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Selected Papers from the Mobile Genetic Elements Conference, Woods Hole...
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Selected Papers from the Mobile Genetic Elements Conference, Woods Hole MA 2019

A special issue of Genes (ISSN 2073-4425).

Deadline for manuscript submissions: closed (31 December 2020) | Viewed by 29369

Special Issue Editors

Dr. Irina R. Arkhipova

E-Mail Website
Guest Editor
Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA, USA
Interests: transposable elements; horizontal gene transfer; retroelements; reverse transcriptase; comparative genomics
Dr. William S. Reznikoff

E-Mail Website
Guest Editor
Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA, USA
Interests: mobile genetic elements; comparative genetic analysis of microbial populations; vertical vs. horizontal gene transfer in bacteria
Dr. Fernando Rodriguez

E-Mail Website
Guest Editor
Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA, USA
Interests: transposable elements; epigenetics; molecular evolution

Special Issue Information

Dear Colleagues,

The 7th Meeting on Mobile Genetic Elements in Woods Hole, MA, USA will be held on August 29–31, 2019. The event website can be accessed at: https://www.mbl.edu/conferences/2019/04/29/mobile-genetic-elements-conference-2019/.

This meeting brings together experimental and computational scientists seeking to narrow the gap between the fast-paced discovery of transposable elements (TEs) in silico and the limited number of experimental models amenable to functional studies of structural, mechanistic, and regulatory properties of transposable elements and their impact on prokaryotic and eukaryotic hosts.

The current Special Issue invites submissions of original research articles as well as review articles related to the topics of the conference describing recent advances in all aspects related to transposable elements and their interaction with host genomes. The key themes include, but are not limited to:

  • Genome-wide characterization of mobilomes (not limited by taxonomic distribution)
  • Genetic and epigenetic processes regulating TE movement in the host
  • Mechanisms of DNA transposition and retrotransposition
  • Molecular domestication of TEs and their influence on host biology
  • Environmental and population genomics of mobile DNA
  • Computational approaches to the investigation of prokaryotic and eukaryotic mobilomes
  • Mobile elements in health and disease

Dr. Irina R. Arkhipova
Dr. William S. Reznikoff
Dr. Fernando Rodriguez
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. Genes 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 2600 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

  • repetitive DNA
  • transposable elements
  • mobile genetic elements
  • genome evolution
  • transposition

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Published Papers (6 papers)

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Research

18 pages, 2152 KiB  
Article
Transposons-Based Clonal Diversity in Trematode Involves Parts of CR1 (LINE) in Eu- and Heterochromatin
by Anna Solovyeva, Ivan Levakin, Evgeny Zorin, Leonid Adonin, Yuri Khotimchenko and Olga Podgornaya
Genes 2021, 12(8), 1129; https://doi.org/10.3390/genes12081129 - 25 Jul 2021
Cited by 5 | Viewed by 2849
Abstract
Trematode parthenitae have long been believed to form clonal populations, but clonal diversity has been discovered in this asexual stage of the lifecycle. Clonal polymorphism in the model species Himasthla elongata has been previously described, but the source of this phenomenon remains unknown. [...] Read more.
Trematode parthenitae have long been believed to form clonal populations, but clonal diversity has been discovered in this asexual stage of the lifecycle. Clonal polymorphism in the model species Himasthla elongata has been previously described, but the source of this phenomenon remains unknown. In this work, we traced cercarial clonal diversity using a simplified amplified fragment length polymorphism (SAFLP) method and characterised the nature of fragments in diverse electrophoretic bands. The repetitive elements were identified in both the primary sequence of the H. elongata genome and in the transcriptome data. Long-interspersed nuclear elements (LINEs) and long terminal repeat retrotransposons (LTRs) were found to represent an overwhelming majority of the genome and the transposon transcripts. Most sequenced fragments from SAFLP pattern contained the reverse transcriptase (RT, ORF2) domains of LINEs, and only a few sequences belonged to ORFs of LTRs and ORF1 of LINEs. A fragment corresponding to a CR1-like (LINE) spacer region was discovered and named CR1-renegade (CR1-rng). In addition to RT-containing CR1 transcripts, we found short CR1-rng transcripts in the redia transcriptome and short contigs in the mobilome. Probes against CR1-RT and CR1-rng presented strikingly different pictures in FISH mapping, despite both being fragments of CR1. In silico data and Southern blotting indicated that CR1-rng is not tandemly organised. CR1 involvement in clonal diversity is discussed. Full article
(This article belongs to the Special Issue Selected Papers from the Mobile Genetic Elements Conference, Woods Hole MA 2019)
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16 pages, 2396 KiB  
Article
A Survey of Transposon Landscapes in the Putative Ancient Asexual Ostracod Darwinula stevensoni
by Isa Schön, Fernando Rodriguez, Matthew Dunn, Koen Martens, Michael Shribak and Irina R. Arkhipova
Genes 2021, 12(3), 401; https://doi.org/10.3390/genes12030401 - 11 Mar 2021
Cited by 2 | Viewed by 5630
Abstract
How asexual reproduction shapes transposable element (TE) content and diversity in eukaryotic genomes remains debated. We performed an initial survey of TE load and diversity in the putative ancient asexual ostracod Darwinula stevensoni. We examined long contiguous stretches of DNA in clones [...] Read more.
How asexual reproduction shapes transposable element (TE) content and diversity in eukaryotic genomes remains debated. We performed an initial survey of TE load and diversity in the putative ancient asexual ostracod Darwinula stevensoni. We examined long contiguous stretches of DNA in clones from a genomic fosmid library, totaling about 2.5 Mb, and supplemented these data with results on TE abundance and diversity from an Illumina draft genome. In contrast to other TE studies in putatively ancient asexuals, which revealed relatively low TE content, we found that at least 19% of the fosmid dataset and 26% of the genome assembly corresponded to known transposons. We observed a high diversity of transposon families, including LINE, gypsy, PLE, mariner/Tc, hAT, CMC, Sola2, Ginger, Merlin, Harbinger, MITEs and helitrons, with the prevalence of DNA transposons. The predominantly low levels of sequence diversity indicate that many TEs are or have recently been active. In the fosmid data, no correlation was found between telomeric repeats and non-LTR retrotransposons, which are present near telomeres in other taxa. Most TEs in the fosmid data were located outside of introns and almost none were found in exons. We also report an N-terminal Myb/SANT-like DNA-binding domain in site-specific R4/Dong non-LTR retrotransposons. Although initial results on transposable loads need to be verified with high quality draft genomes, this study provides important first insights into TE dynamics in putative ancient asexual ostracods. Full article
(This article belongs to the Special Issue Selected Papers from the Mobile Genetic Elements Conference, Woods Hole MA 2019)
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11 pages, 6669 KiB  
Article
TEfinder: A Bioinformatics Pipeline for Detecting New Transposable Element Insertion Events in Next-Generation Sequencing Data
by Vista Sohrab, Cristina López-Díaz, Antonio Di Pietro, Li-Jun Ma and Dilay Hazal Ayhan
Genes 2021, 12(2), 224; https://doi.org/10.3390/genes12020224 - 4 Feb 2021
Cited by 8 | Viewed by 7869
Abstract
Transposable elements (TEs) are mobile elements capable of introducing genetic changes rapidly. Their importance has been documented in many biological processes, such as introducing genetic instability, altering patterns of gene expression, and accelerating genome evolution. Increasing appreciation of TEs has resulted in a [...] Read more.
Transposable elements (TEs) are mobile elements capable of introducing genetic changes rapidly. Their importance has been documented in many biological processes, such as introducing genetic instability, altering patterns of gene expression, and accelerating genome evolution. Increasing appreciation of TEs has resulted in a growing number of bioinformatics software to identify insertion events. However, the application of existing tools is limited by either narrow-focused design of the package, too many dependencies on other tools, or prior knowledge required as input files that may not be readily available to all users. Here, we reported a simple pipeline, TEfinder, developed for the detection of new TE insertions with minimal software and input file dependencies. The external software requirements are BEDTools, SAMtools, and Picard. Necessary input files include the reference genome sequence in FASTA format, an alignment file from paired-end reads, existing TEs in GTF format, and a text file of TE names. We tested TEfinder among several evolving populations of Fusarium oxysporum generated through a short-term adaptation study. Our results demonstrate that this easy-to-use tool can effectively detect new TE insertion events, making it accessible and practical for TE analysis. Full article
(This article belongs to the Special Issue Selected Papers from the Mobile Genetic Elements Conference, Woods Hole MA 2019)
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18 pages, 3168 KiB  
Article
Evolutionary Dynamics of the Pericentromeric Heterochromatin in Drosophila virilis and Related Species
by Alexander P. Rezvykh, Sergei Yu. Funikov, Lyudmila A. Protsenko, Dina A. Kulikova, Elena S. Zelentsova, Lyubov N. Chuvakova, Justin P. Blumenstiel and Michael B. Evgen’ev
Genes 2021, 12(2), 175; https://doi.org/10.3390/genes12020175 - 27 Jan 2021
Cited by 6 | Viewed by 3404
Abstract
Pericentromeric heterochromatin in Drosophila generally consists of repetitive DNA, forming the environment associated with gene silencing. Despite the expanding knowledge of the impact of transposable elements (TEs) on the host genome, little is known about the evolution of pericentromeric heterochromatin, its structural composition, [...] Read more.
Pericentromeric heterochromatin in Drosophila generally consists of repetitive DNA, forming the environment associated with gene silencing. Despite the expanding knowledge of the impact of transposable elements (TEs) on the host genome, little is known about the evolution of pericentromeric heterochromatin, its structural composition, and age. During the evolution of the Drosophilidae, hundreds of genes have become embedded within pericentromeric regions yet retained activity. We investigated a pericentromeric heterochromatin fragment found in D. virilis and related species, describing the evolution of genes in this region and the age of TE invasion. Regardless of the heterochromatic environment, the amino acid composition of the genes is under purifying selection. However, the selective pressure affects parts of genes in varying degrees, resulting in expansion of gene introns due to TEs invasion. According to the divergence of TEs, the pericentromeric heterochromatin of the species of virilis group began to form more than 20 million years ago by invasions of retroelements, miniature inverted repeat transposable elements (MITEs), and Helitrons. Importantly, invasions into the heterochromatin continue to occur by TEs that fall under the scope of piRNA silencing. Thus, the pericentromeric heterochromatin, in spite of its ability to induce silencing, has the means for being dynamic, incorporating the regions of active transcription. Full article
(This article belongs to the Special Issue Selected Papers from the Mobile Genetic Elements Conference, Woods Hole MA 2019)
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17 pages, 3877 KiB  
Article
Domesticated gag Gene of Drosophila LTR Retrotransposons Is Involved in Response to Oxidative Stress
by Pavel Makhnovskii, Yevheniia Balakireva, Lidia Nefedova, Anton Lavrenov, Ilya Kuzmin and Alexander Kim
Genes 2020, 11(4), 396; https://doi.org/10.3390/genes11040396 - 6 Apr 2020
Cited by 12 | Viewed by 3561
Abstract
Drosophila melanogaster is one of the most extensively used genetic model organisms for studying LTR retrotransposons that are represented by various groups in its genome. However, the phenomenon of molecular domestication of LTR retrotransposons has been insufficiently studied in Drosophila, as well [...] Read more.
Drosophila melanogaster is one of the most extensively used genetic model organisms for studying LTR retrotransposons that are represented by various groups in its genome. However, the phenomenon of molecular domestication of LTR retrotransposons has been insufficiently studied in Drosophila, as well as in other invertebrates. The present work is devoted to studying the role of the domesticated gag gene, Gagr, in the Drosophila genome. The Gagr gene has been shown to be involved in the response to stress caused by exposure to ammonium persulfate, but not in the stress response to oligomycin A, zeomycin, and cadmium chloride. Ammonium persulfate tissue specifically activates the expression of Gagr in the tissues of the carcass, but not in the gut. We found that the Gagr gene promoter contains one binding motif for the transcription factor kayak, a component of the JNK signaling pathway, and two binding motifs for the transcription factor Stat92E, a component of the Jak-STAT signaling pathway. Remarkably, Gagr orthologs contain the second binding motif for Stat92E only in D. melanogaster, D. simulans and D. sechellia, whereas in D. yakuba and D. erecta, Gagr orthologs contain a single motif, and there are no binding sites for Stat92E in the promoters of Gagr orthologs in D. ananassae and in species outside the melanogaster group. The data obtained indicate the formation of the protective function of the Gagr gene during evolution. Full article
(This article belongs to the Special Issue Selected Papers from the Mobile Genetic Elements Conference, Woods Hole MA 2019)
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20 pages, 2265 KiB  
Article
The Complete Genome of an Endogenous Nimavirus (Nimav-1_LVa) From the Pacific Whiteleg Shrimp Penaeus (Litopenaeus) Vannamei
by Weidong Bao, Kathy F. J. Tang and Acacia Alcivar-Warren
Genes 2020, 11(1), 94; https://doi.org/10.3390/genes11010094 - 14 Jan 2020
Cited by 17 | Viewed by 4523
Abstract
White spot syndrome virus (WSSV), the lone virus of the genus Whispovirus under the family Nimaviridae, is one of the most devastating viruses affecting the shrimp farming industry. Knowledge about this virus, in particular, its evolution history, has been limited, partly due [...] Read more.
White spot syndrome virus (WSSV), the lone virus of the genus Whispovirus under the family Nimaviridae, is one of the most devastating viruses affecting the shrimp farming industry. Knowledge about this virus, in particular, its evolution history, has been limited, partly due to its large genome and the lack of other closely related free-living viruses for comparative studies. In this study, we reconstructed a full-length endogenous nimavirus consensus genome, Nimav-1_LVa (279,905 bp), in the genome sequence of Penaeus (Litopenaeus) vannamei breed Kehai No. 1 (ASM378908v1). This endogenous virus seemed to insert exclusively into the telomeric pentanucleotide microsatellite (TAACC/GGTTA)n. It encoded 117 putative genes, with some containing introns, such as g012 (inhibitor of apoptosis, IAP), g046 (crustacean hyperglycemic hormone, CHH), g155 (innexin), g158 (Bax inhibitor 1 like). More than a dozen Nimav-1_LVa genes are involved in the pathogen-host interactions. We hypothesized that g046, g155, g158, and g227 (semaphorin 1A like) were recruited host genes for their roles in immune regulation. Sequence analysis indicated that a total of 43 WSSV genes belonged to the ancestral/core nimavirus gene set, including four genes reported in this study: wsv112 (dUTPase), wsv206, wsv226, and wsv308 (nucleocapsid protein). The availability of the Nimav-1_LVa sequence would help understand the genetic diversity, epidemiology, evolution, and virulence of WSSV. Full article
(This article belongs to the Special Issue Selected Papers from the Mobile Genetic Elements Conference, Woods Hole MA 2019)
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