DNA gains and losses in gigantic genomes do not track differences in transposable element-host silencing interactions
Abstract Size evolution among gigantic genomes involves gain and loss of many gigabases of transposable elements (TEs), sequences that parasitize host genomes. Vertebrates suppress TEs using piRNA and KRAB-ZFP pathways. TEs and hosts coevolve in an arms race, where suppression strength reflects TE f...
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| Main Authors: | , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Nature Portfolio
2025-05-01
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| Series: | Communications Biology |
| Online Access: | https://doi.org/10.1038/s42003-025-08127-3 |
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| author | Jie Wang Guangpu Zhang Cheng Sun Liming Chang Yingyong Wang Xin Yang Guiying Chen Michael W. Itgen Ava Haley Jiaxing Tang Rachel Lockridge Mueller |
| author_facet | Jie Wang Guangpu Zhang Cheng Sun Liming Chang Yingyong Wang Xin Yang Guiying Chen Michael W. Itgen Ava Haley Jiaxing Tang Rachel Lockridge Mueller |
| author_sort | Jie Wang |
| collection | DOAJ |
| description | Abstract Size evolution among gigantic genomes involves gain and loss of many gigabases of transposable elements (TEs), sequences that parasitize host genomes. Vertebrates suppress TEs using piRNA and KRAB-ZFP pathways. TEs and hosts coevolve in an arms race, where suppression strength reflects TE fitness costs. In enormous genomes, additional TE costs become miniscule. How, then, do TEs and host suppression invoke further addition of massive DNA amounts? We analyze TE proliferation histories, deletion rates, and community diversities in six salamander genomes (21.3 - 49.9 Gb), alongside gonadal expression of TEs and suppression pathways. We show that TE activity is higher in testes than ovaries, attributable to lower KRAB-ZFP suppression. Unexpectedly, genome size and expansion are uncorrelated with TE deletion rate, proliferation history, expression, and host suppression. Also, TE community diversity increases with genome size, contrasting theoretical predictions. We infer that TE-host antagonism in gigantic genomes produces stochastic TE accumulation, reflecting noisy intermolecular interactions in huge genomes and cells. |
| format | Article |
| id | doaj-art-d68414d5e56241a8ac0fdda1fbf7aa7f |
| institution | OA Journals |
| issn | 2399-3642 |
| language | English |
| publishDate | 2025-05-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Communications Biology |
| spelling | doaj-art-d68414d5e56241a8ac0fdda1fbf7aa7f2025-08-20T01:49:38ZengNature PortfolioCommunications Biology2399-36422025-05-018111610.1038/s42003-025-08127-3DNA gains and losses in gigantic genomes do not track differences in transposable element-host silencing interactionsJie Wang0Guangpu Zhang1Cheng Sun2Liming Chang3Yingyong Wang4Xin Yang5Guiying Chen6Michael W. Itgen7Ava Haley8Jiaxing Tang9Rachel Lockridge Mueller10Chengdu Institute of Biology, Chinese Academy of SciencesChengdu Institute of Biology, Chinese Academy of SciencesCollege of Life Sciences, Capital Normal UniversityChengdu Institute of Biology, Chinese Academy of SciencesSchool of Life Sciences, Sun Yat-sen University, GuangzhouSchool of Life Sciences, Shangrao Normal UniversityCollege of Life Sciences, Sichuan Normal UniversityDepartment of Biology, Colorado State UniversityDepartment of Biology, Colorado State UniversityChengdu Institute of Biology, Chinese Academy of SciencesDepartment of Biology, Colorado State UniversityAbstract Size evolution among gigantic genomes involves gain and loss of many gigabases of transposable elements (TEs), sequences that parasitize host genomes. Vertebrates suppress TEs using piRNA and KRAB-ZFP pathways. TEs and hosts coevolve in an arms race, where suppression strength reflects TE fitness costs. In enormous genomes, additional TE costs become miniscule. How, then, do TEs and host suppression invoke further addition of massive DNA amounts? We analyze TE proliferation histories, deletion rates, and community diversities in six salamander genomes (21.3 - 49.9 Gb), alongside gonadal expression of TEs and suppression pathways. We show that TE activity is higher in testes than ovaries, attributable to lower KRAB-ZFP suppression. Unexpectedly, genome size and expansion are uncorrelated with TE deletion rate, proliferation history, expression, and host suppression. Also, TE community diversity increases with genome size, contrasting theoretical predictions. We infer that TE-host antagonism in gigantic genomes produces stochastic TE accumulation, reflecting noisy intermolecular interactions in huge genomes and cells.https://doi.org/10.1038/s42003-025-08127-3 |
| spellingShingle | Jie Wang Guangpu Zhang Cheng Sun Liming Chang Yingyong Wang Xin Yang Guiying Chen Michael W. Itgen Ava Haley Jiaxing Tang Rachel Lockridge Mueller DNA gains and losses in gigantic genomes do not track differences in transposable element-host silencing interactions Communications Biology |
| title | DNA gains and losses in gigantic genomes do not track differences in transposable element-host silencing interactions |
| title_full | DNA gains and losses in gigantic genomes do not track differences in transposable element-host silencing interactions |
| title_fullStr | DNA gains and losses in gigantic genomes do not track differences in transposable element-host silencing interactions |
| title_full_unstemmed | DNA gains and losses in gigantic genomes do not track differences in transposable element-host silencing interactions |
| title_short | DNA gains and losses in gigantic genomes do not track differences in transposable element-host silencing interactions |
| title_sort | dna gains and losses in gigantic genomes do not track differences in transposable element host silencing interactions |
| url | https://doi.org/10.1038/s42003-025-08127-3 |
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