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Transposable Elements in Plant Genomes
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Transposable Elements in Plant Genomes

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Plant Genetics and Genomics".

Deadline for manuscript submissions: closed (20 November 2021) | Viewed by 21913

Special Issue Editor

Prof. Dr. Dariusz Grzebelus

E-Mail Website
Guest Editor
Institute of Plant Biology and Biotechnology, University of Agriculture in Krakow, Al. 29 Listopada 54, 31-425 Krakow, Poland
Interests: apiaceae; carrot; crop domestication; genetic diversity; molecular markers; plant breeding; plant genomics; transposable elements

Special Issue Information

Dear Colleagues,

Transposable elements (TEs) are DNA segments capable of changing their position in the genome. In plants, TEs occupy a significant portion of genomes and, upon mobilization, are capable of driving dynamic changes through the formation of novel structural variants. These can range from simple insertional polymorphisms, resulting in gene knockouts, to complex rearrangements with profound effects on gene evolution, dosage, and regulation, ultimately resulting in phenotypic diversity.

Even though TEs are essentially considered as parasitic to the host and their activity is mostly deleterious at the individual organism level, they may provide useful genetic variability at the population level, constituting a basis for natural or human-driven selection. Examples have been provided pointing at the significance of TE-derived genetic novelty for adaptability, domestication, and crop improvement.

Rapid progress in high-throughput sequencing technologies allows for more precise identification of TE-associated structural variants (TEASVs) and their functional impact. Also, novel tools facilitating identification of TEASVs and their association with phenotypes are being developed.

In this Special Issue, we invite original research papers, reviews, and concept papers in which the contributing authors explore the interplay between TEs and plant genomes, ranging from the development of novel methods and tools to characterization of the impact of TEs on the host genome structure to examples of the functional impact of TEs on host genes. Papers referring to the global genomic context are welcome.

Prof. Dariusz Grzebelus
Guest Editor

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

  • adaptability
  • genome evolution
  • genome plasticity
  • plants
  • TE-associated structural variants
  • transposable elements
  • transposition

Published Papers (6 papers)

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Research

8 pages, 943 KiB  
Article
DARTS: An Algorithm for Domain-Associated Retrotransposon Search in Genome Assemblies
by Mikhail Biryukov and Kirill Ustyantsev
Genes 2022, 13(1), 9; https://doi.org/10.3390/genes13010009 - 21 Dec 2021
Cited by 6 | Viewed by 2745
Abstract
Retrotransposons comprise a substantial fraction of eukaryotic genomes, reaching the highest proportions in plants. Therefore, identification and annotation of retrotransposons is an important task in studying the regulation and evolution of plant genomes. The majority of computational tools for mining transposable elements (TEs) [...] Read more.
Retrotransposons comprise a substantial fraction of eukaryotic genomes, reaching the highest proportions in plants. Therefore, identification and annotation of retrotransposons is an important task in studying the regulation and evolution of plant genomes. The majority of computational tools for mining transposable elements (TEs) are designed for subsequent genome repeat masking, often leaving aside the element lineage classification and its protein domain composition. Additionally, studies focused on the diversity and evolution of a particular group of retrotransposons often require substantial customization efforts from researchers to adapt existing software to their needs. Here, we developed a computational pipeline to mine sequences of protein-coding retrotransposons based on the sequences of their conserved protein domains—DARTS (Domain-Associated Retrotransposon Search). Using the most abundant group of TEs in plants—long terminal repeat (LTR) retrotransposons (LTR-RTs)—we show that DARTS has radically higher sensitivity for LTR-RT identification compared to the widely accepted tool LTRharvest. DARTS can be easily customized for specific user needs. As a result, DARTS returns a set of structurally annotated nucleotide and amino acid sequences which can be readily used in subsequent comparative and phylogenetic analyses. DARTS may facilitate researchers interested in the discovery and detailed analysis of the diversity and evolution of retrotransposons, LTR-RTs, and other protein-coding TEs. Full article
(This article belongs to the Special Issue Transposable Elements in Plant Genomes)
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14 pages, 1774 KiB  
Article
A Global Landscape of Miniature Inverted-Repeat Transposable Elements in the Carrot Genome
by Alicja Macko-Podgórni, Gabriela Machaj and Dariusz Grzebelus
Genes 2021, 12(6), 859; https://doi.org/10.3390/genes12060859 - 03 Jun 2021
Cited by 5 | Viewed by 3287
Abstract
Miniature inverted-repeat transposable elements (MITEs) are the most abundant group of Class II mobile elements in plant genomes. Their presence in genic regions may alter gene structure and expression, providing a new source of functional diversity. Owing to their small size and lack [...] Read more.
Miniature inverted-repeat transposable elements (MITEs) are the most abundant group of Class II mobile elements in plant genomes. Their presence in genic regions may alter gene structure and expression, providing a new source of functional diversity. Owing to their small size and lack of coding capacity, the identification of MITEs has been demanding. However, the increasing availability of reference genomes and bioinformatic tools provides better means for the genome-wide identification and analysis of MITEs and for the elucidation of their contribution to the evolution of plant genomes. We mined MITEs in the carrot reference genome DH1 using MITE-hunter and developed a curated carrot MITE repository comprising 428 families. Of the 31,025 MITE copies spanning 10.34 Mbp of the carrot genome, 54% were positioned in genic regions. Stowaways and Tourists were frequently present in the vicinity of genes, while Mutator-like MITEs were relatively more enriched in introns. hAT-like MITEs were relatively more frequently associated with transcribed regions, including untranslated regions (UTRs). Some carrot MITE families were shared with other Apiaceae species. We showed that hAT-like MITEs were involved in the formation of new splice variants of insertion-harboring genes. Thus, carrot MITEs contributed to the accretion of new diversity by altering transcripts and possibly affecting the regulation of many genes. Full article
(This article belongs to the Special Issue Transposable Elements in Plant Genomes)
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14 pages, 2732 KiB  
Article
Genetic Variation of the Serine Acetyltransferase Gene Family for Sulfur Assimilation in Maize
by Zhixuan Zhao, Shuai Li, Chen Ji, Yong Zhou, Changsheng Li and Wenqin Wang
Genes 2021, 12(3), 437; https://doi.org/10.3390/genes12030437 - 19 Mar 2021
Viewed by 2559
Abstract
Improving sulfur assimilation in maize kernels is essential due to humans and animals’ inability to synthesize methionine. Serine acetyltransferase (SAT) is a critical enzyme that controls cystine biosynthesis in plants. In this study, all SAT gene members were genome-wide characterized by using a [...] Read more.
Improving sulfur assimilation in maize kernels is essential due to humans and animals’ inability to synthesize methionine. Serine acetyltransferase (SAT) is a critical enzyme that controls cystine biosynthesis in plants. In this study, all SAT gene members were genome-wide characterized by using a sequence homology search. The RNA-seq quantification indicates that they are highly expressed in leaves, other than root and seeds, consistent with their biological functions in sulfur assimilation. With the recently released 25 genomes of nested association mapping (NAM) founders representing the diverse maize stock, we had the opportunity to investigate the SAT genetic variation comprehensively. The abundant transposon insertions into SAT genes indicate their driving power in terms of gene structure and genome evolution. We found that the transposon insertion into exons could change SAT gene transcription, whereas there was no significant correlation between transposable element (TE) insertion into introns and their gene expression, indicating that other regulatory elements such as promoters could also be involved. Understanding the SAT gene structure, gene expression and genetic variation involved in natural selection and species adaption could precisely guide genetic engineering to manipulate sulfur assimilation in maize and to improve nutritional quality. Full article
(This article belongs to the Special Issue Transposable Elements in Plant Genomes)
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17 pages, 2605 KiB  
Article
InpactorDB: A Classified Lineage-Level Plant LTR Retrotransposon Reference Library for Free-Alignment Methods Based on Machine Learning
by Simon Orozco-Arias, Paula A. Jaimes, Mariana S. Candamil, Cristian Felipe Jiménez-Varón, Reinel Tabares-Soto, Gustavo Isaza and Romain Guyot
Genes 2021, 12(2), 190; https://doi.org/10.3390/genes12020190 - 28 Jan 2021
Cited by 13 | Viewed by 3723
Abstract
Long terminal repeat (LTR) retrotransposons are mobile elements that constitute the major fraction of most plant genomes. The identification and annotation of these elements via bioinformatics approaches represent a major challenge in the era of massive plant genome sequencing. In addition to their [...] Read more.
Long terminal repeat (LTR) retrotransposons are mobile elements that constitute the major fraction of most plant genomes. The identification and annotation of these elements via bioinformatics approaches represent a major challenge in the era of massive plant genome sequencing. In addition to their involvement in genome size variation, LTR retrotransposons are also associated with the function and structure of different chromosomal regions and can alter the function of coding regions, among others. Several sequence databases of plant LTR retrotransposons are available for public access, such as PGSB and RepetDB, or restricted access such as Repbase. Although these databases are useful to identify LTR-RTs in new genomes by similarity, the elements of these databases are not fully classified to the lineage (also called family) level. Here, we present InpactorDB, a semi-curated dataset composed of 130,439 elements from 195 plant genomes (belonging to 108 plant species) classified to the lineage level. This dataset has been used to train two deep neural networks (i.e., one fully connected and one convolutional) for the rapid classification of these elements. In lineage-level classification approaches, we obtain up to 98% performance, indicated by the F1-score, precision and recall scores. Full article
(This article belongs to the Special Issue Transposable Elements in Plant Genomes)
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28 pages, 3832 KiB  
Article
Comparative Study of Pine Reference Genomes Reveals Transposable Element Interconnected Gene Networks
by Angelika Voronova, Martha Rendón-Anaya, Pär Ingvarsson, Ruslan Kalendar and Dainis Ruņģis
Genes 2020, 11(10), 1216; https://doi.org/10.3390/genes11101216 - 16 Oct 2020
Cited by 10 | Viewed by 4265
Abstract
Sequencing the giga-genomes of several pine species has enabled comparative genomic analyses of these outcrossing tree species. Previous studies have revealed the wide distribution and extraordinary diversity of transposable elements (TEs) that occupy the large intergenic spaces in conifer genomes. In this study, [...] Read more.
Sequencing the giga-genomes of several pine species has enabled comparative genomic analyses of these outcrossing tree species. Previous studies have revealed the wide distribution and extraordinary diversity of transposable elements (TEs) that occupy the large intergenic spaces in conifer genomes. In this study, we analyzed the distribution of TEs in gene regions of the assembled genomes of Pinus taeda and Pinus lambertiana using high-performance computing resources. The quality of draft genomes and the genome annotation have significant consequences for the investigation of TEs and these aspects are discussed. Several TE families frequently inserted into genes or their flanks were identified in both species’ genomes. Potentially important sequence motifs were identified in TEs that could bind additional regulatory factors, promoting gene network formation with faster or enhanced transcription initiation. Node genes that contain many TEs were observed in multiple potential transposable element-associated networks. This study demonstrated the increased accumulation of TEs in the introns of stress-responsive genes of pines and suggests the possibility of rewiring them into responsive networks and sub-networks interconnected with node genes containing multiple TEs. Many such regulatory influences could lead to the adaptive environmental response clines that are characteristic of naturally spread pine populations. Full article
(This article belongs to the Special Issue Transposable Elements in Plant Genomes)
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24 pages, 2615 KiB  
Article
Bioinformatic and Molecular Analysis of Satellite Repeat Diversity in Vaccinium Genomes
by Nusrat Sultana, Gerhard Menzel, Tony Heitkam, Kenji K. Kojima, Weidong Bao and Sedat Serçe
Genes 2020, 11(5), 527; https://doi.org/10.3390/genes11050527 - 09 May 2020
Cited by 9 | Viewed by 3773
Abstract
Bioinformatic and molecular characterization of satellite repeats was performed to understand the impact of their diversification on Vaccinium genome evolution. Satellite repeat diversity was evaluated in four cultivated and wild species, including the diploid species Vaccinium myrtillus and Vaccinium uliginosum, as well [...] Read more.
Bioinformatic and molecular characterization of satellite repeats was performed to understand the impact of their diversification on Vaccinium genome evolution. Satellite repeat diversity was evaluated in four cultivated and wild species, including the diploid species Vaccinium myrtillus and Vaccinium uliginosum, as well as the tetraploid species Vaccinium corymbosum and Vaccinium arctostaphylos. We comparatively characterized six satellite repeat families using in total 76 clones with 180 monomers. We observed that the monomer units of VaccSat1, VaccSat2, VaccSat5, and VaccSat6 showed a higher order repeat (HOR) structure, likely originating from the organization of two adjacent subunits with differing similarity, length and size. Moreover, VaccSat1, VaccSat3, VaccSat6, and VaccSat7 were found to have sequence similarity to parts of transposable elements. We detected satellite-typical tandem organization for VaccSat1 and VaccSat2 in long arrays, while VaccSat5 and VaccSat6 distributed in multiple sites over all chromosomes of tetraploid V. corymbosum, presumably in long arrays. In contrast, very short arrays of VaccSat3 and VaccSat7 are dispersedly distributed over all chromosomes in the same species, likely as internal parts of transposable elements. We provide a comprehensive overview on satellite species specificity in Vaccinium, which are potentially useful as molecular markers to address the taxonomic complexity of the genus, and provide information for genome studies of this genus. Full article
(This article belongs to the Special Issue Transposable Elements in Plant Genomes)
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