Editorial: Mobile Elements and Plant Genome Evolution, Comparative Analyzes and Computational Tools

Kalendar, Ruslan; Sabot, François; Rodríguez, Fernando; Карлов, Г. И.; Natali, Lucia; Alix, Karine

doi:10.3389/fpls.2021.735134

Cited by 13 publications

(11 citation statements)

References 15 publications

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“…As previously mentioned, all types of TEs from both classes have a unique role in genome instability and evolution and organism adaptation to abnormal conditions [222]. Nevertheless, insertion or transposition of TEs in normal conditions may cause harmful effects to organisms, including plants.…”

Section: Epigenetic Effects Of Tesmentioning

confidence: 99%

The Dynamism of Transposon Methylation for Plant Development and Stress Adaptation

Ramakrishnan

Satish

Kalendar

et al. 2021

IJMS

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Plant development processes are regulated by epigenetic alterations that shape nuclear structure, gene expression, and phenotypic plasticity; these alterations can provide the plant with protection from environmental stresses. During plant growth and development, these processes play a significant role in regulating gene expression to remodel chromatin structure. These epigenetic alterations are mainly regulated by transposable elements (TEs) whose abundance in plant genomes results in their interaction with genomes. Thus, TEs are the main source of epigenetic changes and form a substantial part of the plant genome. Furthermore, TEs can be activated under stress conditions, and activated elements cause mutagenic effects and substantial genetic variability. This introduces novel gene functions and structural variation in the insertion sites and primarily contributes to epigenetic modifications. Altogether, these modifications indirectly or directly provide the ability to withstand environmental stresses. In recent years, many studies have shown that TE methylation plays a major role in the evolution of the plant genome through epigenetic process that regulate gene imprinting, thereby upholding genome stability. The induced genetic rearrangements and insertions of mobile genetic elements in regions of active euchromatin contribute to genome alteration, leading to genomic stress. These TE-mediated epigenetic modifications lead to phenotypic diversity, genetic variation, and environmental stress tolerance. Thus, TE methylation is essential for plant evolution and stress adaptation, and TEs hold a relevant military position in the plant genome. High-throughput techniques have greatly advanced the understanding of TE-mediated gene expression and its associations with genome methylation and suggest that controlled mobilization of TEs could be used for crop breeding. However, development application in this area has been limited, and an integrated view of TE function and subsequent processes is lacking. In this review, we explore the enormous diversity and likely functions of the TE repertoire in adaptive evolution and discuss some recent examples of how TEs impact gene expression in plant development and stress adaptation.

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Section: Epigenetic Effects Of Tesmentioning

confidence: 99%

The Dynamism of Transposon Methylation for Plant Development and Stress Adaptation

Ramakrishnan

Satish

Kalendar

et al. 2021

IJMS

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“…Endogenous viruses and LTR retrotransposons play a unique role in the instability and evolution of the genome, as well as the body’s adaptability to aberrant situations [ 55 ]. They make up a considerable portion of the genome, include cis-regulatory regions comparable to protective transcription factors, and can regulate nearby genes by adjusting their expression in response to stress [ 56 ]. Some LTR retrotransposons are probably deployed directly into the genes that are most susceptible to environmental changes as a result of evolutionary adaptations [ 57 ].…”

Section: Discussionmentioning

confidence: 99%

Genetic Diversity in Natural Populations of Rhodiola Species of Different Adaptation Strategies

Terletskaya

Turzhanova

Хапилина

et al. 2023

Genes

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Representatives of the Crassulaceae family’s genus Rhodiola are succulents, making them distinctive in a changing environment. One of the most significant tools for analyzing plant resources, including numerous genetic processes in wild populations, is the analysis of molecular genetic polymorphism. This work aimed to look at the polymorphisms of allelic variations of the superoxide dismutase (SOD) and auxin response factor (ARF) gene families, as well as the genetic diversity of five Rhodiola species, using the retrotransposons-based fingerprinting approach. The multi-locus exon-primed intron-crossing (EPIC-PCR) profiling approach was used to examine allelic variations in the SOD and ARF gene families. We implemented the inter-primer binding site (iPBS) PCR amplification technique for genome profiling, which demonstrated a significant level of polymorphism in the Rhodiola samples studied. Natural populations of Rhodiola species have a great capacity for adaptation to unfavorable environmental influences. The genetic variety of wild populations of Rhodiola species leads to their improved tolerance of opposing environmental circumstances and species evolutionary divergence based on the diversity of reproductive systems.

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“…The high abundance and expansion of TEs might facilitate evolutionary genome rearrangements in M. beccarii and be responsible for the large structural differences between M. beccarii and other studied Musa species. Structural rearrangements mediated by various families of TE elements have been reported in other plants [ 170 , 171 ]; chromosome-scale assemblies anchored by long-molecule sequencing will enable further study of the association of TEs to chromosomal rearrangements.…”

Section: Discussionmentioning

confidence: 99%

Genome assembly ofMusa beccariishows extensive chromosomal rearrangements and genome expansion during evolution of Musaceae genomes

et al. 2022

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Background Musa beccarii (Musaceae) is a banana species native to Borneo, sometimes grown as an ornamental plant. The basic chromosome number of Musa species is x = 7, 10, or 11; however, M. beccarii has a basic chromosome number of x = 9 (2n = 2x = 18), which is the same basic chromosome number of species in the sister genera Ensete and Musella. Musa beccarii is in the section Callimusa, which is sister to the section Musa. We generated a high-quality chromosome-scale genome assembly of M. beccarii to better understand the evolution and diversity of genomes within the family Musaceae. Findings The M. beccarii genome was assembled by long-read and Hi-C sequencing, and genes were annotated using both long Iso-seq and short RNA-seq reads. The size of M. beccarii was the largest among all known Musaceae assemblies (∼570 Mbp) due to the expansion of transposable elements and increased 45S ribosomal DNA sites. By synteny analysis, we detected extensive genome-wide chromosome fusions and fissions between M. beccarii and the other Musa and Ensete species, far beyond those expected from differences in chromosome number. Within Musaceae, M. beccarii showed a reduced number of terpenoid synthase genes, which are related to chemical defense, and enrichment in lipid metabolism genes linked to the physical defense of the cell wall. Furthermore, type III polyketide synthase was the most abundant biosynthetic gene cluster (BGC) in M. beccarii. BGCs were not conserved in Musaceae genomes. Conclusions The genome assembly of M. beccarii is the first chromosome-scale genome assembly in the Callimusa section in Musa, which provides an important genetic resource that aids our understanding of the evolution of Musaceae genomes and enhances our knowledge of the pangenome.

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Editorial: Mobile Elements and Plant Genome Evolution, Comparative Analyzes and Computational Tools

Cited by 13 publications

References 15 publications

The Dynamism of Transposon Methylation for Plant Development and Stress Adaptation

The Dynamism of Transposon Methylation for Plant Development and Stress Adaptation

Genetic Diversity in Natural Populations of Rhodiola Species of Different Adaptation Strategies

Genome assembly ofMusa beccariishows extensive chromosomal rearrangements and genome expansion during evolution of Musaceae genomes

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