Transposable elements in plants: Recent advancements, tools and prospects

Ramakrishnan, Muthusamy; Satish, Lakkakula; Sharma, Anket; Vinod, K. K.; Emamverdian, Abolghassem; Zhou, Mingbing; Wei, Qiang

doi:10.1007/s11105-022-01342-w

Cited by 14 publications

(18 citation statements)

References 139 publications

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“…These proteins are present in two main open reading frames (ORFs) that specify GAG, the structural protein forming the nucleocapsid, and the POL polyprotein, which is processed by its own aspartic proteinase (AP) domain. The ORF also contains reverse transcriptase (RT) and RNAse H (RH) to perform reverse transcription, and an integrase (IN) to insert the new copy into the genome (Quesneville 2020;Ramakrishnan et al 2022).…”

Section: Ltr Retrotransposons and Retrovirusesmentioning

confidence: 99%

“…Retrotransposons outnumber genes in plant genomes, comprising the bulk of the genome, and they are largely inactive during development (Alzohairy et al 2014). However, they replicate through cycles of transcription, reverse transcription, and integrate new copies, without deleting original copies from the genome during replication (Quesneville 2020; Ramakrishnan et al 2022). The replication of LTR retrotransposons is equivalent to the intracellular phase of the retroviral life cycle .…”

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confidence: 99%

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The role of LTR retrotransposons in plant genetic engineering: how to control their transposition in the genome

Ramakrishnan

Papolu

Mullasseri³

et al. 2022

Plant Cell Rep

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Key message We briefly discuss that the similarity of LTR retrotransposons to retroviruses is a great opportunity for the development of a genetic engineering tool that exploits intragenic elements in the plant genome for plant genetic improvement. Abstract Long terminal repeat (LTR) retrotransposons are very similar to retroviruses but do not have the property of being infectious. While spreading between its host cells, a retrovirus inserts a DNA copy of its genome into the cells. The ability of retroviruses to cause infection with genome integration allows genes to be delivered to cells and tissues. Retrovirus vectors are, however, only specific to animals and insects, and, thus, are not relevant to plant genetic engineering. However, the similarity of LTR retrotransposons to retroviruses is an opportunity to explore the former as a tool for genetic engineering. Although recent long-read sequencing technologies have advanced the knowledge about transposable elements (TEs), the integration of TEs is still unable either to control them or to direct them to specific genomic locations. The use of existing intragenic elements to achieve the desired genome composition is better than using artificial constructs like vectors, but it is not yet clear how to control the process. Moreover, most LTR retrotransposons are inactive and unable to produce complete proteins. They are also highly mutable. In addition, it is impossible to find a full active copy of a LTR retrotransposon out of thousands of its own copies. Theoretically, if these elements were directly controlled and turned on or off using certain epigenetic mechanisms (inducing by stress or infection), LTR retrotransposons could be a great opportunity to develop a genetic engineering tool using intragenic elements in the plant genome. In this review, the recent developments in uncovering the nature of LTR retrotransposons and the possibility of using these intragenic elements as a tool for plant genetic engineering are briefly discussed.

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Section: Ltr Retrotransposons and Retrovirusesmentioning

confidence: 99%

mentioning

confidence: 99%

The role of LTR retrotransposons in plant genetic engineering: how to control their transposition in the genome

Ramakrishnan

Papolu

Mullasseri³

et al. 2022

Plant Cell Rep

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“…Although almost any article devoted to the study of the consequences of introgressive hybridization ends with the statement that the nature of the physiological and molecular mechanisms of the phenotypic changes in the products of introgressive hybridization that are observed remains unclear, today there is a lot of evidence that these mechanisms are epigenetic, which include DNA methylation, histone modification, the involvement of small RNAs in the regulation of gene expression, and the involvement of transposons. Moreover, none of these mechanisms act independently, but are a component of events, the results of which can be a change in gene expression and the appearance of a new phenotype that is not related to the expression of an alien gene [60,61].…”

Section: Attenuation Of Alien Gene Expressionmentioning

confidence: 99%

“…Currently, a huge amount of evidence has been accumulated regarding the participation of transposons in numerous molecular processes that occur when the stability of the genome is disturbed: during hybridization and polyploidization, which constantly accompany the evolution of plants [61,[67][68][69][70]. The activity of transposons induces structural changes in the genome, causes deletions and duplications, and affects gene expression [67][68][69].…”

Section: Epigenetic Mechanisms Of Expansion Of the Variability Of Int...mentioning

confidence: 99%

“…They can contribute to changes in epigenetic patterns [71,72]. Transposons can generate new genes [61,70], affect their exon-intron structure and, because of this, their expression [73]. All this makes transposons a promoter for all those processes that underlie what is now called genome instability.…”

Section: Epigenetic Mechanisms Of Expansion Of the Variability Of Int...mentioning

confidence: 99%

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Significance of introgression hybridization for extension of genetic variability in recipient genome

Аntonyuk

Shpylchyn

Martynenko

et al. 2022

NRPBE

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Alien chromatin (introgressions) can be incorporated into the wheat genome either through recombination or through translocation. Lines of introgressive origin may not contain identified alien chromatin, although they appear to be changed relative to the original wheat sample by some characteristics that are registered at different levels of phenotype assessment. It has been shown numerous facts of the variability of the recipient genome of hybrid origin. They can be caused by irregular behavior of chromosomes in mitoses of somatic cells with hybrid genome, and DNA changes. Wide phenotypic variability was observed among the progeny of hybrid genomes up to appearance of phenotypic novelties. The study of DNA profiles using several methods revealed the presence of numerous genetic and epigenetic changes, including deletions, changes in gene expression, changes in the methylation pattern, and activation of retrotransposons in the recipient genome. When these changes were not directly related to alien fragments, they are considered as possible mechanisms of extension of genetic variability intra genome of hybrid origin. Transcriptomic analysis of lines of hybrid origin and parental plants using the RNA-seq analyses showed that the change of expression affected a different number of genes. The change in the expression of alien genes occurred in the direction of down-regulation, upregulation was typical for wheat genes. Phenotypic variability during introgressive hybridization can be accompanied by attenuation of the expression of an alien gene when it enters the recipient genome. That may be a consequence of the interaction between the alien gene and the genetic environment of the host genome. Today there is a lot of evidence that these mechanisms are epigenetic, which include DNA methylation, histone modification, the involvement of small RNAs in the regulation of gene expression, and the involvement of transposons. Moreover, none of these mechanisms act independently, but are a component of events, the results of which can be a change in gene expression and the appearance of a new phenotype that is not related to the expression of an alien gene.

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Target capture and genome skimming for plant diversity studies

et al. 2023

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Recent technological advances in long‐read high‐throughput sequencing and assembly methods have facilitated the generation of annotated chromosome‐scale whole‐genome sequence data for evolutionary studies; however, generating such data can still be difficult for many plant species. For example, obtaining high‐molecular‐weight DNA is typically impossible for samples in historical herbarium collections, which often have degraded DNA. The need to fast‐freeze newly collected living samples to conserve high‐quality DNA can be complicated when plants are only found in remote areas. Therefore, short‐read reduced‐genome representations, such as target capture and genome skimming, remain important for evolutionary studies. Here, we review the pros and cons of each technique for non‐model plant taxa. We provide guidance related to logistics, budget, the genomic resources previously available for the target clade, and the nature of the study. Furthermore, we assess the available bioinformatic analyses, detailing best practices and pitfalls, and suggest pathways to combine newly generated data with legacy data. Finally, we explore the possible downstream analyses allowed by the type of data generated using each technique. We provide a practical guide to help researchers make the best‐informed choice regarding reduced genome representation for evolutionary studies of non‐model plants in cases where whole‐genome sequencing remains impractical.

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Transposable elements in plants: Recent advancements, tools and prospects

Cited by 14 publications

References 139 publications

The role of LTR retrotransposons in plant genetic engineering: how to control their transposition in the genome

The role of LTR retrotransposons in plant genetic engineering: how to control their transposition in the genome

Significance of introgression hybridization for extension of genetic variability in recipient genome

Target capture and genome skimming for plant diversity studies

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