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Biology
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De Novo Detection of Transposons
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De Novo Detection of Transposons

A special issue of Biology (ISSN 2079-7737). This special issue belongs to the section "Genetics and Genomics".

Deadline for manuscript submissions: 30 September 2024 | Viewed by 4504

Special Issue Editors

Dr. Dongying Gao

E-Mail Website
Guest Editor
Small Grains and Potato Germplasm Research Unit, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Aberdeen, ID, USA
Interests: transposons
Dr. Kenji K. Kojima

E-Mail Website
Guest Editor
Genetic Information Research Institute, Cupertino, CA 95014, USA
Interests: transposons
Dr. Attila Cristian Rațiu

E-Mail Website
Guest Editor
Department of Genetics, Faculty of Biology, University of Bucharest, 060101 Bucharest, Romania
Interests: transposons

Special Issue Information

Dear Colleagues,

Transposons, or transposable elements (TEs), are ubiquitous genomic components identified in all sequenced genomes. Once considered as ‘junk DNA’ or ‘selfish DNA’, TEs are now known to play critical roles in gene and genome evolution, phenotypic variation and the formation of eukaryotic centromeres and telomeres. In addition, TEs have been widely used to develop molecular tools for basic and applied research, such as random and targeted mutagenesis, gene therapy, phenotypic rescue and gene-tagging. They represent the most abundant dispersed type of repeats and constitute a large fraction of some eukaryotic genomes. Therefore, accurate detection of transposons is extremely important for all genome sequencing projects and related research areas. To acknowledge the latest advancements made for improving the efficiency and quality of transposon discovery and for contributing to a better understanding of their evolutionary and functional impacts, we propose the specific topic ‘De Novo Detection of Transposons’. The research areas of interest will cover, but are not limited to, new progresses in transposon annotation, transposon evolution mechanisms and impact, including horizontal transposon transfers in prokaryotes and eukaryotes, the detection of active and domesticated transposons by various molecular biology and bioinformatics approaches, endeavors aiming to update transposon databases and the development of dedicated software for TE analysis. We invite you to submit manuscripts to this Special Issue, including original research articles, reviews, communication letters, commentaries, and others.

Dr. Dongying Gao
Dr. Kenji K. Kojima
Dr. Attila Cristian Rațiu
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. Biology is an international peer-reviewed open access monthly 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 2700 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

  • transposons
  • de novo detection
  • genome
  • evolution
  • activity
  • data analysis pipeline

Published Papers (3 papers)

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Research

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18 pages, 8971 KiB  
Article
Helenus and Ajax, Two Groups of Non-Autonomous LTR Retrotransposons, Represent a New Type of Small RNA Gene-Derived Mobile Elements
by Kenji K. Kojima
Biology 2024, 13(2), 119; https://doi.org/10.3390/biology13020119 - 13 Feb 2024
Cited by 1 | Viewed by 1232
Abstract
Terminal repeat retrotransposons in miniature (TRIMs) are short non-autonomous long terminal repeat (LTR) retrotransposons found from various eukaryotes. Cassandra is a unique TRIM lineage which contains a 5S rRNA-derived sequence in its LTRs. Here, two new groups of TRIMs, designated Helenus and Ajax, [...] Read more.
Terminal repeat retrotransposons in miniature (TRIMs) are short non-autonomous long terminal repeat (LTR) retrotransposons found from various eukaryotes. Cassandra is a unique TRIM lineage which contains a 5S rRNA-derived sequence in its LTRs. Here, two new groups of TRIMs, designated Helenus and Ajax, are reported based on bioinformatics analysis and the usage of Repbase. Helenus is found from fungi, animals, and plants, and its LTRs contain a tRNA-like sequence. It includes two LTRs and between them, a primer-binding site (PBS) and polypurine tract (PPT) exist. Fungal and plant Helenus generate 5 bp target site duplications (TSDs) upon integration, while animal Helenus generates 4 bp TSDs. Ajax includes a 5S rRNA-derived sequence in its LTR and is found from two nemertean genomes. Ajax generates 5 bp TSDs upon integration. These results suggest that despite their unique promoters, Helenus and Ajax are TRIMs whose transposition is dependent on autonomous LTR retrotransposon. These TRIMs can originate through an insertion of SINE in an LTR of TRIM. The discovery of Helenus and Ajax suggests the presence of TRIMs with a promoter for RNA polymerase III derived from a small RNA gene, which is here collectively termed TRIMp3. Full article
(This article belongs to the Special Issue De Novo Detection of Transposons)
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16 pages, 12204 KiB  
Article
PiggyBac Transposon Mining in the Small Genomes of Animals
by Mengke Guo, George A. Addy, Naisu Yang, Emmanuel Asare, Han Wu, Ahmed A. Saleh, Shasha Shi, Bo Gao and Chengyi Song
Biology 2024, 13(1), 24; https://doi.org/10.3390/biology13010024 - 31 Dec 2023
Viewed by 1235
Abstract
TEs, including DNA transposons, are major contributors of genome expansions, and have played a very significant role in shaping the evolution of animal genomes, due to their capacity to jump from one genomic position to the other. In this study, we investigated the [...] Read more.
TEs, including DNA transposons, are major contributors of genome expansions, and have played a very significant role in shaping the evolution of animal genomes, due to their capacity to jump from one genomic position to the other. In this study, we investigated the evolution landscapes of PB transposons, including their distribution, diversity, activity and structure organization in 79 species of small (compact) genomes of animals comprising both vertebrate and invertebrates. Overall, 212 PB transposon types were detected from almost half (37) of the total number of the small genome species (79) investigated. The detected PB transposon types, which were unevenly distributed in various genera and phyla, have been classified into seven distinct clades or families with good bootstrap support (>80%). The PB transposon types that were identified have a length ranging from 1.23 kb to 9.51 kb. They encode transposases of approximately ≥500 amino acids in length, and possess terminal inverted repeats (TIRs) ranging from 4 bp to 24 bp. Though some of the transposon types have long TIRs (528 bp), they still maintain the consistent and reliable 4 bp target site duplication (TSD) of TTAA. However, PiggyBac-2_Cvir transposon originating from the Crassostrea virginica species exhibits a unique TSD of TATG. The TIRs of the transposons in all the seven families display high divergence, with a highly conserved 5′ end motif. The core transposase domains (DDD) were better conserved among the seven different families compared to the other protein domains, which were less prevalent in the vertebrate genome. The divergent evolution dynamics analysis also indicated that the majority of the PB transposon types identified in this study are either relatively young or old, with some being active. Additionally, numerous invasions of PB transposons were found in the genomes of both vertebrate and invertebrate animals. The data reveals that the PB superfamily is widely distributed in these species. PB transposons exhibit high diversity and activity in the small genomes of animals, and might play a crucial role in shaping the evolution of these small genomes of animals. Full article
(This article belongs to the Special Issue De Novo Detection of Transposons)
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Review

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17 pages, 4952 KiB  
Review
Introduction of Plant Transposon Annotation for Beginners
by Dongying Gao
Biology 2023, 12(12), 1468; https://doi.org/10.3390/biology12121468 - 26 Nov 2023
Viewed by 1481
Abstract
Transposons are mobile DNA sequences that contribute large fractions of many plant genomes. They provide exclusive resources for tracking gene and genome evolution and for developing molecular tools for basic and applied research. Despite extensive efforts, it is still challenging to accurately annotate [...] Read more.
Transposons are mobile DNA sequences that contribute large fractions of many plant genomes. They provide exclusive resources for tracking gene and genome evolution and for developing molecular tools for basic and applied research. Despite extensive efforts, it is still challenging to accurately annotate transposons, especially for beginners, as transposon prediction requires necessary expertise in both transposon biology and bioinformatics. Moreover, the complexity of plant genomes and the dynamic evolution of transposons also bring difficulties for genome-wide transposon discovery. This review summarizes the three major strategies for transposon detection including repeat-based, structure-based, and homology-based annotation, and introduces the transposon superfamilies identified in plants thus far, and some related bioinformatics resources for detecting plant transposons. Furthermore, it describes transposon classification and explains why the terms ‘autonomous’ and ‘non-autonomous’ cannot be used to classify the superfamilies of transposons. Lastly, this review also discusses how to identify misannotated transposons and improve the quality of the transposon database. This review provides helpful information about plant transposons and a beginner’s guide on annotating these repetitive sequences. Full article
(This article belongs to the Special Issue De Novo Detection of Transposons)
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