Characteristics of Duplicated Gene Expression and DNA Methylation Regulation in Different Tissues of Allopolyploid Brassica Napus

Overview

Journal BMC Plant Biol

Publisher Biomed Central

Specialty Biology

Date 2024 Jun 8

PMID 38851683

Authors

Weiqi Sun

Mengdi Li

Jianbo Wang

Affiliations

Soon will be listed here.

Abstract

Plant polyploidization increases the complexity of epigenomes and transcriptional regulation, resulting in genome evolution and enhanced adaptability. However, few studies have been conducted on the relationship between gene expression and epigenetic modification in different plant tissues after allopolyploidization. In this study, we studied gene expression and DNA methylation modification patterns in four tissues (stems, leaves, flowers and siliques) of Brassica napusand its diploid progenitors. On this basis, the alternative splicing patterns and cis-trans regulation patterns of four tissues in B. napus and its diploid progenitors were also analyzed. It can be seen that the number of alternative splicing occurs in the B. napus is higher than that in the diploid progenitors, and the IR type increases the most during allopolyploidy. In addition, we studied the fate changes of duplicated genes after allopolyploidization in B. napus. We found that the fate of most duplicated genes is conserved, but the number of neofunctionalization and specialization is also large. The genetic fate of B. napus was classified according to five replication types (WGD, PD, DSD, TD, TRD). This study also analyzed generational transmission analysis of expression and DNA methylation patterns. Our study provides a reference for the fate differentiation of duplicated genes during allopolyploidization.

References

Tatarinova T, Elhaik E, Pellegrini M . Cross-species analysis of genic GC3 content and DNA methylation patterns. Genome Biol Evol. 2013; 5(8):1443-56. PMC: 3762193. DOI: 10.1093/gbe/evt103. View

Bird K, VanBuren R, Puzey J, Edger P . The causes and consequences of subgenome dominance in hybrids and recent polyploids. New Phytol. 2018; 220(1):87-93. DOI: 10.1111/nph.15256. View

Rensing S . Gene duplication as a driver of plant morphogenetic evolution. Curr Opin Plant Biol. 2014; 17:43-8. DOI: 10.1016/j.pbi.2013.11.002. View

Lu K, Wei L, Li X, Wang Y, Wu J, Liu M . Whole-genome resequencing reveals Brassica napus origin and genetic loci involved in its improvement. Nat Commun. 2019; 10(1):1154. PMC: 6411957. DOI: 10.1038/s41467-019-09134-9. View

Nordborg M . Structured coalescent processes on different time scales. Genetics. 1997; 146(4):1501-14. PMC: 1208092. DOI: 10.1093/genetics/146.4.1501. View

Edger P, Pires J . Gene and genome duplications: the impact of dosage-sensitivity on the fate of nuclear genes. Chromosome Res. 2009; 17(5):699-717. DOI: 10.1007/s10577-009-9055-9. View

Panchy N, Lehti-Shiu M, Shiu S . Evolution of Gene Duplication in Plants. Plant Physiol. 2016; 171(4):2294-316. PMC: 4972278. DOI: 10.1104/pp.16.00523. View

Hughes T, Ekman D, Ardawatia H, Elofsson A, Liberles D . Evaluating dosage compensation as a cause of duplicate gene retention in Paramecium tetraurelia. Genome Biol. 2007; 8(5):213. PMC: 1929130. DOI: 10.1186/gb-2007-8-5-213. View

Leitch A, Leitch I . Genomic plasticity and the diversity of polyploid plants. Science. 2008; 320(5875):481-3. DOI: 10.1126/science.1153585. View

10.

Panchy N, Azodi C, Winship E, OMalley R, Shiu S . Expression and regulatory asymmetry of retained Arabidopsis thaliana transcription factor genes derived from whole genome duplication. BMC Evol Biol. 2019; 19(1):77. PMC: 6416927. DOI: 10.1186/s12862-019-1398-z. View

11.

Kenchanmane Raju S . Gene Dosage Balance Immediately following Whole-Genome Duplication in Arabidopsis. Plant Cell. 2020; 32(5):1344-1345. PMC: 7203935. DOI: 10.1105/tpc.20.00205. View

12.

Lynch M, Conery J . The evolutionary fate and consequences of duplicate genes. Science. 2000; 290(5494):1151-5. DOI: 10.1126/science.290.5494.1151. View

13.

Yoo M, Wendel J . Comparative evolutionary and developmental dynamics of the cotton (Gossypium hirsutum) fiber transcriptome. PLoS Genet. 2014; 10(1):e1004073. PMC: 3879233. DOI: 10.1371/journal.pgen.1004073. View

14.

Teufel A, Liu L, Liberles D . Models for gene duplication when dosage balance works as a transition state to subsequent neo-or sub-functionalization. BMC Evol Biol. 2016; 16:45. PMC: 4761171. DOI: 10.1186/s12862-016-0616-1. View

15.

Yin L, Xu G, Yang J, Zhao M . The Heterogeneity in the Landscape of Gene Dominance in Maize is Accompanied by Unique Chromatin Environments. Mol Biol Evol. 2022; 39(10). PMC: 9547528. DOI: 10.1093/molbev/msac198. View

16.

Cantalapiedra C, Hernandez-Plaza A, Letunic I, Bork P, Huerta-Cepas J . eggNOG-mapper v2: Functional Annotation, Orthology Assignments, and Domain Prediction at the Metagenomic Scale. Mol Biol Evol. 2021; 38(12):5825-5829. PMC: 8662613. DOI: 10.1093/molbev/msab293. View

17.

Jackson S, Chen Z . Genomic and expression plasticity of polyploidy. Curr Opin Plant Biol. 2009; 13(2):153-9. PMC: 2880571. DOI: 10.1016/j.pbi.2009.11.004. View

18.

Assis R, Bachtrog D . Rapid divergence and diversification of mammalian duplicate gene functions. BMC Evol Biol. 2015; 15:138. PMC: 4502564. DOI: 10.1186/s12862-015-0426-x. View

19.

Otto S . The evolutionary consequences of polyploidy. Cell. 2007; 131(3):452-62. DOI: 10.1016/j.cell.2007.10.022. View

20.

Li L, Briskine R, Schaefer R, Schnable P, Myers C, Flagel L . Co-expression network analysis of duplicate genes in maize (Zea mays L.) reveals no subgenome bias. BMC Genomics. 2016; 17(1):875. PMC: 5097351. DOI: 10.1186/s12864-016-3194-0. View