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Transposable elements (TEs) represent approximately 45% of the human genome and 50-90% of some grass genomes. While most elements contain inactivating mutations, others are reversibly inactivated (silenced) by epigenetic mechanisms, including cytosine methylation. Previous studies have shown that retrotransposons can influence the expression of adj...
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Citations
... Based on the sequence structure of the transposon, the distribution on the chromosome, and the element chimerism in this transpose, it is speculated that the Dasheng transposon is activated by RIRE2 [38]. Previous studies have shown that Dasheng belongs to the high-copy-number family and can be activated under normal circumstances [39], which is consistent with our results (Table 1). Osr13 belongs to the Ty1-copia family and has a very high copy number in rice, which is closely involved in the formation of rice species and may be involved in tissue differentiation [40,41]. ...
High-energy heavy ion beams are a new type of physical mutagen that can produce a wide range of phenotypic variations. In order to understand the mechanism of high-energy heavy ion beams, we resequenced the whole genome of individual plants with obvious phenotypic variations in rice. The sequence alignment results revealed a large number of SNPs and InDels, as well as genetic variations related to grain type and heading date. The distribution of SNP and InDel on chromosomes is random, but they often occur in the up/downstream regions and the intergenic region. Mutagenesis can cause changes in transposons such as Dasheng, mPing, Osr13 and RIRE2, affecting the stability of the genome. This study obtained the major gene mutation types, discovered differentially active transposons, screened out gene variants related to phenotype, and explored the mechanism of high-energy heavy ion beam radiation on rice genes.
... Hybridization and introgression also occur extensively in natural populations and contribute to diversification and speciation. Along with genomic changes, hybridization can result in epigenomic changes like activation of transposable elements (Kashkush and Khasdan, 2007;Rathore et al., 2020), small RNA changes, as well as changes in DNA methylation and histone modifications (Ha et al., 2009;Marfil et al., 2009;Kraitshtein et al., 2010;Zhao et al., 2011) which can lead to the establishment of new species via these stabilizing mechanisms (Feldman and Levy, 2005). In genus Spartina, the hybridization of an European native and an American hexaploid resulted in two genetically uniform hybrids that showed massive methylation changes in their genomes compared to their ancestors (Salmon et al., 2005). ...
Recent research in plant epigenetics has increased our understanding of how epigenetic variability can contribute to adaptive phenotypic plasticity in natural populations. Studies show that environmental changes induce epigenetic switches either independently or in complementation with the genetic variation. Although most of the induced epigenetic variability gets reset between generations and is short-lived, some variation becomes transgenerational and results in heritable phenotypic traits. The short-term epigenetic responses provide the first tier of transient plasticity required for local adaptations while transgenerational epigenetic changes contribute to stress memory and help the plants respond better to recurring or long-term stresses. These transgenerational epigenetic variations translate into an additional tier of diversity which results in stable epialleles. In recent years, studies have been conducted on epigenetic variation in natural populations related to various biological processes, ecological factors, communities, and habitats. With the advent of advanced NGS-based technologies, epigenetic studies targeting plants in diverse environments have increased manifold to enhance our understanding of epigenetic responses to environmental stimuli in facilitating plant fitness. Taking all points together in a frame, the present review is a compilation of present-day knowledge and understanding of the role of epigenetics and its fitness benefits in diverse ecological systems in natural populations.
... Methylation does not have to strictly occur directly within a gene's promoter or gene body to alter its transcription. In fact, retrotransposons can be activated typically via demethylation and their methylation status can influence the expression of surrounding genes (Kashkush and Khasdan 2007). Plant studies showed that these transposable elements are usually hypermethylated to maintain their inactivation and avoid disruption of proximal gene coding regions. ...
... For Oryza sativa L. (cultivated rice), studies have shown high methylation levels for transposable elements and repetitive sequences in its genome (He et al. 2010;Yan et al. 2010). Methylation patterns of long terminal repeats (LTR) which flank the Dasheng retrotransposon were compared with the expression of adjacent genes in rice leaves (Kashkush and Khasdan 2007). Differential methylation was correlated with altered gene expression of nearby genes in a tissue-specific manner indicating the potential role of transposable elements in gene transcription regulation via methylation (Kashkush and Khasdan 2007). ...
... Methylation patterns of long terminal repeats (LTR) which flank the Dasheng retrotransposon were compared with the expression of adjacent genes in rice leaves (Kashkush and Khasdan 2007). Differential methylation was correlated with altered gene expression of nearby genes in a tissue-specific manner indicating the potential role of transposable elements in gene transcription regulation via methylation (Kashkush and Khasdan 2007). Garg et al. (2015) provided evidence suggesting that DNA methylation plays an important role in abiotic stress adaptation/response by regulating expression of a set of stress-responsive genes in rice largely via methylation/ demethylation of proximal TEs. ...
BackgroundA review of research shows that methylation in plants is more complex and sophisticated than in microorganisms and animals. Overall, studies on the effects of abiotic stress on epigenetic modifications in plants are still scarce and limited to few species. Epigenetic regulation of plant responses to environmental stresses has not been elucidated. This study summarizes key effects of abiotic stressors on DNA methylation and histone modifications in plants.DiscussionPlant DNA methylation and histone modifications in responses to abiotic stressors varied and depended on the type and level of stress, plant tissues, age, and species. A critical analysis of the literature available revealed that 44% of the epigenetic modifications induced by abiotic stressors in plants involved DNA hypomethylation, 40% DNA hypermethylation, and 16% histone modification. The epigenetic changes in plants might be underestimated since most authors used methods such as methylation-sensitive amplification polymorphism (MSAP), High performance liquid chromatography (HPLC), and immunolabeling that are less sensitive compared to bisulfite sequencing and single-base resolution methylome analyses. More over, mechanisms underlying epigenetic changes in plants have not yet been determined since most reports showed only the level or/and distribution of DNA methylation and histone modifications.Conclusions
Various epigenetic mechanisms are involved in response to abiotic stressors, and several of them are still unknown. Integrated analysis of the changes in the genome by omic approaches should help to identify novel components underlying mechanisms involved in DNA methylation and histone modifications associated with plant response to environmental stressors.
... However, non-methylated LTR-REs can become transcriptionally active, resulting in transcriptional activation that extends into the flanking sequences (Kashkush et al., 2003). Dasheng is an RE that is polymorphic in numerous rice species and subspecies (Jiang et al., 2002); the expression of some Dasheng presents tissue-specific DNA methylation correlating with nearby gene expression tissue specificity (Kashkush and Khasdan, 2007). Furthermore, non methylated copies of Dasheng REs impact host gene expression by producing antisense chimeric transcripts that putatively promote mRNA degradation (Kashkush and Khasdan, 2007). ...
... Dasheng is an RE that is polymorphic in numerous rice species and subspecies (Jiang et al., 2002); the expression of some Dasheng presents tissue-specific DNA methylation correlating with nearby gene expression tissue specificity (Kashkush and Khasdan, 2007). Furthermore, non methylated copies of Dasheng REs impact host gene expression by producing antisense chimeric transcripts that putatively promote mRNA degradation (Kashkush and Khasdan, 2007). ...
Transposable elements (TEs) contribute to genomic innovations, as well as genome instability, across a wide variety of species. Popular designations such as ‘selfish DNA’ and ‘junk DNA,’ common in the 1980s, may be either inaccurate or misleading, while a more enlightened view of the TE-host relationship covers a range from parasitism to mutualism. Both plant and animal hosts have evolved epigenetic mechanisms to reduce the impact of TEs, both by directly silencing them and by reducing their ability to transpose in the genome. However, TEs have also been co-opted by both plant and animal genomes to perform a variety of physiological functions, ranging from TE-derived proteins acting directly in normal biological functions to innovations in transcription factor activity and also influencing gene expression. Their presence, in fact, can affect a range of features at genome, phenotype, and population levels. The impact that TEs have had on evolution is multifaceted, and many aspects still remain unexplored. In this review, the epigenetic control of TEs is contextualised according to the evolution of complex living systems.
... Transposon display (TD) and transposon methylation display (TMD) are powerful techniques to investigate TE genetic and epigenetic variation, respectively. TD is capable to identify the integration site of transposons in gene tagging (Takagi et al., 2003), whereas TMD surveys CCGG methylation in DNA on the flanks of transposons by applying two CCGG methylation-sensitive isoschizomers MspI and HpaII (Kashkush & Khasdan, 2007;Yaakov & Kashkush, 2011). MspI is sensitive only when the external cytosine is methylated, whereas HpaII is sensitive to methylation of either cytosine (except when the external cytosine is hemi-methylated) (Kashkush & Khasdan, 2007;Yaakov & Kashkush, 2011). ...
... TD is capable to identify the integration site of transposons in gene tagging (Takagi et al., 2003), whereas TMD surveys CCGG methylation in DNA on the flanks of transposons by applying two CCGG methylation-sensitive isoschizomers MspI and HpaII (Kashkush & Khasdan, 2007;Yaakov & Kashkush, 2011). MspI is sensitive only when the external cytosine is methylated, whereas HpaII is sensitive to methylation of either cytosine (except when the external cytosine is hemi-methylated) (Kashkush & Khasdan, 2007;Yaakov & Kashkush, 2011). A combined use of the two enzymes leads to the detection of cytosine methylation status. ...
... We used a modified TMD protocol as previously described (Kashkush & Khasdan, 2007;Yaakov & Kashkush, 2011 Transposon display was achieved using the methylationinsensitive restriction enzyme MseI, rather than HpaII and MspI used in TMD. The MseI-adaptor pair and the TE-specific primer were shown in Table 1 and Table S2. ...
Why invasive species can rapidly adapt to novel environments is a puzzling question known as the genetic paradox of invasive species. This paradox is explainable in terms of transposable elements (TEs) activity, which are theorized to be powerful mutational forces to create genetic variation. Mikania micrantha, a noxious invasive weed, in this sense provides an excellent opportunity to test the explanation. The genetic and epigenetic variation of 21 invasive populations of M. micrantha in southern China have been examined by using transposon display (TD) and transposon methylation display (TMD) techniques to survey 12 TE superfamilies. Our results showed that M. micrantha populations maintained an almost equally high level of TE-based genetic and epigenetic variation and they have been differentiated into subpopulations genetically and epigenetically. A similar positive spatial genetic and epigenetic structure pattern was observed within 300 m. Six and seven TE superfamilies presented significant genetic and epigenetic isolation by distance (IBD) pattern. In total, 59 genetic and 86 epigenetic adaptive TE loci were identified. Of them, 51 genetic and 44 epigenetic loci were found to correlate with 25 environmental variables (including precipitation, temperature, vegetation coverage, and soil metals). Twenty-five transposon-inserted genes were sequenced and homology-based annotated, which are found to be involved in a variety of molecular and cellular functions. Our research consolidates the importance of TE-associated genetic and epigenetic variation in the rapid adaptation and invasion of M. micrantha.
... Dasheng is a retroelement, polymorphic in numerous rice species and subspecies (Jiang, Jordan, & Wessler, 2002). The expression of some Dasheng elements can cause a reduction in the transcription of rice genes adjacent to these elements (Kashkush & Khasdan, 2007). ...
Transposable elements (TEs) are DNA sequences that can change their position within genomes. TEs are present in most organisms and can be an important genomic component. Their activities are manifold: restructuring of genome size, chromosomal rearrangements, induction of gene mutations, and alteration of gene activity by insertion near or within promoters, intronic regions, or enhancer. There are several examples of mutations and other genetic variations determined by the activity of TEs, associated with the evolution of prokaryotic and eukaryotic organisms and the domestication of plants. Generally, TE mobilization occurs when the organism is subjected to stress, which can include both biotic and abiotic stresses, polyploidy conditions , and interspecific hybridizations, very common events in plants. TEs are widely distributed among organisms. TEs also play essential roles in evolution, but most of them are either dormant or inactive. This is mainly determined by epigenetic silencing mechanisms, regulatory systems, and control systems that aim to limit its proliferation. Furthermore, the host has recruited many genes originated from TEs as tran-scriptional regulators, especially in defense against pathogens and invasive genetic elements; this phenomenon is called molecular domestication. Therefore, TEs are responsible for horizontal gene transfer and the movement of genetic material between organisms, even phylogenetically distant, with a consequent remixing of their gene pools.
... The modification participates in various important biological responses, e.g., repressing the expression of transposons and repetitive elements, responding to biotic/abiotic stress, and taking part in early embryogenesis, stem cell differentiation, X chromosome inactivation, and genomic imprinting [19][20][21][22][23][24]. Differences in the extent of DNA methylation can give rise to varied gene expression patterns, leading to phenotypic variation [25]; furthermore, specific sites showing different patterns of 5 mC (either hypermethylation or demethylation) between different individuals or tissues can affect genetic transcription, resulting in morphological changes [26][27][28]. ...
Growth and wood formation are crucial and complex biological processes during tree development. These biological regulatory processes are presumed to be controlled by DNA methylation. However, there is little direct evidence to show that genes taking part in wood regulation are affected by cytosine methylation, resulting in phenotypic variations. Here, we detected epimarkers using a methylation-sensitive amplification polymorphism (MSAP) method and performed epimarker–trait association analysis on the basis of nine growth and wood property traits within populations of 432 genotypes of Populus tomentosa. Tree height was positively correlated with relative full-methylation level, and 1101 out of 2393 polymorphic epimarkers were associated with phenotypic traits, explaining 1.1–7.8% of the phenotypic variation. In total, 116 epimarkers were successfully sequenced, and 96 out of these sequences were linked to putative genes. Among them, 13 candidate genes were randomly selected for verification using quantitative real-time PCR (qRT-PCR), and it also showed the expression of nine putative genes of PtCYP450, PtCpn60, PtPME, PtSCP, PtGH, PtMYB, PtWRKY, PtSTP, and PtABC were negatively correlated with DNA methylation level. Therefore, it suggested that changes in DNA methylation might contribute to regulating tree growth and wood property traits.
... In rice, whole genome methylation patterns are similar among mature leaves, embryos, and seedling shoots and roots, but hypomethylation levels are correlated with expression levels of genes that are preferentially expressed in endosperm [25]. Patterns of 5mC in long terminal repeat (LTR) transposable elements differ between rice leaves and roots [26] and affect neighboring gene expression in A. thaliana [27,28]. Tissue-specific characteristics of genome methylation are also evident in natural populations of Chinese white poplar [29]. ...
Abstract Background As an important epigenetic mark, 5-methylcytosine (5mC) methylation is involved in many DNA-dependent biological processes and plays a role during development and differentiation of multicellular organisms. However, there is still a lack of knowledge about the dynamic aspects and the roles of global 5mC methylation in wood formation in tree trunks. In this study, we not only scrutinized single-base resolution methylomes of primary stems (PS), transitional stems (TS), and secondary stems (SS) of Populus trichocarpa using a high-throughput bisulfite sequencing technique, but also analyzed the effects of 5mC methylation on the expression of genes involved in wood formation. Results The overall average percentages of CG, CHG, and CHH methylation in poplar stems were ~ 53.6%, ~ 37.7%, and ~ 8.5%, respectively, and the differences of 5mC in genome-wide CG/CHG/CHH contexts among PS, TS, and SS were statistically significant (p
... For example, inserting into protein-coding sequences results in pseudogenization. LTR-Rs adjacent to protein-coding genes can downregulate or silence the expression of flanking genes by extending methylation regions or by producing antisense transcripts [52][53][54][55]. LTR-Rs also mediate gene retroposition, capturing genes back into the genome [51]. ...
Background
The African eggplant (Solanum aethiopicum) is a nutritious traditional vegetable used in many African countries, including Uganda and Nigeria. It is thought to have been domesticated in Africa from its wild relative, Solanum anguivi. S. aethiopicum has been routinely used as a source of disease resistance genes for several Solanaceae crops, including Solanum melongena. A lack of genomic resources has meant that breeding of S. aethiopicum has lagged behind other vegetable crops.
Results
We assembled a 1.02-Gb draft genome of S. aethiopicum, which contained predominantly repetitive sequences (78.9%). We annotated 37,681 gene models, including 34,906 protein-coding genes. Expansion of disease resistance genes was observed via 2 rounds of amplification of long terminal repeat retrotransposons, which may have occurred ∼1.25 and 3.5 million years ago, respectively. By resequencing 65 S. aethiopicum and S. anguivi genotypes, 18,614,838 single-nucleotide polymorphisms were identified, of which 34,171 were located within disease resistance genes. Analysis of domestication and demographic history revealed active selection for genes involved in drought tolerance in both “Gilo” and “Shum” groups. A pan-genome of S. aethiopicum was assembled, containing 51,351 protein-coding genes; 7,069 of these genes were missing from the reference genome.
Conclusions
The genome sequence of S. aethiopicum enhances our understanding of its biotic and abiotic resistance. The single-nucleotide polymorphisms identified are immediately available for use by breeders. The information provided here will accelerate selection and breeding of the African eggplant, as well as other crops within the Solanaceae family.
... For example, inserting into protein coding sequences results into the pseudogenization. LTR-Rs adjacent to protein coding genes can down regulate or silence the expression of flanking genes by extending methylation region or by producing anti-sense transcripts [41][42][43][44]. In addition, LTR-Rs also mediate gene retroposition, capturing genes back into the genome [40]. ...
Background
S. aethiopicum is a close relative to S. melongena and has been routinely used to improve disease resistance in S. melongena . However, these efforts have been greatly limited by the lack of a reference genome and the clear understanding of the genes involved during biotic and abiotic stress response.
Results
We present here a draft genome assembly of S. aethiopicum of 1.02 Gb in size, which is predominantly occupied by repetitive sequences (76.2%), particularly long terminal repeat elements. We annotated 37,681 gene models including 34,905 protein-coding genes. We observed an expansion of resistance genes through two rounds of amplification of LTR-Rs, occurred around 1.25 and 3.5 million years ago, respectively. The expansion also occurred in gene families related to drought tolerance. A number of 14,995,740 SNPs are identified by re-sequencing 65 S. aethiopicum genotypes including “Gilo” and “Shum” accessions, 41,046 of which are closely linked to resistance genes. The domestication and demographic history analysis reveals selection of genes involved in drought tolerance in both “Gilo” and “Shum” groups. A pan-genome of S. aethiopicum with a total of 36,250 protein-coding genes was assembled, of which 1,345 genes are missing in the reference genome.
Conclusions
Overall, the genome sequence of S. aethiopicum increases our understanding of the genomic mechanisms of its extraordinary disease resistance and drought tolerance. The SNPs identified are available for potential use by breeders. The information provided here will greatly accelerate the selection and breeding of the African eggplant as well as other crops within the Solanaceae family.
