Nested plant LTR retrotransposons target specific regions of other elements, while all LTR retrotransposons often target palindromes and nucleosome-occupied regions: in silico study

Jedlička, Pavel; Lexa, Matej; Vanat, I.; Hobza, Roman; Kejnovský, Eduard

doi:10.1186/s13100-019-0186-z

Cited by 16 publications

(10 citation statements)

References 71 publications

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“…Each TE is distributed in the plant genome with a specific insertion preference [130]. LTR-RTEs, such as the Ty3/gypsy and Ty1/copia superfamilies, are present in the centromere regions of the plant genome and play significant and perilous parts in the formation and function of centromeres [12,106,131].…”

Section: Distribution Of Tes In the Plant Genomementioning

confidence: 99%

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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: Distribution Of Tes In the Plant Genomementioning

confidence: 99%

“…This suggests that nesting of LTR-RTEs is not random and depends on chromatin modifications. Class II TEs can also lead to TE nesting, although nesting is common in LTR-RTEs [130].…”

Section: Distribution Of Tes In the Plant Genomementioning

confidence: 99%

The Dynamism of Transposon Methylation for Plant Development and Stress Adaptation

Ramakrishnan

Satish

Kalendar

et al. 2021

IJMS

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“…Specifically, the Gypsy superfamily accounts for over half the size of the T. arvense genome assembly, and the athila and crm lineages made a great proportion to the proliferation of the Gypsy superfamily ( Figure 2A and Table 2 ). For further study of the evolution of LTR-RTs, nested LTR-RTs and relevant pipelines should be considered ( Jedlicka et al, 2019 ; Lexa et al, 2020 ). Overall, LTR-RT proliferation largely contributes to the enlargement of the T. arvense genome size, which is consistent with a recent report ( Geng et al, 2021 ).…”

Section: Discussionmentioning

confidence: 99%

Rapid Genome Evolution and Adaptation of Thlaspi arvense Mediated by Recurrent RNA-Based and Tandem Gene Duplications

Jin

et al. 2022

Front. Plant Sci.

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Retrotransposons are the most abundant group of transposable elements (TEs) in plants, providing an extraordinarily versatile source of genetic variation. Thlaspi arvense, a close relative of the model plant Arabidopsis thaliana with worldwide distribution, thrives from sea level to above 4,000 m elevation in the Qinghai-Tibet Plateau (QTP), China. Its strong adaptability renders it an ideal model system for studying plant adaptation in extreme environments. However, how the retrotransposons affect the T. arvense genome evolution and adaptation is largely unknown. We report a high-quality chromosome-scale genome assembly of T. arvense with a scaffold N50 of 59.10 Mb. Long terminal repeat retrotransposons (LTR-RTs) account for 56.94% of the genome assembly, and the Gypsy superfamily is the most abundant TEs. The amplification of LTR-RTs in the last six million years primarily contributed to the genome size expansion in T. arvense. We identified 351 retrogenes and 303 genes flanked by LTRs, respectively. A comparative analysis showed that orthogroups containing those retrogenes and genes flanked by LTRs have a higher percentage of significantly expanded orthogroups (SEOs), and these SEOs possess more recent tandem duplicated genes. All present results indicate that RNA-based gene duplication (retroduplication) accelerated the subsequent tandem duplication of homologous genes resulting in family expansions, and these expanded gene families were implicated in plant growth, development, and stress responses, which were one of the pivotal factors for T. arvense’s adaptation to the harsh environment in the QTP regions. In conclusion, the high-quality assembly of the T. arvense genome provides insights into the retroduplication mediated mechanism of plant adaptation to extreme environments.

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“…This can be gene-poor heterochromatic regions for some TE families, or open, transcriptionally active regions for others [23,77]. Examples of TEs inserting favorably in transcriptionally active regions in plants are Mutator elements in maize [78] and mPing MITEs in rice [54], while helitrons preferentially insert in intergenic regions [79] and LTR retrotransposons show a higher preference to insert into older copies of the same family [80]. Nevertheless, it is important to note that selection may obscure initial insertion preferences, so the picture we have now may be biased [23].…”

Section: Tes Facilitate Transcription Factor Network Evolutionmentioning

confidence: 99%

Mobility connects: transposable elements wire new transcriptional networks by transferring transcription factor binding motifs

Qiu

Köhler

2020

Biochemical Society Transactions

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Transposable elements (TEs) constitute major fractions of plant genomes. Their potential to be mobile provides them with the capacity to cause major genome rearrangements. Those effects are potentially deleterious and enforced the evolution of epigenetic suppressive mechanisms controlling TE activity. However, beyond their deleterious effects, TE insertions can be neutral or even advantageous for the host, leading to long-term retention of TEs in the host genome. Indeed, TEs are increasingly recognized as major drivers of evolutionary novelties by regulating the expression of nearby genes. TEs frequently contain binding motifs for transcription factors and capture binding motifs during transposition, which they spread through the genome by transposition. Thus, TEs drive the evolution and diversification of gene regulatory networks by recruiting lineage-specific targets under the regulatory control of specific transcription factors. This process can explain the rapid and repeated evolution of developmental novelties, such as C4 photosynthesis and a wide spectrum of stress responses in plants. It also underpins the convergent evolution of embryo nourishing tissues, the placenta in mammals and the endosperm in flowering plants. Furthermore, the gene regulatory network underlying flower development has also been largely reshaped by TE-mediated recruitment of regulatory elements; some of them being preserved across long evolutionary timescales. In this review, we highlight the potential role of TEs as evolutionary toolkits in plants by showcasing examples of TE-mediated evolutionary novelties.

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Nested plant LTR retrotransposons target specific regions of other elements, while all LTR retrotransposons often target palindromes and nucleosome-occupied regions: in silico study

Cited by 16 publications

References 71 publications

The Dynamism of Transposon Methylation for Plant Development and Stress Adaptation

The Dynamism of Transposon Methylation for Plant Development and Stress Adaptation

Rapid Genome Evolution and Adaptation of Thlaspi arvense Mediated by Recurrent RNA-Based and Tandem Gene Duplications

Mobility connects: transposable elements wire new transcriptional networks by transferring transcription factor binding motifs

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