Epigenetic modification brings new opportunities for gene capture by transposable elements in allopolyploid Brassica napus

Abstract

Polyploids are widespread in plants and are important drivers for evolution and biodiversity. Allopolyploidy activates transposable elements (TEs) and causes genomic shock. Plant genomes can regulate gene expression by changing the epigenetic modification of TEs, but the mechanism for TEs to capture genes remains to be explored. Helitron TEs used the ‘peel-and-paste’ mechanism to achieve gene capture. We identified 3156 capture events and 326 donor genes of Helitron TEs in Brassica napus (A_nA_nC_nC_n). The donor genes captured by TEs were related to the number, length, and location of their exons. The gene-capturing TEs carrying donor gene fragments were evenly distributed on the genome, and more than half of them were involved in the construction of pseudogenes, becoming the reserve force for polyploid evolution. Gene fragment copies enhanced information storage, providing opportunities for gene mutation and the formation of new genes. Simultaneously, the siRNAs targeting TEs may act on the donor genes due to siRNA crosstalk, and the gene methylation levels increased and the expression levels decreased. The genome sought a balance between sacrificing donor gene expression and silencing TEs, allowing TEs to hide in the genome. In addition, epigenetic modifications may temporarily relax the control of gene capture during allopolyploidization. Our study identified and characterized gene capture events in B. napus, analyzed the effects of DNA methylation and siRNA on gene capture events, and explored the regulation mechanism of gene expression by TE epigenetic modification during allopolyploidization, which will contribute to understanding the formation and evolution mechanism of allopolyploidy.

Acknowledgements

We thank Dr Xiaoming Wu for providing the seeds. This work was supported by the National Natural Science Foundation of China (32470234).

Author contributions

J.W. and Y.X. designed the study. Y.X. performed the data analysis and wrote the manuscript. M.L. was involved in data analysis of gene expression and DNA methylation. J.W. contributed suggestions and revisions.

Data availability

The raw data that support this study are available in the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA) database (RNA-seq, SRR13302173-13302184; Small RNA-seq, SRR24296930-24296941; WGBS, SRR13306925-13306936).

Conflict of interest statement

The authors declare no conflicts of interest.

Supplementary Data

Supplementary data is available at Horticulture Research online.

References

[1] Fox DT, Soltis DE, Soltis PS. et al. Polyploidy: a biological force from cells to ecosystems. Trends Cell Biol. 2020;30:688-94

[2] Van de Peer Y, Ashman TL, Soltis PS. et al. Polyploidy: an evolu-tionary and ecological force in stressful times. Plant Cell. 2021;33: 11-26

[3] McClintock B. The significance of responses of the genome to challenge. Science. 1984;226:792-801

[4] Edger PP, Poorten TJ, VanBuren R. et al. Origin and evolution of the octoploid strawberry genome. Nat Genet. 2019;51:541-7

[5] Morgan C, Zhang H, Henry CE. et al. Derived alleles of two axis proteins affect meiotic traits in autotetraploid Arabidopsis arenosa. Proc Natl Acad Sci USA. 2020;117:8980-8

[6] Tian T, Wang S, Yang S. et al. Genome assembly and genetic dissection of a prominent drought-resistant maize germplasm. Nat Genet. 2023;55:496-506

[7] Qin P, Lu H, Du H. et al. Pan-genome analysis of 33 genetically diverse rice accessions reveals hidden genomic variations. Cell. 2021;184:3542-3558.e16

[8] Zhang L, Liang J, Chen H. et al. A near-complete genome assem-bly of Brassica rapa provides new insights into the evolution of centromeres. Plant Biotechnol J. 2023;21:1022-32

[9] Zhang L, Hu J, Han X. et al. A high-quality apple genome assem-bly reveals the association of a retrotransposon and red fruit colour. Nat Commun. 2019;10:1494

[10] Catlin NS, Josephs EB.The important contribution of transpos-able elements to phenotypic variation and evolution. Curr Opin Plant Biol. 2022; 65:102140

[11] Roessner C, Bhide AS, Hoffmeier A. et al. Conservation of the restricted expression of Brassicaceae Bsister-like genes in seeds requires a transposable element in Arabidopsis thaliana. Mol Biol Evol. 2023;40:msad114

[12] Chow HT, Mosher RA. Small RNA-mediated DNA methylation during plant reproduction. Plant Cell. 2023;35:1787-800

[13] Zhou M, Coruh C, Xu G. et al. The CLASSY family controls tissue-specific DNA methylation patterns in Arabidopsis. Nat Commun. 2022;13:244

[14] Frost JM, Rhee JH, Choi Y. Dynamics of DNA methylation and its impact on plant embryogenesis. Curr Opin Plant Biol. 2024;81: 102593

[15] Kawashima T, Berger F. Epigenetic reprogramming in plant sex-ual reproduction. Nat Rev Genet. 2014;15:613-24

[16] Xu L, Yuan K, Yuan M. et al. Regulation of rice tillering by RNA-directed DNA methylation at miniature inverted-repeat transposable elements. Mol Plant. 2020;13:851-63

[17] Sun S, Zhu J, Guo R. et al. DNA methylation is involved in accli-mation to iron-deficiency in rice (Oryza sativa). Plant J. 2021;107: 727-39

[18] Ziegler DJ, Khan D, Pulgar-Vidal N. et al. Genomic asymmetry of the Brassica napus seed: epigenetic contributions of DNA methy-lation and small RNAs to subgenome bias. Plant J. 2023;115: 690-708

[19] Grabundzija I, Messing SA, Thomas J. et al. A Helitron transposon reconstructed from bats reveals a novel mechanism of genome shuffling in eukaryotes. Nat Commun. 2016;7:10716

[20] Zhao D, Hamilton JP, Vaillancourt B. et al. The unique epigenetic features of Pack-MULEs and their impact on chromosomal base composition and expression spectrum. Nucleic Acids Res. 2018;46: 2380-97

[21] Barro-Trastoy D, Köhler C. Helitrons: genomic parasites that generate developmental novelties. Trends Genet. 2024;40:437-48

[22] Muyle A, Seymour D, Darzentas N. et al. Gene capture by trans-posable elements leads to epigenetic conflict in maize. Mol Plant. 2021;14:237-52

[23] Wu J, Liang J, Lin R. et al. Investigation of Brassica and its relative genomes in the post-genomics era. Hortic Res. 2022;9: uhac182

[24] Chalhoub B, Denoeud F, Liu S. et al. Early allopolyploid evolu-tion in the post-Neolithic Brassica napus oilseed genome. Science. 2014;345:950-3

[25] Chen X, Tong C, Zhang X. et al. A high-quality Brassica napus genome reveals expansion of transposable elements, subgenome evolution and disease resistance. Plant Biotechnol J. 2021;19:615-30

[26] Xiao Y, Xi Z, Wang F. et al. Genomic asymmetric epigenetic mod-ification of transposable elements is involved in gene expres-sion regulation of allopolyploid Brassica napus. Plant J. 2024;117: 226-41

[27] Li M, Sun W, Wang F. et al. Asymmetric epigenetic modifica-tion and homoeolog expression bias in the establishment and evolution of allopolyploid Brassica napus. New Phytol. 2021;232: 898-913

[28] Jiang L, Shen W, Liu C. et al. Engineering drought-tolerant apple by knocking down six GH3 genes and potential application of transgenic apple as a rootstock. Hortic Res. 2022;9:uhac122

[29] Berthelier J, Furci L, Asai S. et al. Long-read direct RNA sequenc-ing reveals epigenetic regulation of chimeric gene-transposon transcripts in Arabidopsis thaliana. Nat Commun. 2023;14:3248

[30] Castanera R, Morales-Díaz N, Gupta S. et al. Transposons are important contributors to gene expression variability under selection in rice populations. eLife. 2023;12:RP86324

[31] SongB, NingW, WeiD. et al. Plant genome resequencing and population genomics: current status and future prospects. Mol Plant. 2023;16:1252-68

[32] Ye L, Lam SZ, Yang L. et al. AAV-mediated delivery of a Sleeping Beauty transposon and an mRNA-encoded transposase for the engineering of therapeutic immune cells. Nat Biomed Eng. 2023;8: 132-48

[33] Jameson N, Georgelis N, Fouladbash E. et al. Helitron medi-ated amplification of cytochrome P450 monooxygenase gene in maize. Plant Mol Biol. 2008;67:295-304

[34] Yang L, Bennetzen JL. Distribution, diversity, evolution, and sur-vival of Helitrons in the maize genome. Proc Natl Acad Sci USA. 2009;106:19922-7

[35] Liu B, Zhao M. How transposable elements are recognized and epigenetically silenced in plants? Curr Opin Plant Biol. 2023;75: 102428

[36] Lawlor MA, Ellison CE. Evolutionary dynamics between transposable elements and their host genomes: mechanisms of suppression and escape. Curr Opin Genet Dev. 2023;82: 102092

[37] Cheetham SW, Faulkner GJ, Dinger ME. Overcoming challenges and dogmas to understand the functions of pseudogenes. Nat Rev Genet. 2020;21:191-201

[38] Troskie RL, Faulkner GJ, Cheetham SW. Processed pseudo-genes: a substrate for evolutionary innovation. BioEssays. 2021; 43:e2100186

[39] Ma Y, Liu S, Gao J. et al. Genome-wide analysis of pseudogenes reveals HBBP1’s human-specific essentiality in erythropoiesis and implication in β-thalassemia. Dev Cell. 2021;56:478-493.e11

[40] Barbaglia AM, Klusman KM, Higgins J. et al. Gene capture by Helitron transposons reshuffles the transcriptome of maize. Genetics. 2012;190:965-75

[41] Kuzmin E, VanderSluis B, Nguyen Ba AN. et al. Exploring whole-genome duplicate gene retention with complex genetic interac-tion analysis. Science. 2020;368:eaaz5667

[42] Birchler JA, Yang H. The multiple fates of gene duplications: deletion, hypofunctionalization, subfunctionalization, neofunc-tionalization, dosage balance constraints, and neutral variation. Plant Cell. 2022;34:2466-74

[43] Xie G, Du X, Hu H. et al. Molecular mechanisms of the RNA polymerases in plant RNA-directed DNA methylation. Trends Biochem Sci. 2024;49:247-56

[44] Wang L, Zheng K, Zeng L. et al. Reinforcement of CHH methy-lation through RNA-directed DNA methylation ensures sexual reproduction in rice. Plant Physiol. 2022;188:1189-209

[45] Shahzad Z, Eaglesfield R, Carr C. et al. Cryptic variation in RNA-directed DNA-methylation controls lateral root development when auxin signalling is perturbed. Nat Commun. 2020;11:218

[46] Ou S, Su W, Liao Y. et al. Benchmarking transposable element annotation methods for creation of a streamlined, comprehen-sive pipeline. Genome Biol. 2019;20:275

[47] Chen C, Chen H, Zhang Y. et al. TBtools: an integrative toolkit developed for interactive analyses of big biological data. Mol Plant. 2020;13:1194-202

[48] Garewal N, Goyal N, Pathania S. et al. Gauging the trends of pseudogenes in plants. Crit Rev Biotechnol. 2021;41:1114-29

[49] Quinlan AR. BEDTools: the Swiss-army tool forgenome feature analysis. Curr Protoc Bioinformatics. 2014;47:11.12.1-34

[50] Zhou Q, Lim J-Q, Sung W-K. et al. An integrated package for bisulfite DNA methylation data analysis with Indel-sensitive mapping. BMC Bioinformatics. 2019;20:47