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Transposable Elements and Phenotypic Variation in Plants

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A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Plant Sciences".

Deadline for manuscript submissions: closed (30 July 2023) | Viewed by 13585

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Special Issue Editors

Prof. Dr. Andrea Cavallini

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Department of Agricultural, Food, and Environmental Sciences, University of Pisa, Via del Borghetto 80, I-56124 Pisa, Italy
Interests: plant genomics; genome sequencing; plant breeding; repetitive DNA; transposons
Special Issues, Collections and Topics in MDPI journals

Dr. Flavia Mascagni

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Guest Editor

Department of Agriculture, Food and Environment (DAFE), University of Pisa, Via del Borghetto 80, I-56124 Pisa, Italy
Interests: bioinformatics application to plant breeding; plant structural and functional genomics; bioinformatics; genome structure and evolution; genome sequencing; crop improvement
Special Issues, Collections and Topics in MDPI journals

Dr. Gabriele Usai

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Guest Editor

Department of Agricultural, Food, and Environmental Sciences, University of Pisa, Via del Borghetto 80, I-56124 Pisa, Italy
Interests: plant genetics and structural genomics; genome sequencing; bioinformatics; genome structure and evolution

Special Issue Information

Dear Colleagues,

Transposable elements (TEs) are mobile DNA sequences that are able to change their chromosomal location. These sequences, which are present in the nuclear genomes of all eukaryotes, were first isolated in consequence of the polymorphisms they induced in hosts. The huge abundance of TEs in plant genomes necessarily results in their interaction with genes over long evolutionary scales. The mutagenic action of TEs creates substantial genetic variability. The proliferation of TEs introduces novel functions via fine-tuning gene activity, contributing, through epigenetic regulation, to the organization of the genome or, after the elements become transcriptionally inactive, introducing a structural variation in insertion sites. Transposition-related changes rarely offer an immediate fitness benefit to their host; rather, they produce neutral mutations that become fixed in the population because of genetic drift. However, in some cases, TE activity can result in phenotypic variations.

In this Special Issue, the contributing authors explore these subjects from a range of perspectives, especially focusing on the potential role of TEs in adaptive evolution and on their impact on gene expression both at locus and genome level, with a look to the effect of transposition in determining changes in phenotypic traits.

Prof. Dr. Andrea Cavallini
Dr. Flavia Mascagni
Dr. Gabriele Usai
Guest Editors

Manuscript Submission Information

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Keywords

Transposable elements
Plant mobile elements
Retrotransposons
Transposon-related structural variations
Transposon-related phenotypic variations
Transposon activation
Transposon silencing
Transposon structure
Transposon dynamics
Transposon evolution

Published Papers (4 papers)

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Research

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17 pages, 4799 KiB

Open AccessArticle

Bioinformatics Analysis of MSH1 Genes of Green Plants: Multiple Parallel Length Expansions, Intron Gains and Losses, Partial Gene Duplications, and Alternative Splicing

by Ming-Zhu Bai and Yan-Yan Guo

Int. J. Mol. Sci. 2023, 24(17), 13620; https://doi.org/10.3390/ijms241713620 - 03 Sep 2023

Cited by 1 | Viewed by 1035

Abstract

MutS homolog 1 (MSH1) is involved in the recombining and repairing of organelle genomes and is essential for maintaining their stability. Previous studies indicated that the length of the gene varied greatly among species and detected species-specific partial gene duplications in Physcomitrella patens. However, there are critical gaps in the understanding of the gene size expansion, and the extent of the partial gene duplication of MSH1 remains unclear. Here, we screened MSH1 genes in 85 selected species with genome sequences representing the main clades of green plants (Viridiplantae). We identified the MSH1 gene in all lineages of green plants, except for nine incomplete species, for bioinformatics analysis. The gene is a singleton gene in most of the selected species with conserved amino acids and protein domains. Gene length varies greatly among the species, ranging from 3234 bp in Ostreococcus tauri to 805,861 bp in Cycas panzhihuaensis. The expansion of MSH1 repeatedly occurred in multiple clades, especially in Gymnosperms, Orchidaceae, and Chloranthus spicatus. MSH1 has exceptionally long introns in certain species due to the gene length expansion, and the longest intron even reaches 101,025 bp. And the gene length is positively correlated with the proportion of the transposable elements (TEs) in the introns. In addition, gene structure analysis indicated that the MSH1 of green plants had undergone parallel intron gains and losses in all major lineages. However, the intron number of seed plants (gymnosperm and angiosperm) is relatively stable. All the selected gymnosperms contain 22 introns except for Gnetum montanum and Welwitschia mirabilis, while all the selected angiosperm species preserve 21 introns except for the ANA grade. Notably, the coding region of MSH1 in algae presents an exceptionally high GC content (47.7% to 75.5%). Moreover, over one-third of the selected species contain species-specific partial gene duplications of MSH1, except for the conserved mosses-specific partial gene duplication. Additionally, we found conserved alternatively spliced MSH1 transcripts in five species. The study of MSH1 sheds light on the evolution of the long genes of green plants. Full article

(This article belongs to the Special Issue Transposable Elements and Phenotypic Variation in Plants)

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17 pages, 2021 KiB

Open AccessArticle

Characterisation of LTR-Retrotransposons of Stevia rebaudiana and Their Use for the Analysis of Genetic Variability

by Samuel Simoni, Clarissa Clemente, Gabriele Usai, Alberto Vangelisti, Lucia Natali, Silvia Tavarini, Luciana G. Angelini, Andrea Cavallini, Flavia Mascagni and Tommaso Giordani

Int. J. Mol. Sci. 2022, 23(11), 6220; https://doi.org/10.3390/ijms23116220 - 01 Jun 2022

Cited by 4 | Viewed by 2088

Abstract

Stevia rebaudiana is one of the most important crops belonging to the Asteraceae family. Stevia is cultivated all over the world as it represents a valid natural alternative to artificial sweeteners thanks to its leaves, which produce steviol glycosides that have high sweetening power and reduced caloric value. In this work, the stevia genome sequence was used to isolate and characterise full-length long-terminal repeat retrotransposons (LTR-REs), which account for more than half of the genome. The Gypsy retrotransposons were twice as abundant as the Copia ones. A disproportionate abundance of elements belonging to the Chromovirus/Tekay lineage was observed among the Gypsy elements. Only the SIRE and Angela lineages represented significant portions of the genome among the Copia elements. The dynamics with which LTR-REs colonised the stevia genome were also estimated; all isolated full-length elements turned out to be relatively young, with a proliferation peak around 1–2 million years ago. However, a different analysis conducted by comparing sequences encoding retrotranscriptase showed the occurrence of an older period in which there was a lot of LTR-RE proliferation. Finally, a group of isolated full-length elements belonging to the lineage Angela was used to analyse the genetic variability in 25 accessions of S. rebaudiana using the Inter-Retrotransposon Amplified Polymorphism (IRAP) protocol. The obtained fingerprints highlighted a high degree of genetic variability and were used to study the genomic structures of the different accessions. It was hypothesised that there are four ancestral subpopulations at the root of the analysed accessions, which all turned out to be admixed. Overall, these data may be useful for genome sequence annotations and for evaluating genetic variability in this species, which may be useful in stevia breeding. Full article

(This article belongs to the Special Issue Transposable Elements and Phenotypic Variation in Plants)

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Review

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40 pages, 4083 KiB

Open AccessReview

The Dynamism of Transposon Methylation for Plant Development and Stress Adaptation

by Muthusamy Ramakrishnan, Lakkakula Satish, Ruslan Kalendar, Mathiyazhagan Narayanan, Sabariswaran Kandasamy, Anket Sharma, Abolghassem Emamverdian, Qiang Wei and Mingbing Zhou

Int. J. Mol. Sci. 2021, 22(21), 11387; https://doi.org/10.3390/ijms222111387 - 21 Oct 2021

Cited by 43 | Viewed by 8219 | Correction

Abstract

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. Full article

(This article belongs to the Special Issue Transposable Elements and Phenotypic Variation in Plants)

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