of Sailor (DD82E), a new superfamily of IS630-Tc1-Mariner DNA transposons // Biology (Basel). 2021. V. 10. № 10. https://doi.org/10.3390/biology10101005
- 18. Shi S., Puzakov M.V., Puzakova L.V. et al. Hiker, a new family of DNA transposons encoding transposases with DD35E motifs, displays a distinct phylogenetic relationship with most known DNA transposon families of IS630-Tc1-mariner (ITm) // Mol. Phylogenet. Evol. 2023. V. 188. https://doi.org/10.1016/j.ympev.2023.107906
- 19. Пузаков М.В., Пузакова Л.В. Структура и эволюция ДНК-транспозонов надсемейства L31 двустворчатых моллюсков // Мол. биология. 2024. Т. 58. № 1. С. 54–72. https://doi.org/10.31857/S0026898424010051
- 20. Пузакова Л.В., Пузаков М.В., Пузакова Л.М. L31-транспозоны шестилучевых кораллов (Hexacorallia): распространение, разнообразие и эволюция // Генетика. 2024. Т. 60. № 6. С. 22–30. https://doi.org/10.31857/S0016675824060027
- 21. Liu Y., Zong W., Diaby M. et al. Diversity and evolution of pogo and Tc1/mariner transposons in the Apoidea genomes // Biology. 2021. V. 10. https://doi.org/10.3390/biology10090940
- 22. Wang S., Diaby M., Puzakov M. et al. Divergent evolution profiles of DD37D and DD39D families of Tc1/mariner transposons in eukaryotes // Mol. Phylogenet. Evol. 2021. V. 161. https://doi.org/10.1016/j.ympev.2021.107143
- 23. Dupeyron M., Baril T., Bass C., Hayward A. Phylogenetic analysis of the Tc1/mariner superfamily reveals the unexplored diversity of pogo-like elements // Mobile DNA. 2020. V. 11. P. 21. https://doi.org/10.1186/s13100-020-00212-0
- 24. Ivics Z., Hackett P.B., Plasterk R.H., Izsvák Z. Molecular reconstruction of Sleeping Beauty, a Tc1-like transposon from fish, and its transposition in human cells // Cell. 1997. V. 91. № 4. P. 501–510. https://doi.org/10.1016/s0092-8674 (00)80436-5
- 25. Plasterk R.H., Izsvák Z., Ivics Z. Resident aliens: The Tc1/mariner superfamily of transposable elements // Trends in Genetics. 1999. V. 15. № 8. P. 326–332. https://doi.org/10.1016/s0168-9525 (99)01777-1
- 26. Shao H., Tu Z. Expanding the diversity of the IS630-Tc1-mariner superfamily: Discovery of a unique DD37E transposon and reclassification of the DD37D and DD39D transposons // Genetics. 2001. V. 159. № 3. P. 1103–1115. https://doi.org/10.1093/genetics/159.3.1103
- 27. Zhang H.H., Li G.Y., Xiong X.M. et al. TRT, a vertebrate and protozoan Tc1-like transposon: Current activity and horizontal transfer // Genome Biol. and Evol. 2016. V. 8. № 9. P. 2994–3005. https://doi.org/10.1093/gbe/evw213
- 28. Shen D., Gao B., Miskey C. et al. Multiple invasions of visitor, a DD41D family of Tc1/mariner transposons, throughout the evolution of vertebrates // Genome Biol. and Evol. 2020. V. 12. № 7. P. 1060–1073. https://doi.org/10.1093/gbe/evaa135
- 29. Пузаков М.В., Пузакова Л.В. Распространенность, разнообразие и эволюция ДНК-транспозонов L18 (DD37E) в геномах стрекающих (Cnidaria) // Мол. биология. 2022. Т. 56. № 3. С. 476–490. https://doi.org/10.31857/S0026898422030120
- 30. Xiang K., Puzakov M., Shi S. et al. Mosquito (MS), a DD37E family of Tc1/Mariner, displaying a distinct evolution profile from DD37E/TRT and DD37E/L18 // Genes. 2023. V. 14. № 7. https://doi.org/10.3390/genes14071379
- 31. Bleykasten-Grosshans C., Fabrizio R., Friedrich A., Schacherer J. Species-wide transposable element repertoires retrace the evolutionary history of the Saccharomyces cerevisiae host // Mol. Biol. Evol. 2021. V. 38. № 10. P. 4334–4345. https://doi.org/10.1093/molbev/msab171
- 32. Bleykasten-Grosshans C., Neuvéglise C. Transposable elements in yeasts // Comptes Rendus Biol. 2011. V. 334. № 8–9. P. 679–686. https://doi.org/10.1016/j.crvi.2011.05.017
- 33. Пузакова Л.В., Пузаков М.В. Zvezda – новое подсемейство Tc1-подобных транспозонов в геномах Asterozoa // Генетика. 2022. Т. 58. № 2. С. 137–147. https://doi.org/10.31857/S001667582201009X
- 34. Puzakov M.V., Puzakova L.V., Shi S., Cheresiz S.V. maf and mosquito transposons in cnidarians: Evolutionary history and intraspecific differences // Funct. and Integr. Genomics. 2023. V. 23. № 3. P. 15. https://doi.org/10.1007/s10142-023-01175-0
- 35. Puzakov M.V., Puzakova L.V., Cheresiz S.V. An analysis of IS630/Tc1/mariner transposons in the genome of a Pacific oyster, Crassostrea gigas // J. Mol. Evol. 2018. V. 86. № 8. P. 566–580. https://doi.org/10.1007/s00239-018-9868-2
- 36. Altschul S.F., Madden T.L., Schäffer A.A. et al. Gapped BLAST and PSI-BLAST: A new generation of protein database search programs // Nucl. Acids Res. 1997. V. 25. № 17. P. 3389–3402. https://doi.org/10.1093/nar/25.17.3389
- 37. Yamada K.D., Tomii K., Katoh K. Application of the MAFFT sequence alignment program to large data-reexamination of the usefulness of chained guide trees // Bioinform. 2016. V. 32. № 21. P. 3246–3251. https://doi.org/10.1093/bioinformatics/btw412
- 38. Okonechnikov K., Golosova O., Fursov M. Unipro UGENE: A unified bioinformatics toolkit // Bioinform. 2012. V. 28. № 8. P. 1166–1167. https://doi.org/10.1093/bioinformatics/bts091
- 39. Bray N.L., Pimentel H., Meisted P., Pachter L. Near-optimal probabilistic RNA-seq quantification // Nat. Biotechnol. 2016. V. 34. № 5. P. 525–527. https://doi.org/10.1038/nbt.3519
- 40. Almeida M.V., Vernaz G., Putman A.L., Miska E.A. Taming transposable elements in vertebrates: From epigenetic silencing to domestication // Trends in Genet. 2022. V. 38. № 6. P. 529–553. https://doi.org/10.1016/j.tig.2022.02.009
- 41. Loubalova Z., Konstantinidou P., Haase A.D. Themes and variations on piRNA-guided transposon control // Mobile DNA. 2023. V. 14. № 1. P. 10. https://doi.org/10.1186/s13100-023-00298-2
- 42. Юрченко Н.Н., Коваленко Л.В., Захаров И.К. Мобильные генетические элементы: нестабильность генов и геномов // Вавил. журн. генетики и селекции. 2011. V. 15. № 2. P. 261–270.
- 43. Grundy E.E., Diab N., Chiappinelli K.B. Transposable element regulation and expression in cancer // The FEBS J. 2022. V. 289. № 5. P. 1160–1179. https://doi.org/10.1111/febs.15722
- 44. Schwarz R., Koch P., Wilbrandt J., Hoffmann S. Locus-specific expression analysis of transposable elements // Brief. Bioinform. 2022. V. 23. № 1. https://doi.org/10.1093/bib/bbab417