Age‐associated alterations in the somatic mutation and <scp>DNA</scp> methylation levels in plants

Dubrovina, Alexandra S.; Kiselev, Konstantin V.

doi:10.1111/plb.12375

Cited by 65 publications

(55 citation statements)

References 116 publications

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“…Furthermore, C. revoluta is known to exhibit very slow growth (2–3 inches a year) and a relatively long life span (more than 1000 years). Perhaps, methylation-induced mutations may accumulate during extended periods of vegetative growth (Dubrovina and Kiselev 2015 ). Potentially, the meiotic correction system is failing because the reduced homology between repeats inhibits rDNA recombination.…”

Section: Discussionmentioning

confidence: 99%

Astonishing 35S rDNA diversity in the gymnosperm species Cycas revoluta Thunb

Wang

Becher

et al. 2015

Chromosoma

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In all eukaryotes, the highly repeated 35S ribosomal DNA (rDNA) sequences encoding 18S-5.8S-26S ribosomal RNA (rRNA) typically show high levels of intragenomic uniformity due to homogenisation processes, leading to concerted evolution of 35S rDNA repeats. Here, we compared 35S rDNA divergence in several seed plants using next generation sequencing and a range of molecular and cytogenetic approaches. Most species showed similar 35S rDNA homogeneity indicating concerted evolution. However, Cycas revoluta exhibits an extraordinary diversity of rDNA repeats (nucleotide sequence divergence of different copies averaging 12 %), influencing both the coding and non-coding rDNA regions nearly equally. In contrast, its rRNA transcriptome was highly homogeneous suggesting that only a minority of genes (<20 %) encode functional rRNA. The most common SNPs were C > T substitutions located in symmetrical CG and CHG contexts which were also highly methylated. Both functional genes and pseudogenes appear to cluster on chromosomes. The extraordinary high levels of 35S rDNA diversity in C. revoluta, and probably other species of cycads, indicate that the frequency of repeat homogenisation has been much lower in this lineage, compared with all other land plant lineages studied. This has led to the accumulation of methylation-driven mutations and pseudogenisation. Potentially, the reduced homology between paralogs prevented their elimination by homologous recombination, resulting in long-term retention of rDNA pseudogenes in the genome.Electronic supplementary materialThe online version of this article (doi:10.1007/s00412-015-0556-3) contains supplementary material, which is available to authorized users.

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Section: Discussionmentioning

confidence: 99%

Astonishing 35S rDNA diversity in the gymnosperm species Cycas revoluta Thunb

Wang

Becher

et al. 2015

Chromosoma

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“…Additionally, there is evidence about the role of miR156 in redifferentiation during the induction of organogenesis (Liu et al, 2014) and somatic embryo induction (Wu et al, 2011). Moreover, it is well documented that prolonged cultivation of plant cells in vitro induces single nucleotide substitutions and increases the global DNA methylation level in a time-dependent fashion, which is associated with aging in plants (Dubrovina and Kiselev, 2016). …”

Section: Discussionmentioning

confidence: 99%

AGING GENE PATHWAY OF MICRORNAS 156/157 AND 172 IS ALTERED IN JUVENILE AND ADULT PLANTS FROM IN VITRO PROPAGATED Prunus sp.

Bastías

Almada²,

Rojas

et al. 2016

Cienc. Inv. Agr.

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Plants that undergo tissue culture processes often change their morphology and behavior due to the "rejuvenation" caused by the plant growth regulators included in the medium. To evaluate the effects of rejuvenation by tissue culture in Prunus sp., the expression patterns of the aging gene pathway described in plant models, which include the highly conserved microRNA (miRNA or miR) 156/157 and 172 families and several of their respective target genes, were analyzed in distinct Prunus sp. genotypes at different phases of maturity, including true seedling and tissue culture micropropagated plants. In genotypes from true seedling plants, the expression of miR156 and miR157 was higher in the leaves of juvenile plants (one year old) than in those of adult plants (six year old). The opposite pattern was observed with miRNA172 expression. Our results suggest that the aging gene pathway is relatively conserved in Prunus and likely plays a key role in vegetative phase change. However, Prunus sp. plants that were rejuvenated and propagated by in vitro methods showed more erratic behavior for miR156 and miR157 and their target genes, suggesting that tissue culture alters the normal control of the aging pathway.

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“…However, this mechanism, that in natural populations acts as an adaptive tool, may cause changes that could affect the phenotype, which would endanger the maintenance of the characteristics of the conserved plants. In the conservation context, epigenetic changes take on a greater dimension if we consider that many studies relate them with genetic mutations [ 23 ]. Jiang et al [ 24 ] found higher frequency of mutations and epimutations (changes in cytosine methylation status) in Arabidopsis thaliana under salinity stress.…”

Section: Epigenetic Variation In Ex Situ Plant Conservation: the Rmentioning

confidence: 99%

Application of the MSAP Technique to Evaluate Epigenetic Changes in Plant Conservation

González‐Benito

Ibáñez

Pirredda

et al. 2020

IJMS

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Epigenetic variation, and particularly DNA methylation, is involved in plasticity and responses to changes in the environment. Conservation biology studies have focused on the measurement of this variation to establish demographic parameters, diversity levels and population structure to design the appropriate conservation strategies. However, in ex situ conservation approaches, the main objective is to guarantee the characteristics of the conserved material (phenotype and epi-genetic). We review the use of the Methylation Sensitive Amplified Polymorphism (MSAP) technique to detect changes in the DNA methylation patterns of plant material conserved by the main ex situ plant conservation methods: seed banks, in vitro slow growth and cryopreservation. Comparison of DNA methylation patterns before and after conservation is a useful tool to check the fidelity of the regenerated plants, and, at the same time, may be related with other genetic variations that might appear during the conservation process (i.e., somaclonal variation). Analyses of MSAP profiles can be useful in the management of ex situ plant conservation but differs in the approach used in the in situ conservation. Likewise, an easy-to-use methodology is necessary for a rapid interpretation of data, in order to be readily implemented by conservation managers.

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Age‐associated alterations in the somatic mutation and DNA methylation levels in plants

Cited by 65 publications

References 116 publications

Astonishing 35S rDNA diversity in the gymnosperm species Cycas revoluta Thunb

Astonishing 35S rDNA diversity in the gymnosperm species Cycas revoluta Thunb

AGING GENE PATHWAY OF MICRORNAS 156/157 AND 172 IS ALTERED IN JUVENILE AND ADULT PLANTS FROM IN VITRO PROPAGATED Prunus sp.

Application of the MSAP Technique to Evaluate Epigenetic Changes in Plant Conservation

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