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Animals
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Evolution and Diversity of Transposable Elements in Fish Genomes
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Evolution and Diversity of Transposable Elements in Fish Genomes

A special issue of Animals (ISSN 2076-2615). This special issue belongs to the section "Animal Genetics and Genomics".

Deadline for manuscript submissions: closed (15 June 2022) | Viewed by 5493

Special Issue Editors

Dr. Federica Carducci

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Guest Editor
Laboratory of Evolutionary Genetics, Department of Life and Environmental Sciences (DiSVA), Polytechnic University of Marche, Via Brecce Bianche, I-60131 Ancona, Italy
Interests: genome evolution; transposable elements; gene families; genomic and transcriptomic data; evolutionary genetics
Special Issues, Collections and Topics in MDPI journals
Dr. Marco Barucca

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Guest Editor
Dipartimento di Scienze della Vita e Dell’Ambiente, Università Politecnica delle Marche, Via Brecce Bianche, 60131 Ancona, Italy
Interests: genome evolution; repetitive DNA; transposable elements; gene families; genomic and transcriptomic data; evolutionary genetics
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Ray-finned fishes (Actinopterygii) are a remarkably diverse group of vertebrates with over 30,000 species listed. They have adapted to aquatic environments worldwide, from salt- to freshwaters, from cold to warm seas, and from high-elevation mountain lakes to extreme sea depths. The transposable elements (TEs), able to replicate and move throughout the genome, have been suggested to play a role in the extraordinary environmental adaptation of actinopterygians. Moreover, a huge variation in the ray-finned fish genome size has emerged, and one of the main protagonists in shaping their genomes are TEs.

Studies performed to date provide evidence of the presence of many TE superfamilies in actinopterygians, with a prevalence of class II DNA transposons. Moreover, in ray-finned fish, specific TEs that have been hypothesized to be the result of an intricate relationship between TE evolution and the environment have also been reported. Therefore, the presence of mobile elements in ray-finned fish genomes most likely contributes to shaping their genomes, providing advantageous features that would allow them to successfully adapt to different environments. However, due to the high number of species and their different features related to different lifestyles, TEs and their role in genome evolution are not yet completely understood. Therefore, further studies in this field of research are necessary.

For this Special Issue, we invite original manuscripts on the characterization of TEs, TE evolution, the role of mobile elements in genome evolution, the influence of TEs on transcriptional activity, and their role related to adaptation to environmental conditions. Moreover, studies on TEs conducted through genomic and transcriptomic high-throughput sequencing are welcome, as are reviews on all these aforementioned aspects.

Dr. Federica Carducci
Prof. Dr. Marco Barucca
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Animals is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2400 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • transposable elements (TEs)
  • genome evolution
  • environmental adaptation
  • TEs and transcriptional activity
  • actinopterygians

Published Papers (2 papers)

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Research

11 pages, 2157 KiB  
Article
Transposable Element Tissue-Specific Response to Temperature Stress in the Stenothermal Fish Puntius tetrazona
by Elisa Carotti, Federica Carducci, Adriana Canapa, Marco Barucca and Maria Assunta Biscotti
Animals 2023, 13(1), 1; https://doi.org/10.3390/ani13010001 - 20 Dec 2022
Cited by 2 | Viewed by 2131
Abstract
Ray-finned fish represent a very interesting group of vertebrates comprising a variety of organisms living in different aquatic environments worldwide. In the case of stenothermal fish, thermal fluctuations are poorly tolerated, thus ambient temperature represents a critical factor. In this paper, we considered [...] Read more.
Ray-finned fish represent a very interesting group of vertebrates comprising a variety of organisms living in different aquatic environments worldwide. In the case of stenothermal fish, thermal fluctuations are poorly tolerated, thus ambient temperature represents a critical factor. In this paper, we considered the tiger barb Puntius tetrazona, a freshwater fish belonging to the family Cyprinidae, living at 21–28 °C. We analyzed the available RNA-Seq data obtained from specimens exposed at 27 °C and 13 °C to investigate the transcriptional activity of transposable elements (TEs) and genes encoding for proteins involved in their silencing in the brain, gill, and liver. TEs are one of the tools generating genetic variability that underlies biological evolution, useful for organisms to adapt to environmental changes. Our findings highlighted a different response of TEs in the three analyzed tissues. While in the brain and gill, no variation in TE transcriptional activity was observed, a remarkable increase at 13 °C was recorded in the liver. Moreover, the transcriptional analysis of genes encoding proteins involved in TE silencing such as heterochromatin formation, the NuRD complex, and the RISC complex (e.g., AGO and GW182 proteins) highlighted their activity in the hepatic tissue. Overall, our findings suggested that this tissue is a target organ for this kind of stress, since TE activation might regulate the expression of stress-induced genes, leading to a better response of the organism to temperature changes. Therefore, this view corroborates once again the idea of a potential role of TEs in organism rapid adaptation, hence representing a promising molecular tool for species resilience. Full article
(This article belongs to the Special Issue Evolution and Diversity of Transposable Elements in Fish Genomes)
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17 pages, 7617 KiB  
Article
Diversity of Harbinger-like Transposons in Teleost Fish Genomes
by Ema Etchegaray, Corentin Dechaud, Jérémy Barbier, Magali Naville and Jean-Nicolas Volff
Animals 2022, 12(11), 1429; https://doi.org/10.3390/ani12111429 - 31 May 2022
Cited by 1 | Viewed by 2635
Abstract
Harbinger elements are DNA transposons that are widespread from plants to vertebrates but absent from mammalian genomes. Among vertebrates, teleost fish are the clade presenting not only the largest number of species but also the highest diversity of transposable elements, both quantitatively and [...] Read more.
Harbinger elements are DNA transposons that are widespread from plants to vertebrates but absent from mammalian genomes. Among vertebrates, teleost fish are the clade presenting not only the largest number of species but also the highest diversity of transposable elements, both quantitatively and qualitatively, making them a very attractive group to investigate the evolution of mobile sequences. We studied Harbinger DNA transposons and the distantly related ISL2EU elements in fish, focusing on representative teleost species compared to the spotted gar, the coelacanth, the elephant shark and the amphioxus. We observed high variability in the genomic composition of Harbinger-like sequences in teleost fish, as they covered 0.002–0.14% of the genome, when present. While Harbinger transposons might have been present in a common ancestor of all the fish species studied here, with secondary loss in elephant shark, our results suggests that ISL2EU elements were gained by horizontal transfer at the base of teleost fish 200–300 million years ago, and that there was secondary loss in a common ancestor of pufferfishes and stickleback. Harbinger transposons code for a transposase and a Myb-like protein. We reconstructed and compared molecular phylogenies of both proteins to get insights into the evolution of Harbinger transposons in fish. Transposase and Myb-like protein phylogenies showed global congruent evolution, indicating unique origin of the association between both genes and suggesting rare recombination between transposon sublineages. Finally, we report one case of Harbinger horizontal transfer between divergent fish species and the transcriptional activity of both Harbinger and ISL2EU transposons in teleost fish. There was male-biased expression in the gonads of the medaka fish. Full article
(This article belongs to the Special Issue Evolution and Diversity of Transposable Elements in Fish Genomes)
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