Epigenetics and Genome Evolution in Plants

A special issue of Plants (ISSN 2223-7747). This special issue belongs to the section "Plant Genetics, Genomics and Biotechnology".

Deadline for manuscript submissions: 30 June 2024 | Viewed by 14557

Special Issue Editor


E-Mail Website
Guest Editor
Forest Genetics and Forest Tree Breeding, Georg-August University of Göttingen, Busgenweg 2, D-37077 Gottingen, Germany
Interests: plant genomics; epigenetics; plant physiology; plant development; genome evolution; plant cytogenetics; stress tolerance; next-generation sequencing; ChIP-seq; proteomics; protein–protein interaction; genome editing
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Accumulating evidence many of those were from plant systems suggests the contribution of epigenetic mechanisms to genome evolution. For example, DNA methylation is vital for the silencing of transposable elements, enabling the colonization of a substantial proportion of repetitive sequences in plant genomes. During evolution, these genomic elements are capable of moving and self-replicating in germlines in waves (i.e., epigenetic assimilation), potentially resulting in genetic diversity and genome plasticity. Furthermore, these epigenetically controlled dynamics may also steer the ecological and evolutionary advantage of hybridization and polyploid events by perhaps modulating the transcriptional expression of nearby genes. This special issue aims to collect a wide body of research studies dealing with epigenomics, population epigenetics, and functional genomics in model and non-model plant species that have significant relevance in genome evolution, adaptation, ecological speciation, and diversification.

Dr. Xuan Hieu Cao
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Plants is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • ecological speciation
  • environmental adaptation
  • epialleles
  • epigenetic and transcriptional networks
  • epigenetic inheritance
  • epigenomics
  • genome evolution
  • genome/epigenetic editing
  • population epigenetics
  • microRNA
  • non-coding RNA
  • DNA methylation
  • histone modification

Published Papers (8 papers)

Order results
Result details
Select all
Export citation of selected articles as:

Research

Jump to: Review

22 pages, 12189 KiB  
Article
Epigenetic Regulation of Subgenomic Gene Expression in Allotetraploid Brassica napus
by Meimei Hu, Zengde Xi and Jianbo Wang
Plants 2023, 12(14), 2608; https://doi.org/10.3390/plants12142608 - 10 Jul 2023
Viewed by 1002
Abstract
The allotetraploid Brasscia napus has now been extensively utilized to reveal the genetic processes involved in hybridization and polyploidization. Here, transcriptome, WGBS, and Chip-Seq sequencing data were obtained to explore the regulatory consequences of DNA methylation and histone modifications on gene expression in [...] Read more.
The allotetraploid Brasscia napus has now been extensively utilized to reveal the genetic processes involved in hybridization and polyploidization. Here, transcriptome, WGBS, and Chip-Seq sequencing data were obtained to explore the regulatory consequences of DNA methylation and histone modifications on gene expression in B. napus. When compared with diploid parents, the expression levels of 14,266 (about 32%) and 17,054 (about 30%) genes were altered in the An and Cn subgenomes, respectively, and a total of 4982 DEGs were identified in B. napus. Genes with high or no expression in diploid parents often shifted to medium or low expression in B. napus. The number of genes with elevated methylation levels in gene promoters and gene body regions has increased in An and Cn subgenomes. The peak number of H3K4me3 modification increased, while the peak number of H3K27ac and H3K27me3 decreased in An and Cn subgenomes, and more genes that maintained parental histone modifications were identified in Cn subgenome. The differential multiples of DEGs in B. napus were positively correlated with DNA methylation levels in promoters and the gene body, and the differential multiples of these DEGs were also affected by the degree of variation in DNA methylation levels. Further analysis revealed that about 99% of DEGs were of DNA methylation, and about 68% of DEGs were modified by at least two types of DNA methylation and H3K4me3, H3K27ac, and H3K27me3 histone modifications. These results demonstrate that DNA methylation is crucial for gene expression regulation, and different epigenetic modifications have an essential function in regulating the differential expression of genes in B. napus. Full article
(This article belongs to the Special Issue Epigenetics and Genome Evolution in Plants)
Show Figures

Figure 1

18 pages, 4134 KiB  
Article
The Contribution of Epigenetics to Evolutionary Adaptation in Zingiber kawagoii Hayata (Zingiberaceae) Endemic to Taiwan
by Yi-Shao Li, Pei-Chun Liao, Chung-Te Chang and Shih-Ying Hwang
Plants 2023, 12(7), 1558; https://doi.org/10.3390/plants12071558 - 4 Apr 2023
Viewed by 1353
Abstract
We epigenotyped 211 individuals from 17 Zingiber kawagoii populations using methylation-sensitive amplification polymorphism (MSAP) and investigated the associations of methylated (mMSAP) and unmethylated (uMSAP) loci with 16 environmental variables. Data regarding genetic variation based on amplified fragment length polymorphism (AFLP) were obtained from [...] Read more.
We epigenotyped 211 individuals from 17 Zingiber kawagoii populations using methylation-sensitive amplification polymorphism (MSAP) and investigated the associations of methylated (mMSAP) and unmethylated (uMSAP) loci with 16 environmental variables. Data regarding genetic variation based on amplified fragment length polymorphism (AFLP) were obtained from an earlier study. We found a significant positive correlation between genetic and epigenetic variation. Significantly higher mean mMSAP and uMSAP uHE (unbiased expected heterozygosity: 0.223 and 0.131, respectively, p < 0.001) per locus than that estimated based on AFLP (uHE = 0.104) were found. Genome scans detected 10 mMSAP and 9 uMSAP FST outliers associated with various environmental variables. A significant linear fit for 11 and 12 environmental variables with outlier mMSAP and uMSAP ordination, respectively, generated using full model redundancy analysis (RDA) was found. When conditioned on geography, partial RDA revealed that five and six environmental variables, respectively, were the most important variables influencing outlier mMSAP and uMSAP variation. We found higher genetic (average FST = 0.298) than epigenetic (mMSAP and uMSAP average FST = 0.044 and 0.106, respectively) differentiation and higher genetic isolation-by-distance (IBD) than epigenetic IBD. Strong epigenetic isolation-by-environment (IBE) was found, particularly based on the outlier data, controlling either for geography (mMSAP and uMSAP βE = 0.128 and 0.132, respectively, p = 0.001) or for genetic structure (mMSAP and uMSAP βE = 0.105 and 0.136, respectively, p = 0.001). Our results suggest that epigenetic variants can be substrates for natural selection linked to environmental variables and complement genetic changes in the adaptive evolution of Z. kawagoii populations. Full article
(This article belongs to the Special Issue Epigenetics and Genome Evolution in Plants)
Show Figures

Figure 1

17 pages, 3365 KiB  
Article
Epigenetic Stress and Long-Read cDNA Sequencing of Sunflower (Helianthus annuus L.) Revealed the Origin of the Plant Retrotranscriptome
by Ilya Kirov, Pavel Merkulov, Ekaterina Polkhovskaya, Zakhar Konstantinov, Mikhail Kazancev, Ksenia Saenko, Alexander Polkhovskiy, Maxim Dudnikov, Tsovinar Garibyan, Yakov Demurin and Alexander Soloviev
Plants 2022, 11(24), 3579; https://doi.org/10.3390/plants11243579 - 19 Dec 2022
Cited by 2 | Viewed by 2264
Abstract
Transposable elements (TEs) contribute not only to genome diversity but also to transcriptome diversity in plants. To unravel the sources of LTR retrotransposon (RTE) transcripts in sunflower, we exploited a recently developed transposon activation method (‘TEgenesis’) along with long-read cDNA Nanopore sequencing. This [...] Read more.
Transposable elements (TEs) contribute not only to genome diversity but also to transcriptome diversity in plants. To unravel the sources of LTR retrotransposon (RTE) transcripts in sunflower, we exploited a recently developed transposon activation method (‘TEgenesis’) along with long-read cDNA Nanopore sequencing. This approach allows for the identification of 56 RTE transcripts from different genomic loci including full-length and non-autonomous RTEs. Using the mobilome analysis, we provided a new set of expressed and transpositional active sunflower RTEs for future studies. Among them, a Ty3/Gypsy RTE called SUNTY3 exhibited ongoing transposition activity, as detected by eccDNA analysis. We showed that the sunflower genome contains a diverse set of non-autonomous RTEs encoding a single RTE protein, including the previously described TR-GAG (terminal repeat with the GAG domain) as well as new categories, TR-RT-RH, TR-RH, and TR-INT-RT. Our results demonstrate that 40% of the loci for RTE-related transcripts (nonLTR-RTEs) lack their LTR sequences and resemble conventional eucaryotic genes encoding RTE-related proteins with unknown functions. It was evident based on phylogenetic analysis that three nonLTR-RTEs encode GAG (HadGAG1-3) fused to a host protein. These HadGAG proteins have homologs found in other plant species, potentially indicating GAG domestication. Ultimately, we found that the sunflower retrotranscriptome originated from the transcription of active RTEs, non-autonomous RTEs, and gene-like RTE transcripts, including those encoding domesticated proteins. Full article
(This article belongs to the Special Issue Epigenetics and Genome Evolution in Plants)
Show Figures

Figure 1

15 pages, 1682 KiB  
Article
Intraspecific Variability of Wild-Growing Common Valerian (Valeriana officinalis L.)
by Katarzyna Barbara Bączek, Olga Kosakowska, Maja Boczkowska, Paulina Bolc, Rafał Chmielecki, Ewelina Pióro-Jabrucka, Kavana Raj and Zenon Węglarz
Plants 2022, 11(24), 3455; https://doi.org/10.3390/plants11243455 - 9 Dec 2022
Cited by 2 | Viewed by 1501
Abstract
Common valerian (Valeriana officinalis L.) is an important medicinal plant revealing sedative, hypotensive, anti-spasmodic and anxiolytic activity. The purpose of the study was to determine the intraspecific variability of the common valerian growing wild in Poland and the ‘Lubelski’ landrace, as to [...] Read more.
Common valerian (Valeriana officinalis L.) is an important medicinal plant revealing sedative, hypotensive, anti-spasmodic and anxiolytic activity. The purpose of the study was to determine the intraspecific variability of the common valerian growing wild in Poland and the ‘Lubelski’ landrace, as to their developmental traits, chemical composition and selected genetic parameters. Both wild-growing populations (19) and the landrace (1) were evaluated under ex situ conditions. Observations of the underground organs parameters, both developmental and chemical (according to the European Pharmacopoeia) were carried out in the first year of the plant’s development, while the characteristics of the aboveground organs, followed by the sowing value of seeds (according to the International Seed Testing Association)—in the second year. The genetic analyses were performed using the NGS-DArT-seq method. Results indicate the presence of five different gene pools covering the regions of population’s origin, with a gene flow within and between them. A high level of developmental and chemical variabilities among the wild-growing populations was noticed, however without a clear relation to the region of the origin. The mass of underground organs ranged from 107.4 to 403.6 g FW × plant−1 with the content of sesquiterpenic acids at the level of 0.004–0.094%. Population no 18 was distinguished by the highest content of sesquiterpenic acids and the relatively high mass of underground organs, followed by the admixture of the gene pool, typical for the ‘Lubelski’ landrace. Unlike the ‘Lubelski’ landrace, the wild-growing populations were characterized by a high amount of an essential oils (3.90 to 10.04 mL/kg), which may be promising from the perspective of their potential use. In turn, the sowing value of the seeds obtained from the populations, expressed as the germinability, was rather low (25.25–62.25%). Full article
(This article belongs to the Special Issue Epigenetics and Genome Evolution in Plants)
Show Figures

Figure 1

Review

Jump to: Research

14 pages, 797 KiB  
Review
Biological Activity of Artificial Plant Peptides Corresponding to the Translational Products of Small ORFs in Primary miRNAs and Other Long “Non-Coding” RNAs
by T. N. Erokhina, D. Y. Ryazantsev, S. K. Zavriev and S. Y. Morozov
Plants 2024, 13(8), 1137; https://doi.org/10.3390/plants13081137 - 18 Apr 2024
Viewed by 627
Abstract
Generally, lncPEPs (peptides encoded by long non-coding RNAs) have been identified in many plant species of several families and in some animal species. Importantly, molecular mechanisms of the miPEPs (peptides encoded by primary microRNAs, pri-miRNAs) are often poorly understood in different flowering plants. [...] Read more.
Generally, lncPEPs (peptides encoded by long non-coding RNAs) have been identified in many plant species of several families and in some animal species. Importantly, molecular mechanisms of the miPEPs (peptides encoded by primary microRNAs, pri-miRNAs) are often poorly understood in different flowering plants. Requirement for the additional studies in these directions is highlighted by alternative findings concerning positive regulation of pri-miRNA/miRNA expression by synthetic miPEPs in plants. Further extensive studies are also needed to understand the full set of their roles in eukaryotic organisms. This review mainly aims to consider the available data on the regulatory functions of the synthetic miPEPs. Studies of chemically synthesized miPEPs and analyzing the fine molecular mechanisms of their functional activities are reviewed. Brief description of the studies to identify lncORFs (open reading frames of long non-coding RNAs) and the encoded protein products is also provided. Full article
(This article belongs to the Special Issue Epigenetics and Genome Evolution in Plants)
Show Figures

Figure 1

16 pages, 1082 KiB  
Review
Unlocking the Secret to Higher Crop Yield: The Potential for Histone Modifications
by Weiwei Fang, Carlo Fasano and Giorgio Perrella
Plants 2023, 12(8), 1712; https://doi.org/10.3390/plants12081712 - 20 Apr 2023
Cited by 2 | Viewed by 1634
Abstract
Histone modifications are epigenetic mechanisms, termed relative to genetics, and they refer to the induction of heritable changes without altering the DNA sequence. It is widely known that DNA sequences precisely modulate plant phenotypes to adapt them to the changing environment; however, epigenetic [...] Read more.
Histone modifications are epigenetic mechanisms, termed relative to genetics, and they refer to the induction of heritable changes without altering the DNA sequence. It is widely known that DNA sequences precisely modulate plant phenotypes to adapt them to the changing environment; however, epigenetic mechanisms also greatly contribute to plant growth and development by altering chromatin status. An increasing number of recent studies have elucidated epigenetic regulations on improving plant growth and adaptation, thus making contributions to the final yield. In this review, we summarize the recent advances of epigenetic regulatory mechanisms underlying crop flowering efficiency, fruit quality, and adaptation to environmental stimuli, especially to abiotic stress, to ensure crop improvement. In particular, we highlight the major discoveries in rice and tomato, which are two of the most globally consumed crops. We also describe and discuss the applications of epigenetic approaches in crop breeding programs. Full article
(This article belongs to the Special Issue Epigenetics and Genome Evolution in Plants)
Show Figures

Figure 1

30 pages, 2794 KiB  
Review
Miniature Inverted-Repeat Transposable Elements: Small DNA Transposons That Have Contributed to Plant MICRORNA Gene Evolution
by Joseph L. Pegler, Jackson M. J. Oultram, Christopher W. G. Mann, Bernard J. Carroll, Christopher P. L. Grof and Andrew L. Eamens
Plants 2023, 12(5), 1101; https://doi.org/10.3390/plants12051101 - 1 Mar 2023
Cited by 2 | Viewed by 2207
Abstract
Angiosperms form the largest phylum within the Plantae kingdom and show remarkable genetic variation due to the considerable difference in the nuclear genome size of each species. Transposable elements (TEs), mobile DNA sequences that can amplify and change their chromosome position, account for [...] Read more.
Angiosperms form the largest phylum within the Plantae kingdom and show remarkable genetic variation due to the considerable difference in the nuclear genome size of each species. Transposable elements (TEs), mobile DNA sequences that can amplify and change their chromosome position, account for much of the difference in nuclear genome size between individual angiosperm species. Considering the dramatic consequences of TE movement, including the complete loss of gene function, it is unsurprising that the angiosperms have developed elegant molecular strategies to control TE amplification and movement. Specifically, the RNA-directed DNA methylation (RdDM) pathway, directed by the repeat-associated small-interfering RNA (rasiRNA) class of small regulatory RNA, forms the primary line of defense to control TE activity in the angiosperms. However, the miniature inverted-repeat transposable element (MITE) species of TE has at times avoided the repressive effects imposed by the rasiRNA-directed RdDM pathway. MITE proliferation in angiosperm nuclear genomes is due to their preference to transpose within gene-rich regions, a pattern of transposition that has enabled MITEs to gain further transcriptional activity. The sequence-based properties of a MITE results in the synthesis of a noncoding RNA (ncRNA), which, after transcription, folds to form a structure that closely resembles those of the precursor transcripts of the microRNA (miRNA) class of small regulatory RNA. This shared folding structure results in a MITE-derived miRNA being processed from the MITE-transcribed ncRNA, and post-maturation, the MITE-derived miRNA can be used by the core protein machinery of the miRNA pathway to regulate the expression of protein-coding genes that harbor homologous MITE insertions. Here, we outline the considerable contribution that the MITE species of TE have made to expanding the miRNA repertoire of the angiosperms. Full article
(This article belongs to the Special Issue Epigenetics and Genome Evolution in Plants)
Show Figures

Figure 1

16 pages, 1756 KiB  
Review
DDM1-Mediated TE Silencing in Plants
by Ruth Y. Akinmusola, Catherine-Axa Wilkins and James Doughty
Plants 2023, 12(3), 437; https://doi.org/10.3390/plants12030437 - 18 Jan 2023
Cited by 2 | Viewed by 2971
Abstract
Epigenetic modifications are indispensable for regulating gene bodies and TE silencing. DECREASE IN DNA METHYLATION 1 (DDM1) is a chromatin remodeller involved in histone modifications and DNA methylation. Apart from maintaining the epigenome, DDM1 also maintains key plant traits such as flowering time [...] Read more.
Epigenetic modifications are indispensable for regulating gene bodies and TE silencing. DECREASE IN DNA METHYLATION 1 (DDM1) is a chromatin remodeller involved in histone modifications and DNA methylation. Apart from maintaining the epigenome, DDM1 also maintains key plant traits such as flowering time and heterosis. The role of DDM1 in epigenetic regulation is best characterised in plants, especially arabidopsis, rice, maize and tomato. The epigenetic changes induced by DDM1 establish the stable inheritance of many plant traits for at least eight generations, yet DDM1 does not methylate protein-coding genes. The DDM1 TE silencing mechanism is distinct and has evolved independently of other silencing pathways. Unlike the RNA-directed DNA Methylation (RdDM) pathway, DDM1 does not depend on siRNAs to enforce the heterochromatic state of TEs. Here, we review DDM1 TE silencing activity in the RdDM and non-RdDM contexts. The DDM1 TE silencing machinery is strongly associated with the histone linker H1 and histone H2A.W. While the linker histone H1 excludes the RdDM factors from methylating the heterochromatin, the histone H2A.W variant prevents TE mobility. The DDM1-H2A.W strategy alone silences nearly all the mobile TEs in the arabidopsis genome. Thus, the DDM1-directed TE silencing essentially preserves heterochromatic features and abolishes mobile threats to genome stability. Full article
(This article belongs to the Special Issue Epigenetics and Genome Evolution in Plants)
Show Figures

Figure 1

Back to TopTop