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Transposable Elements and Phenotypic Variation in Plants
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Transposable Elements and Phenotypic Variation in Plants

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 (31 October 2019) | Viewed by 10745

Special Issue Editors

Prof. Dr. Andrea Cavallini

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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 genomics; genome sequencing; plant breeding; repetitive DNA; transposons
Special Issues, Collections and Topics in MDPI journals
Dr. Flavia Mascagni

E-Mail Website
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. Alexandros Bousios

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Guest Editor
School of Life Sciences, University of Sussex, Brighton, UK
Interests: plant genome evolution; transposable elements; epigenetics; bioinformatics
Prof. Dr. Lucia Natali

E-Mail Website
Guest Editor
Department of Agricultural, Food, and Environmental Sciences, University of Pisa, 80-56124 Pisa, Italy
Interests: plant structural and functional genomics; stress tolerance in plants; genome structure and evolution; transposable elements; repetitive DNA

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 or genome level, with a look to the effect of transposition in determining changes in phenotypic traits.

Dr. Flavia Mascagni
Dr. Alexandros Bousios
Prof. Dr. Andrea Cavallini
Prof. Dr. Lucia Natali
Guest Editors

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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

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Published Papers (2 papers)

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Research

15 pages, 3684 KiB  
Article
On the Trail of Tetu1: Genome-Wide Discovery of CACTA Transposable Elements in Sunflower Genome
by Maria Ventimiglia, Claudio Pugliesi, Alberto Vangelisti, Gabriele Usai, Tommaso Giordani, Lucia Natali, Andrea Cavallini and Flavia Mascagni
Int. J. Mol. Sci. 2020, 21(6), 2021; https://doi.org/10.3390/ijms21062021 - 16 Mar 2020
Cited by 4 | Viewed by 3933
Abstract
Much has been said about sunflower (Helianthus annuus L.) retrotransposons, representing the majority of the sunflower’s repetitive component. By contrast, class II transposons remained poorly described within this species, as they present low sequence conservation and are mostly lacking coding domains, making [...] Read more.
Much has been said about sunflower (Helianthus annuus L.) retrotransposons, representing the majority of the sunflower’s repetitive component. By contrast, class II transposons remained poorly described within this species, as they present low sequence conservation and are mostly lacking coding domains, making the identification and characterization of these transposable elements difficult. The transposable element Tetu1, is a non-autonomous CACTA-like element that has been detected in the coding region of a CYCLOIDEA (CYC) gene of a sunflower mutant, tubular ray flower (turf). Based on our knowledge of Tetu1, the publicly available genome of sunflower was fully scanned. A combination of bioinformatics analyses led to the discovery of 707 putative CACTA sequences: 84 elements with complete ends and 623 truncated elements. A detailed characterization of the identified elements allowed further classification into three subgroups of 347 elements on the base of their terminal repeat sequences. Only 39 encode a protein similar to known transposases (TPase), with 10 TPase sequences showing signals of activation. Finally, an analysis of the proximity of CACTA transposons to sunflower genes showed that the majority of CACTA elements are close to the nearest gene, whereas a relevant fraction resides within gene-encoding sequences, likely interfering with sunflower genome functionality and organization. Full article
(This article belongs to the Special Issue Transposable Elements and Phenotypic Variation in Plants)
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16 pages, 2989 KiB  
Article
Affinities of Terminal Inverted Repeats to DNA Binding Domain of Transposase Affect the Transposition Activity of Bamboo Ppmar2 Mariner-Like Element
by Muthusamy Ramakrishnan, Mingbing Zhou, Chunfang Pan, Heikki Hänninen, Kim Yrjälä, Kunnummal Kurungara Vinod and Dingqin Tang
Int. J. Mol. Sci. 2019, 20(15), 3692; https://doi.org/10.3390/ijms20153692 - 28 Jul 2019
Cited by 9 | Viewed by 6000
Abstract
Mariner-like elements (MLE) are a super-family of DNA transposons widespread in animal and plant genomes. Based on their transposition characteristics, such as random insertions and high-frequency heterogeneous transpositions, several MLEs have been developed to be used as tools in gene tagging and gene [...] Read more.
Mariner-like elements (MLE) are a super-family of DNA transposons widespread in animal and plant genomes. Based on their transposition characteristics, such as random insertions and high-frequency heterogeneous transpositions, several MLEs have been developed to be used as tools in gene tagging and gene therapy. Two active MLEs, Ppmar1 and Ppmar2, have previously been identified in moso bamboo (Phyllostachys edulis). Both of these have a preferential insertion affinity to AT-rich region and their insertion sites are close to random in the host genome. In Ppmar2 element, we studied the affinities of terminal inverted repeats (TIRs) to DNA binding domain (DBD) and their influence on the transposition activity. We could identify two putative boxes in the TIRs which play a significant role in defining the TIR’s affinities to the DBD. Seven mutated TIRs were constructed, differing in affinities based on similarities with those of other plant MLEs. Gel mobility shift assays showed that the TIR mutants with mutation sites G669A-C671A had significantly higher affinities than the mutants with mutation sites C657T-A660T. The high-affinity TIRs indicated that their transposition frequency was 1.5–2.0 times higher than that of the wild type TIRs in yeast transposition assays. The MLE mutants with low-affinity TIRs had relatively lower transposition frequency from that of wild types. We conclude that TIR affinity to DBD significantly affects the transposition activity of Ppmar2. The mutant MLEs highly active TIRs constructed in this study can be used as a tool for bamboo genetic studies. Full article
(This article belongs to the Special Issue Transposable Elements and Phenotypic Variation in Plants)
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