1
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Gluck-Thaler E, Vogan A. Systematic identification of cargo-mobilizing genetic elements reveals new dimensions of eukaryotic diversity. Nucleic Acids Res 2024; 52:5496-5513. [PMID: 38686785 PMCID: PMC11162782 DOI: 10.1093/nar/gkae327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 03/12/2024] [Accepted: 04/15/2024] [Indexed: 05/02/2024] Open
Abstract
Cargo-mobilizing mobile elements (CMEs) are genetic entities that faithfully transpose diverse protein coding sequences. Although common in bacteria, we know little about eukaryotic CMEs because no appropriate tools exist for their annotation. For example, Starships are giant fungal CMEs whose functions are largely unknown because they require time-intensive manual curation. To address this knowledge gap, we developed starfish, a computational workflow for high-throughput eukaryotic CME annotation. We applied starfish to 2 899 genomes of 1 649 fungal species and found that starfish recovers known Starships with 95% combined precision and recall while expanding the number of annotated elements ten-fold. Extant Starship diversity is partitioned into 11 families that differ in their enrichment patterns across fungal classes. Starship cargo changes rapidly such that elements from the same family differ substantially in their functional repertoires, which are predicted to contribute to diverse biological processes such as metabolism. Many elements have convergently evolved to insert into 5S rDNA and AT-rich sequence while others integrate into random locations, revealing both specialist and generalist strategies for persistence. Our work establishes a framework for advancing mobile element biology and provides the means to investigate an emerging dimension of eukaryotic genetic diversity, that of genomes within genomes.
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Affiliation(s)
- Emile Gluck-Thaler
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, Neuchâtel, Neuchâtel 2000, Switzerland
- Department of Plant Pathology, University of Wisconsin-Madison, Madison, WI 53706, USA
- Wisconsin Institute for Discovery, Madison, WI 53706, USA
| | - Aaron A Vogan
- Systematic Biology, Department of Organismal Biology, Uppsala University, Uppsala, 752 36, Sweden
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2
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Shao F, Zeng M, Xu X, Zhang H, Peng Z. FishTEDB 2.0: an update fish transposable element (TE) database with new functions to facilitate TE research. Database (Oxford) 2024; 2024:baae044. [PMID: 38829853 PMCID: PMC11146639 DOI: 10.1093/database/baae044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 04/04/2024] [Accepted: 05/15/2024] [Indexed: 06/05/2024]
Abstract
We launched the initial version of FishTEDB in 2018, which aimed to establish an open-source, user-friendly, data-rich transposable element (TE) database. Over the past 5 years, FishTEDB 1.0 has gained approximately 10 000 users, accumulating more than 450 000 interactions. With the unveiling of extensive fish genome data and the increasing emphasis on TE research, FishTEDB needs to extend the richness of data and functions. To achieve the above goals, we introduced 33 new fish species to FishTEDB 2.0, encompassing a wide array of fish belonging to 48 orders. To make the updated database more functional, we added a genome browser to visualize the positional relationship between TEs and genes and the estimated TE insertion time in different species. In conclusion, we released a new version of the fish TE database, FishTEDB 2.0, designed to assist researchers in the future study of TE functions and promote the progress of biological theories related to TEs. Database URL: https://www.fishtedb.com/.
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Affiliation(s)
- Feng Shao
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Southwest University School of Life Sciences, 2 Tiansheng Road, Chongqing 400715, China
| | - Minzhi Zeng
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Southwest University School of Life Sciences, 2 Tiansheng Road, Chongqing 400715, China
| | - Xiaofei Xu
- School of Computing Technologies, RMIT University, 124 La Trobe Street, Victoria 3000, Australia
| | - Huahao Zhang
- College of Pharmacy and Life Science, Jiujiang University, 551 Qianjin East Road, Jiujiang 332005, China
| | - Zuogang Peng
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Southwest University School of Life Sciences, 2 Tiansheng Road, Chongqing 400715, China
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3
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Kirsch JM, Hryckowian AJ, Duerkop BA. A metagenomics pipeline reveals insertion sequence-driven evolution of the microbiota. Cell Host Microbe 2024; 32:739-754.e4. [PMID: 38565143 PMCID: PMC11081829 DOI: 10.1016/j.chom.2024.03.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 02/06/2024] [Accepted: 03/08/2024] [Indexed: 04/04/2024]
Abstract
Insertion sequence (IS) elements are mobile genetic elements in bacterial genomes that support adaptation. We developed a database of IS elements coupled to a computational pipeline that identifies IS element insertions in the microbiota. We discovered that diverse IS elements insert into the genomes of intestinal bacteria regardless of human host lifestyle. These insertions target bacterial accessory genes that aid in their adaptation to unique environmental conditions. Using IS expansion in Bacteroides, we show that IS activity leads to the insertion of "hot spots" in accessory genes. We show that IS insertions are stable and can be transferred between humans. Extreme environmental perturbations force IS elements to fall out of the microbiota, and many fail to rebound following homeostasis. Our work shows that IS elements drive bacterial genome diversification within the microbiota and establishes a framework for understanding how strain-level variation within the microbiota impacts human health.
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Affiliation(s)
- Joshua M Kirsch
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, School of Medicine, Aurora, CO 80045, USA
| | - Andrew J Hryckowian
- Department of Medicine, Division of Gastroenterology and Hepatology, University of Wisconsin School of Medicine and Public Health, Madison, WI 53706, USA; Department of Medical Microbiology & Immunology, University of Wisconsin School of Medicine and Public Health, Madison, WI 53706, USA
| | - Breck A Duerkop
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, School of Medicine, Aurora, CO 80045, USA.
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4
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Hwang J, Ye DY, Jung GY, Jang S. Mobile genetic element-based gene editing and genome engineering: Recent advances and applications. Biotechnol Adv 2024; 72:108343. [PMID: 38521283 DOI: 10.1016/j.biotechadv.2024.108343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Revised: 03/14/2024] [Accepted: 03/16/2024] [Indexed: 03/25/2024]
Abstract
Genome engineering has revolutionized several scientific fields, ranging from biochemistry and fundamental research to therapeutic uses and crop development. Diverse engineering toolkits have been developed and used to effectively modify the genome sequences of organisms. However, there is a lack of extensive reviews on genome engineering technologies based on mobile genetic elements (MGEs), which induce genetic diversity within host cells by changing their locations in the genome. This review provides a comprehensive update on the versatility of MGEs as powerful genome engineering tools that offers efficient solutions to challenges associated with genome engineering. MGEs, including DNA transposons, retrotransposons, retrons, and CRISPR-associated transposons, offer various advantages, such as a broad host range, genome-wide mutagenesis, efficient large-size DNA integration, multiplexing capabilities, and in situ single-stranded DNA generation. We focused on the components, mechanisms, and features of each MGE-based tool to highlight their cellular applications. Finally, we discussed the current challenges of MGE-based genome engineering and provided insights into the evolving landscape of this transformative technology. In conclusion, the combination of genome engineering with MGE demonstrates remarkable potential for addressing various challenges and advancing the field of genetic manipulation, and promises to revolutionize our ability to engineer and understand the genomes of diverse organisms.
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Affiliation(s)
- Jaeseong Hwang
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-gu, Pohang, Gyeongbuk 37673, Republic of Korea
| | - Dae-Yeol Ye
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-gu, Pohang, Gyeongbuk 37673, Republic of Korea
| | - Gyoo Yeol Jung
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-gu, Pohang, Gyeongbuk 37673, Republic of Korea; Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-gu, Pohang, Gyeongbuk 37673, Republic of Korea.
| | - Sungho Jang
- Department of Bioengineering and Nano-Bioengineering, Incheon National University, 119 Academy-ro, Yeonsu-gu, Incheon 22012, Republic of Korea; Division of Bioengineering, College of Life Sciences and Bioengineering, Incheon National University, 119 Academy-ro, Yeonsu-gu, Incheon 22012, Republic of Korea; Research Center for Bio Materials & Process Development, Incheon National University, 119 Academy-ro, Yeonsu-gu, Incheon 22012, Republic of Korea.
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5
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Schmidt N, Sielemann K, Breitenbach S, Fuchs J, Pucker B, Weisshaar B, Holtgräwe D, Heitkam T. Repeat turnover meets stable chromosomes: repetitive DNA sequences mark speciation and gene pool boundaries in sugar beet and wild beets. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 118:171-190. [PMID: 38128038 DOI: 10.1111/tpj.16599] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 12/05/2023] [Accepted: 12/08/2023] [Indexed: 12/23/2023]
Abstract
Sugar beet and its wild relatives share a base chromosome number of nine and similar chromosome morphologies. Yet, interspecific breeding is impeded by chromosome and sequence divergence that is still not fully understood. Since repetitive DNAs are among the fastest evolving parts of the genome, we investigated, if repeatome innovations and losses are linked to chromosomal differentiation and speciation. We traced genome and chromosome-wide evolution across 13 beet species comprising all sections of the genera Beta and Patellifolia. For this, we combined short and long read sequencing, flow cytometry, and cytogenetics to build a comprehensive framework that spans the complete scale from DNA to chromosome to genome. Genome sizes and repeat profiles reflect the separation into three gene pools with contrasting evolutionary patterns. Among all repeats, satellite DNAs harbor most genomic variability, leading to fundamentally different centromere architectures, ranging from chromosomal uniformity in Beta and Patellifolia to the formation of patchwork chromosomes in Corollinae/Nanae. We show that repetitive DNAs are causal for the genome expansions and contractions across the beet genera, providing insights into the genomic underpinnings of beet speciation. Satellite DNAs in particular vary considerably between beet genomes, leading to the evolution of distinct chromosomal setups in the three gene pools, likely contributing to the barriers in beet breeding. Thus, with their isokaryotypic chromosome sets, beet genomes present an ideal system for studying the link between repeats, genomic variability, and chromosomal differentiation and provide a theoretical fundament for understanding barriers in any crop breeding effort.
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Affiliation(s)
- Nicola Schmidt
- Faculty of Biology, Technische Universität Dresden, 01069, Dresden, Germany
| | - Katharina Sielemann
- Genetics and Genomics of Plants, Center for Biotechnology (CeBiTec) & Faculty of Biology, Bielefeld University, 33615, Bielefeld, Germany
- Graduate School DILS, Bielefeld Institute for Bioinformatics Infrastructure (BIBI), Bielefeld University, 33615, Bielefeld, Germany
| | - Sarah Breitenbach
- Faculty of Biology, Technische Universität Dresden, 01069, Dresden, Germany
| | - Jörg Fuchs
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466, Stadt Seeland, Germany
| | - Boas Pucker
- Plant Biotechnology and Bioinformatics, Institute of Plant Biology & Braunschweig Integrated Centre of Systems Biology (BRICS), TU Braunschweig, 38106, Braunschweig, Germany
| | - Bernd Weisshaar
- Genetics and Genomics of Plants, Center for Biotechnology (CeBiTec) & Faculty of Biology, Bielefeld University, 33615, Bielefeld, Germany
| | - Daniela Holtgräwe
- Genetics and Genomics of Plants, Center for Biotechnology (CeBiTec) & Faculty of Biology, Bielefeld University, 33615, Bielefeld, Germany
| | - Tony Heitkam
- Faculty of Biology, Technische Universität Dresden, 01069, Dresden, Germany
- Institute of Biology, NAWI Graz, Karl-Franzens-Universität, A-8010 Graz, Graz, Austria
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6
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Liu X, Zhao L, Majid M, Huang Y. Orthoptera-TElib: a library of Orthoptera transposable elements for TE annotation. Mob DNA 2024; 15:5. [PMID: 38486291 PMCID: PMC10941475 DOI: 10.1186/s13100-024-00316-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Accepted: 03/08/2024] [Indexed: 03/17/2024] Open
Abstract
Transposable elements (TEs) are a major component of eukaryotic genomes and are present in almost all eukaryotic organisms. TEs are highly dynamic between and within species, which significantly affects the general applicability of the TE databases. Orthoptera is the only known group in the class Insecta with a significantly enlarged genome (0.93-21.48 Gb). When analyzing the large genome using the existing TE public database, the efficiency of TE annotation is not satisfactory. To address this limitation, it becomes imperative to continually update the available TE resource library and the need for an Orthoptera-specific library as more insect genomes are publicly available. Here, we used the complete genome data of 12 Orthoptera species to de novo annotate TEs, then manually re-annotate the unclassified TEs to construct a non-redundant Orthoptera-specific TE library: Orthoptera-TElib. Orthoptera-TElib contains 24,021 TE entries including the re-annotated results of 13,964 unknown TEs. The naming of TE entries in Orthoptera-TElib adopts the same naming as RepeatMasker and Dfam and is encoded as the three-level form of "level1/level2-level3". Orthoptera-TElib can be directly used as an input reference database and is compatible with mainstream repetitive sequence analysis software such as RepeatMasker and dnaPipeTE. When analyzing TEs of Orthoptera species, Orthoptera-TElib performs better TE annotation as compared to Dfam and Repbase regardless of using low-coverage sequencing or genome assembly data. The most improved TE annotation result is Angaracris rhodopa, which has increased from 7.89% of the genome to 53.28%. Finally, Orthoptera-TElib is stored in Sqlite3 for the convenience of data updates and user access.
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Affiliation(s)
- Xuanzeng Liu
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Lina Zhao
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Muhammad Majid
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Yuan Huang
- College of Life Sciences, Shaanxi Normal University, Xi'an, China.
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7
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Kirsch JM, Hryckowian AJ, Duerkop BA. A metagenomics pipeline reveals insertion sequence-driven evolution of the microbiota. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.10.06.561241. [PMID: 37873088 PMCID: PMC10592638 DOI: 10.1101/2023.10.06.561241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Insertion sequence (IS) elements are mobile genetic elements in bacterial genomes that support adaptation. We developed a database of IS elements coupled to a computational pipeline that identifies IS element insertions in the microbiota. We discovered that diverse IS elements insert into the genomes of intestinal bacteria regardless of human host lifestyle. These insertions target bacterial accessory genes that aid in their adaptation to unique environmental conditions. Using IS expansion in Bacteroides, we show that IS activity leads to insertion "hot spots" in accessory genes. We show that IS insertions are stable and can be transferred between humans. Extreme environmental perturbations force IS elements to fall out of the microbiota and many fail to rebound following homeostasis. Our work shows that IS elements drive bacterial genome diversification within the microbiota and establishes a framework for understanding how strain level variation within the microbiota impacts human health.
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Affiliation(s)
- Joshua M. Kirsch
- Department of Immunology and Microbiology, University of Colorado - Anschutz Medical Campus, School of Medicine, Aurora, Colorado, 80045, USA
| | - Andrew J. Hryckowian
- Department of Medicine, Division of Gastroenterology and Hepatology, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, 53706, USA
- Department of Medical Microbiology & Immunology, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, 53706, USA
| | - Breck A. Duerkop
- Department of Immunology and Microbiology, University of Colorado - Anschutz Medical Campus, School of Medicine, Aurora, Colorado, 80045, USA
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8
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Westerberg I, Ament-Velásquez SL, Vogan AA, Johannesson H. Evolutionary dynamics of the LTR-retrotransposon crapaud in the Podospora anserina species complex and the interaction with repeat-induced point mutations. Mob DNA 2024; 15:1. [PMID: 38218923 PMCID: PMC10787394 DOI: 10.1186/s13100-023-00311-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 12/22/2023] [Indexed: 01/15/2024] Open
Abstract
BACKGROUND The genome of the filamentous ascomycete Podospora anserina shows a relatively high abundance of retrotransposons compared to other interspersed repeats. The LTR-retrotransposon family crapaud is particularly abundant in the genome, and consists of multiple diverged sequence variations specifically localized in the 5' half of both long terminal repeats (LTRs). P. anserina is part of a recently diverged species-complex, which makes the system ideal to classify the crapaud family based on the observed LTR variation and to study the evolutionary dynamics, such as the diversification and bursts of the elements over recent evolutionary time. RESULTS We developed a sequence similarity network approach to classify the crapaud repeats of seven genomes representing the P. anserina species complex into 14 subfamilies. This method does not utilize a consensus sequence, but instead it connects any copies that share enough sequence similarity over a set sequence coverage. Based on phylogenetic analyses, we found that the crapaud repeats likely diversified in the ancestor of the complex and have had activity at different time points for different subfamilies. Furthermore, while we hypothesized that the evolution into multiple subfamilies could have been a direct effect of escaping the genome defense system of repeat induced point mutations, we found this not to be the case. CONCLUSIONS Our study contributes to the development of methods to classify transposable elements in fungi, and also highlights the intricate patterns of retrotransposon evolution over short timescales and under high mutational load caused by nucleotide-altering genome defense.
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Affiliation(s)
- Ivar Westerberg
- Department of Ecology, environmental and Plant Sciences, Stockholm University, Stockholm, 106 91, Sweden
| | - S Lorena Ament-Velásquez
- Division of Population Genetics, Department of Zoology, Stockholm University, Stockholm, 106 91, Sweden
| | - Aaron A Vogan
- Systematic Biology, Department of Organismal Biology, Uppsala University, Norbyvägen 18D, Uppsala, 752 36, Sweden.
| | - Hanna Johannesson
- Department of Ecology, environmental and Plant Sciences, Stockholm University, Stockholm, 106 91, Sweden.
- The Royal Swedish Academy of Sciences, Stockholm, 114 18, Sweden.
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Bonté PE, Metoikidou C, Heurtebise-Chretien S, Arribas YA, Sutra Del Galy A, Ye M, Niborski LL, Zueva E, Piaggio E, Seguin-Givelet A, Girard N, Alanio C, Burbage M, Goudot C, Amigorena S. Selective control of transposable element expression during T cell exhaustion and anti-PD-1 treatment. Sci Immunol 2023; 8:eadf8838. [PMID: 37889984 DOI: 10.1126/sciimmunol.adf8838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 09/01/2023] [Indexed: 10/29/2023]
Abstract
In chronic infections and cancer, T cells are exposed to prolonged antigen stimulation, resulting in loss of function (or exhaustion) and impairment of effective immunological protection. Exhausted T cells are heterogeneous and include early progenitors (Tpex) and terminally exhausted cells (Tex). Here, we used bulk and single-cell transcriptomics to analyze expression of transposable elements (TEs) in subpopulations of mouse and human CD8+ tumor-infiltrating T lymphocytes (TILs). We show that in mice, members of the virus-like murine VL30 TE family (mostly intact, evolutionary young ERV1s) are strongly repressed in terminally exhausted CD8+ T cells in both tumor and viral models of exhaustion. Tpex expression of these VL30s, which are mainly intergenic and transcribed independently of their closest gene neighbors, was driven by Fli1, a transcription factor involved in progression from Tpex to Tex. Immune checkpoint blockade (ICB) in both mice and patients with cancer increased TE expression (including VL30 in mice), demonstrating that TEs may be applicable as ICB response biomarkers. We conclude that expression of TEs is tightly regulated in TILs during establishment of exhaustion and reprogramming by ICB. Analyses of TE expression on single cells and bulk populations open opportunities for understanding immune cell identity and heterogeneity, as well as for defining cellular gene expression signatures and disease biomarkers.
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Affiliation(s)
- Pierre-Emmanuel Bonté
- Institut Curie, PSL University, Inserm U932, Immunity and Cancer, Paris 75005, France
| | - Christina Metoikidou
- Institut Curie, PSL University, Inserm U932, Immunity and Cancer, Paris 75005, France
| | | | - Yago A Arribas
- Institut Curie, PSL University, Inserm U932, Immunity and Cancer, Paris 75005, France
| | | | - Mengliang Ye
- Institut Curie, PSL University, Inserm U932, Immunity and Cancer, Paris 75005, France
| | | | - Elina Zueva
- Institut Curie, PSL University, Inserm U932, Immunity and Cancer, Paris 75005, France
| | - Eliane Piaggio
- Institut Curie, PSL University, Inserm U932, Immunity and Cancer, Paris 75005, France
| | | | - Nicolas Girard
- Institut Curie, PSL University, Inserm U932, Immunity and Cancer, Paris 75005, France
- Institut Curie, Institut du Thorax Curie Montsouris, Paris 75005, France
- Paris Saclay, UVSQ, UFR Simmone Veil, Versailles 78000, France
| | - Cécile Alanio
- Institut Curie, PSL University, Inserm U932, Immunity and Cancer, Paris 75005, France
- Laboratoire d'immunologie clinique, Institut Curie, Paris 75005, France
- Parker Institute of Cancer Immunotherapy, San Francisco, CA, USA
| | - Marianne Burbage
- Institut Curie, PSL University, Inserm U932, Immunity and Cancer, Paris 75005, France
| | - Christel Goudot
- Institut Curie, PSL University, Inserm U932, Immunity and Cancer, Paris 75005, France
| | - Sebastian Amigorena
- Institut Curie, PSL University, Inserm U932, Immunity and Cancer, Paris 75005, France
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Sproul JS, Hotaling S, Heckenhauer J, Powell A, Marshall D, Larracuente AM, Kelley JL, Pauls SU, Frandsen PB. Analyses of 600+ insect genomes reveal repetitive element dynamics and highlight biodiversity-scale repeat annotation challenges. Genome Res 2023; 33:1708-1717. [PMID: 37739812 PMCID: PMC10691545 DOI: 10.1101/gr.277387.122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 09/20/2023] [Indexed: 09/24/2023]
Abstract
Repetitive elements (REs) are integral to the composition, structure, and function of eukaryotic genomes, yet remain understudied in most taxonomic groups. We investigated REs across 601 insect species and report wide variation in RE dynamics across groups. Analysis of associations between REs and protein-coding genes revealed dynamic evolution at the interface between REs and coding regions across insects, including notably elevated RE-gene associations in lineages with abundant long interspersed nuclear elements (LINEs). We leveraged this large, empirical data set to quantify impacts of long-read technology on RE detection and investigate fundamental challenges to RE annotation in diverse groups. In long-read assemblies, we detected ∼36% more REs than short-read assemblies, with long terminal repeats (LTRs) showing 162% increased detection, whereas DNA transposons and LINEs showed less respective technology-related bias. In most insect lineages, 25%-85% of repetitive sequences were "unclassified" following automated annotation, compared with only ∼13% in Drosophila species. Although the diversity of available insect genomes has rapidly expanded, we show the rate of community contributions to RE databases has not kept pace, preventing efficient annotation and high-resolution study of REs in most groups. We highlight the tremendous opportunity and need for the biodiversity genomics field to embrace REs and suggest collective steps for making progress toward this goal.
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Affiliation(s)
- John S Sproul
- Department of Biology, Brigham Young University, Provo, Utah 84602, USA;
- Department of Biology, University of Nebraska Omaha, Omaha, Nebraska 68182, USA
- Department of Biology, University of Rochester, Rochester, New York 14627, USA
| | - Scott Hotaling
- School of Biological Sciences, Washington State University, Pullman, Washington 99163, USA
- Department of Watershed Sciences, Utah State University, Logan, Utah 84322, USA
| | - Jacqueline Heckenhauer
- LOEWE Center for Translational Biodiversity Genomics (LOEWE-TBG), 60325 Frankfurt, Germany
- Senckenberg Research Institute and Natural History Museum Frankfurt, 60325 Frankfurt, Germany
| | - Ashlyn Powell
- Department of Plant and Wildlife Sciences, Brigham Young University, Provo, Utah 84602, USA
| | - Dez Marshall
- Department of Biology, University of Nebraska Omaha, Omaha, Nebraska 68182, USA
| | | | - Joanna L Kelley
- School of Biological Sciences, Washington State University, Pullman, Washington 99163, USA
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, California 95064, USA
| | - Steffen U Pauls
- LOEWE Center for Translational Biodiversity Genomics (LOEWE-TBG), 60325 Frankfurt, Germany
- Senckenberg Research Institute and Natural History Museum Frankfurt, 60325 Frankfurt, Germany
- Department of Insect Biotechnology, Justus-Liebig-University Gießen, 35392 Gießen, Germany
| | - Paul B Frandsen
- LOEWE Center for Translational Biodiversity Genomics (LOEWE-TBG), 60325 Frankfurt, Germany
- Department of Plant and Wildlife Sciences, Brigham Young University, Provo, Utah 84602, USA
- Data Science Lab, Smithsonian Institution, Washington, District of Columbia 20560, USA
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11
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Chakrabarty P, Sen R, Sengupta S. From parasites to partners: exploring the intricacies of host-transposon dynamics and coevolution. Funct Integr Genomics 2023; 23:278. [PMID: 37610667 DOI: 10.1007/s10142-023-01206-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 08/01/2023] [Accepted: 08/07/2023] [Indexed: 08/24/2023]
Abstract
Transposable elements, often referred to as "jumping genes," have long been recognized as genomic parasites due to their ability to integrate and disrupt normal gene function and induce extensive genomic alterations, thereby compromising the host's fitness. To counteract this, the host has evolved a plethora of mechanisms to suppress the activity of the transposons. Recent research has unveiled the host-transposon relationships to be nuanced and complex phenomena, resulting in the coevolution of both entities. Transposition increases the mutational rate in the host genome, often triggering physiological pathways such as immune and stress responses. Current gene transfer technologies utilizing transposable elements have potential drawbacks, including off-target integration, induction of mutations, and modifications of cellular machinery, which makes an in-depth understanding of the host-transposon relationship imperative. This review highlights the dynamic interplay between the host and transposable elements, encompassing various factors and components of the cellular machinery. We provide a comprehensive discussion of the strategies employed by transposable elements for their propagation, as well as the mechanisms utilized by the host to mitigate their parasitic effects. Additionally, we present an overview of recent research identifying host proteins that act as facilitators or inhibitors of transposition. We further discuss the evolutionary outcomes resulting from the genetic interactions between the host and the transposable elements. Finally, we pose open questions in this field and suggest potential avenues for future research.
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Affiliation(s)
- Prayas Chakrabarty
- Department of Life Sciences, Presidency University Kolkata, 86/1 College Street, Kolkata, 700073, India
| | - Raneet Sen
- Department of Life Sciences, Presidency University Kolkata, 86/1 College Street, Kolkata, 700073, India
- Institute of Bioorganic Chemistry, Department of RNA Metabolism, Polish Academy of Sciences, Poznan, Poland
| | - Sugopa Sengupta
- Department of Life Sciences, Presidency University Kolkata, 86/1 College Street, Kolkata, 700073, India.
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Zuo B, Nneji LM, Sun YB. Comparative genomics reveals insights into anuran genome size evolution. BMC Genomics 2023; 24:379. [PMID: 37415107 DOI: 10.1186/s12864-023-09499-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 06/30/2023] [Indexed: 07/08/2023] Open
Abstract
BACKGROUND Amphibians, particularly anurans, display an enormous variation in genome size. Due to the unavailability of whole genome datasets in the past, the genomic elements and evolutionary causes of anuran genome size variation are poorly understood. To address this, we analyzed whole-genome sequences of 14 anuran species ranging in size from 1.1 to 6.8 Gb. By annotating multiple genomic elements, we investigated the genomic correlates of anuran genome size variation and further examined whether the genome size relates to habitat types. RESULTS Our results showed that intron expansions or contraction and Transposable Elements (TEs) diversity do not contribute significantly to genome size variation. However, the recent accumulation of transposable elements (TEs) and the lack of deletion of ancient TEs primarily accounted for the evolution of anuran genome sizes. Our study showed that the abundance and density of simple repeat sequences positively correlate with genome size. Ancestral state reconstruction revealed that genome size exhibits a taxon-specific pattern of evolution, with families Bufonidae and Pipidae experiencing extreme genome expansion and contraction events, respectively. Our result showed no relationship between genome size and habitat types, although large genome-sized species are predominantly found in humid habitats. CONCLUSIONS Overall, our study identified the genomic element and their evolutionary dynamics accounting for anuran genome size variation, thus paving a path to a greater understanding of the size evolution of the genome in amphibians.
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Affiliation(s)
- Bin Zuo
- Ministry of Education Key Laboratory for Transboundary Ecosecurity of Southwest China, Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology, Institute of Biodiversity, School of Ecology and Environmental Science, Yunnan University, Kunming, Yunnan, 650504, China
| | - Lotanna Micah Nneji
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, 08544, USA
| | - Yan-Bo Sun
- Ministry of Education Key Laboratory for Transboundary Ecosecurity of Southwest China, Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology, Institute of Biodiversity, School of Ecology and Environmental Science, Yunnan University, Kunming, Yunnan, 650504, China.
- Laboratory for Conservation and Utilization of Bio-resources, Yunnan University, Kunming, 650091, China.
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13
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Yushkova E, Moskalev A. Transposable elements and their role in aging. Ageing Res Rev 2023; 86:101881. [PMID: 36773759 DOI: 10.1016/j.arr.2023.101881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 01/16/2023] [Accepted: 02/07/2023] [Indexed: 02/12/2023]
Abstract
Transposable elements (TEs) are an important part of eukaryotic genomes. The role of somatic transposition in aging, carcinogenesis, and other age-related diseases has been determined. This review discusses the fundamental properties of TEs and their complex interactions with cellular processes, which are crucial for understanding the diverse effects of their activity on the genetics and epigenetics of the organism. The interactions of TEs with recombination, replication, repair, and chromosomal regulation; the ability of TEs to maintain a balance between their own activity and repression, the involvement of TEs in the creation of new or alternative genes, the expression of coding/non-coding RNA, and the role in DNA damage and modification of regulatory networks are reviewed. The contribution of the derepressed TEs to age-dependent effects in individual cells/tissues in different organisms was assessed. Conflicting information about TE activity under stress as well as theories of aging mechanisms related to TEs is discussed. On the one hand, transposition activity in response to stressors can lead to organisms acquiring adaptive innovations of great importance for evolution at the population level. On the other hand, the TE expression can cause decreased longevity and stress tolerance at the individual level. The specific features of TE effects on aging processes in germline and soma and the ways of their regulation in cells are highlighted. Recent results considering somatic mutations in normal human and animal tissues are indicated, with the emphasis on their possible functional consequences. In the context of aging, the correlation between somatic TE activation and age-related changes in the number of proteins required for heterochromatin maintenance and longevity regulation was analyzed. One of the original features of this review is a discussion of not only effects based on the TEs insertions and the associated consequences for the germline cell dynamics and somatic genome, but also the differences between transposon- and retrotransposon-mediated structural genome changes and possible phenotypic characteristics associated with aging and various age-related pathologies. Based on the analysis of published data, a hypothesis about the influence of the species-specific features of number, composition, and distribution of TEs on aging dynamics of different animal genomes was formulated.
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Affiliation(s)
- Elena Yushkova
- Laboratory of Geroprotective and Radioprotective Technologies, Institute of Biology, Komi Science Center, Ural Branch, Russian Academy of Sciences, 28 Kommunisticheskaya st., 167982 Syktyvkar, Russian Federation
| | - Alexey Moskalev
- Laboratory of Geroprotective and Radioprotective Technologies, Institute of Biology, Komi Science Center, Ural Branch, Russian Academy of Sciences, 28 Kommunisticheskaya st., 167982 Syktyvkar, Russian Federation; Laboratory of Genetics and Epigenetics of Aging, Russian Clinical Research Center for Gerontology, Pirogov Russian National Research Medical University, Moscow 129226, Russian Federation; Longaevus Technologies, London, UK.
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14
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Pezenti LF, Dionisio JF, Sosa-Gómez DR, de Souza RF, da Rosa R. Transposable elements in the transcriptome of the velvetbean caterpillar Anticarsia gemmatalis Hübner, 1818 (Lepidoptera: Erebidae). Genome 2023. [DOI: 10.1139/gen-2022-0066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023]
Abstract
Transposable elements (TEs) are DNA sequences that possess the ability to move from one genomic location to another. These sequences contribute to a significant fraction of the genomes of most eukaryotes and can impact their architecture and regulation. In this paper, we present the first data related to the identification and characterization of TEs present in the transcriptome of Anticarsia gemmatalis. Approximately, 835 transcripts showed significant similarity to TEs and (or) characteristic domains. Retrotransposons accounted for 71.2% (595 sequences) of the identified elements, while DNA transposons were less abundant, with 240 annotations (28.8%). TEs were classified into 30 superfamilies, with SINE3/5S and Gypsy being the most abundant. Based on the sequences of TEs found in the transcriptome, we were able to locate conserved regions in the chromosomes of this species. The analysis of differential expression of TEs in susceptible and resistant strains, challenged and not challenged with Bacillus thuringiensis ( Bt) from in silico analysis, indicated that exposure to Bt can regulate the transcription of mobile genetic elements in the velvetbean caterpillar. Thus, these data contribute significantly to the knowledge of the structure and composition of these elements in the genome of this species, and suggest the role of stress on their expression.
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15
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Gasparotto E, Burattin FV, Di Gioia V, Panepuccia M, Ranzani V, Marasca F, Bodega B. Transposable Elements Co-Option in Genome Evolution and Gene Regulation. Int J Mol Sci 2023; 24:ijms24032610. [PMID: 36768929 PMCID: PMC9917352 DOI: 10.3390/ijms24032610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 01/26/2023] [Accepted: 01/28/2023] [Indexed: 01/31/2023] Open
Abstract
The genome is no longer deemed as a fixed and inert item but rather as a moldable matter that is continuously evolving and adapting. Within this frame, Transposable Elements (TEs), ubiquitous, mobile, repetitive elements, are considered an alive portion of the genomes to date, whose functions, although long considered "dark", are now coming to light. Here we will review that, besides the detrimental effects that TE mobilization can induce, TEs have shaped genomes in their current form, promoting genome sizing, genomic rearrangements and shuffling of DNA sequences. Although TEs are mostly represented in the genomes by evolutionarily old, short, degenerated, and sedentary fossils, they have been thoroughly co-opted by the hosts as a prolific and original source of regulatory instruments for the control of gene transcription and genome organization in the nuclear space. For these reasons, the deregulation of TE expression and/or activity is implicated in the onset and progression of several diseases. It is likely that we have just revealed the outermost layers of TE functions. Further studies on this portion of the genome are required to unlock novel regulatory functions that could also be exploited for diagnostic and therapeutic approaches.
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Affiliation(s)
- Erica Gasparotto
- Fondazione INGM, Istituto Nazionale di Genetica Molecolare “Enrica e Romeo Invernizzi”, 20122 Milan, Italy
- SEMM, European School of Molecular Medicine, 20139 Milan, Italy
| | - Filippo Vittorio Burattin
- Fondazione INGM, Istituto Nazionale di Genetica Molecolare “Enrica e Romeo Invernizzi”, 20122 Milan, Italy
- Department of Biosciences, University of Milan, 20133 Milan, Italy
| | - Valeria Di Gioia
- Fondazione INGM, Istituto Nazionale di Genetica Molecolare “Enrica e Romeo Invernizzi”, 20122 Milan, Italy
- SEMM, European School of Molecular Medicine, 20139 Milan, Italy
| | - Michele Panepuccia
- Fondazione INGM, Istituto Nazionale di Genetica Molecolare “Enrica e Romeo Invernizzi”, 20122 Milan, Italy
| | - Valeria Ranzani
- Fondazione INGM, Istituto Nazionale di Genetica Molecolare “Enrica e Romeo Invernizzi”, 20122 Milan, Italy
| | - Federica Marasca
- Fondazione INGM, Istituto Nazionale di Genetica Molecolare “Enrica e Romeo Invernizzi”, 20122 Milan, Italy
- Department of Clinical Sciences and Community Health, University of Milan, 20122 Milan, Italy
| | - Beatrice Bodega
- Fondazione INGM, Istituto Nazionale di Genetica Molecolare “Enrica e Romeo Invernizzi”, 20122 Milan, Italy
- Department of Biosciences, University of Milan, 20133 Milan, Italy
- Correspondence:
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16
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Bernardt TM, Treviso EM, Cancian M, Silva MDM, da Rocha JBT, Loreto ELS. Chemotherapy Drugs Act Differently in the Expression and Somatic Mobilization of the mariner Transposable Element in Drosophila simulans. Genes (Basel) 2022; 13:genes13122374. [PMID: 36553641 PMCID: PMC9777735 DOI: 10.3390/genes13122374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 12/10/2022] [Accepted: 12/14/2022] [Indexed: 12/23/2022] Open
Abstract
Transposable elements (TEs) are abundant in genomes. Their mobilization can lead to genetic variability that is useful for evolution, but can also have deleterious biological effects. Somatic mobilization (SM) has been linked to degenerative diseases, such as Alzheimer's disease and cancer. We used a Drosophila simulans strain, in which SM can be measured by counting red spots in the eyes, to investigate how chemotherapeutic agents affect expression and SM of the mariner TE. Flies were treated with Cisplatin, Dacarbazine, and Daunorubicin. After acute exposure, relative expression of mariner was quantified by RT-qPCR and oxidative stress was measured by biochemical assays. Exposure to 50 and 100 µg/mL Cisplatin increased mariner expression and ROS levels; catalase activity increased at 100 µg/mL. With chronic exposure, the number of spots also increased, indicating higher mariner SM. Dacarbazine (50 and 100 µg/mL) did not significantly alter mariner expression or mobilization or ROS levels, but decreased catalase activity (100 µg/mL). Daunorubicin (25 and 50 µM) increased mariner expression, but decreased mariner SM. ROS and catalase activity were also reduced. Our data suggest that stress factors may differentially affect the expression and SM of TEs. The increase in mariner transposase gene expression is necessary, but not sufficient for mariner SM.
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Affiliation(s)
- Taís Maus Bernardt
- Biological Sciences, Federal University of Santa Maria (UFSM), Santa Maria 97105-000, RS, Brazil
| | - Estéfani Maria Treviso
- Biological Sciences, Federal University of Santa Maria (UFSM), Santa Maria 97105-000, RS, Brazil
| | - Mariana Cancian
- Genetic and Molecular Biology, Federal University of Rio Grande do Sul (UFRGS), Porto Alegre 91501-970, RS, Brazil
| | - Monica de Medeiros Silva
- Department of Biochemistry and Molecular Biology, Federal University of Santa Maria (UFSM), Av. Roraima 1000, Camobi, Santa Maria 97105-900, RS, Brazil
| | - João Batista Teixeira da Rocha
- Department of Biochemistry and Molecular Biology, Federal University of Santa Maria (UFSM), Av. Roraima 1000, Camobi, Santa Maria 97105-900, RS, Brazil
| | - Elgion Lucio Silva Loreto
- Department of Biochemistry and Molecular Biology, Federal University of Santa Maria (UFSM), Av. Roraima 1000, Camobi, Santa Maria 97105-900, RS, Brazil
- Correspondence:
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17
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Orooji F, Mirzaghaderi G, Kuo YT, Fuchs J. Variation in the Number and Position of rDNA Loci Contributes to the Diversification and Speciation in Nigella (Ranunculaceae). FRONTIERS IN PLANT SCIENCE 2022; 13:917310. [PMID: 35812971 PMCID: PMC9261981 DOI: 10.3389/fpls.2022.917310] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 05/16/2022] [Indexed: 06/15/2023]
Abstract
Nigella is a small genus belonging to the Ranunculaceae family which is presumably originated and distributed in Aegean and the adjacent Western-Irano-Turanian region. Comparative repeat analysis of N. sativa, N. damascena and N. bucharica was performed using low-pass Illumina genomic reads followed by karyotyping and FISH mapping of seven Nigella species using the in silico identified repeats and ribosomal DNA (rDNA) probes. High- and moderate-copy repeat sequences occupy 57.52, 59.01, and 64.73% of N. sativa, N. damascena and N. bucharica genomes, respectively. Roughly, half of the genomes are retrotransposons (class I transposons), while DNA transposons (class II transposons) contributed to only about 2% of the genomes. The analyzed Nigella species possess large genomes of about 7.4 to 12.4 Gbp/1C. Only two satellite repeats in N. sativa, one in N. damascena and four in N. bucharica were identified, which were mostly (peri)centromeric and represented about 1% of each genome. A high variation in number and position of 45S rDNA loci were found among Nigella species. Interestingly, in N. hispanica, each chromosome revealed at least one 45S rDNA site and one of them occurs in hemizygous condition. Based on the chromosome numbers, genome size and (peri)centromeric satellites, three karyotype groups were observed: Two with 2n = 2x = 12 and a karyotype formula of 10m + 2t (including N. sativa, N. arvensis, N. hispanica as the first group and N. damascena and N. orientalis as the second group) and a more distant group with 2n = 2x = 14 and a karyotype formula of 8m + 2st + 4t (including N. integrifolia and N. bucharica). These karyotype groups agreed with the phylogenetic analysis using ITS and rbcL sequences. We conclude that variation in (peri)centromeric sequences, number and localization of rDNA sites as well as chromosome number (dysploidy) are involved in the diversification of the genus Nigella.
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Affiliation(s)
- Fatemeh Orooji
- Department of Agronomy and Plant Breeding, Faculty of Agriculture, University of Kurdistan, Sanandaj, Iran
| | - Ghader Mirzaghaderi
- Department of Agronomy and Plant Breeding, Faculty of Agriculture, University of Kurdistan, Sanandaj, Iran
| | - Yi-Tzu Kuo
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Jörg Fuchs
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
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18
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Sicat JPA, Visendi P, Sewe SO, Bouvaine S, Seal SE. Characterization of transposable elements within the Bemisia tabaci species complex. Mob DNA 2022; 13:12. [PMID: 35440097 PMCID: PMC9017028 DOI: 10.1186/s13100-022-00270-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Accepted: 03/30/2022] [Indexed: 12/24/2022] Open
Abstract
Background Whiteflies are agricultural pests that cause negative impacts globally to crop yields resulting at times in severe economic losses and food insecurity. The Bemisia tabaci whitefly species complex is the most damaging in terms of its broad crop host range and its ability to serve as vector for over 400 plant viruses. Genomes of whiteflies belonging to this species complex have provided valuable genomic data; however, transposable elements (TEs) within these genomes remain unexplored. This study provides the first accurate characterization of TE content within the B. tabaci species complex. Results This study identified that an average of 40.61% of the genomes of three whitefly species (MEAM1, MEDQ, and SSA-ECA) consists of TEs. The majority of the TEs identified were DNA transposons (22.85% average) while SINEs (0.14% average) were the least represented. This study also compared the TE content of the three whitefly genomes with three other hemipteran genomes and found significantly more DNA transposons and less LINEs in the whitefly genomes. A total of 63 TE superfamilies were identified to be present across the three whitefly species (39 DNA transposons, six LTR, 16 LINE, and two SINE). The sequences of the identified TEs were clustered which generated 5766 TE clusters. A total of 2707 clusters were identified as uniquely found within the whitefly genomes while none of the generated clusters were from both whitefly and non-whitefly TE sequences. This study is the first to characterize TEs found within different B. tabaci species and has created a standardized annotation workflow that could be used to analyze future whitefly genomes. Conclusion This study is the first to characterize the landscape of TEs within the B. tabaci whitefly species complex. The characterization of these elements within the three whitefly genomes shows that TEs occupy significant portions of B. tabaci genomes, with DNA transposons representing the vast majority. This study also identified TE superfamilies and clusters of TE sequences of potential interest, providing essential information, and a framework for future TE studies within this species complex. Supplementary Information The online version contains supplementary material available at 10.1186/s13100-022-00270-6.
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Affiliation(s)
- Juan Paolo A Sicat
- Natural Resources Institute, University of Greenwich, Central Avenue, Gillingham, Chatham, ME4 4TB, UK.
| | - Paul Visendi
- Centre for Agriculture and the Bioeconomy, Queensland University of Technology, Brisbane, QLD, 4000, Australia
| | - Steven O Sewe
- Natural Resources Institute, University of Greenwich, Central Avenue, Gillingham, Chatham, ME4 4TB, UK
| | - Sophie Bouvaine
- Natural Resources Institute, University of Greenwich, Central Avenue, Gillingham, Chatham, ME4 4TB, UK
| | - Susan E Seal
- Natural Resources Institute, University of Greenwich, Central Avenue, Gillingham, Chatham, ME4 4TB, UK
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19
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Hoyt SJ, Storer JM, Hartley GA, Grady PGS, Gershman A, de Lima LG, Limouse C, Halabian R, Wojenski L, Rodriguez M, Altemose N, Rhie A, Core LJ, Gerton JL, Makalowski W, Olson D, Rosen J, Smit AFA, Straight AF, Vollger MR, Wheeler TJ, Schatz MC, Eichler EE, Phillippy AM, Timp W, Miga KH, O’Neill RJ. From telomere to telomere: The transcriptional and epigenetic state of human repeat elements. Science 2022; 376:eabk3112. [PMID: 35357925 PMCID: PMC9301658 DOI: 10.1126/science.abk3112] [Citation(s) in RCA: 121] [Impact Index Per Article: 60.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Mobile elements and repetitive genomic regions are sources of lineage-specific genomic innovation and uniquely fingerprint individual genomes. Comprehensive analyses of such repeat elements, including those found in more complex regions of the genome, require a complete, linear genome assembly. We present a de novo repeat discovery and annotation of the T2T-CHM13 human reference genome. We identified previously unknown satellite arrays, expanded the catalog of variants and families for repeats and mobile elements, characterized classes of complex composite repeats, and located retroelement transduction events. We detected nascent transcription and delineated CpG methylation profiles to define the structure of transcriptionally active retroelements in humans, including those in centromeres. These data expand our insight into the diversity, distribution, and evolution of repetitive regions that have shaped the human genome.
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Affiliation(s)
- Savannah J. Hoyt
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA
| | | | - Gabrielle A. Hartley
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA
| | - Patrick G. S. Grady
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA
| | - Ariel Gershman
- Department of Molecular Biology and Genetics, Johns Hopkins University, Baltimore, MD, USA
| | | | - Charles Limouse
- Department of Biochemistry, Stanford University, Stanford, CA, USA
| | - Reza Halabian
- Institute of Bioinformatics, Faculty of Medicine, University of Münster, Münster, Germany
| | - Luke Wojenski
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA
| | - Matias Rodriguez
- Institute of Bioinformatics, Faculty of Medicine, University of Münster, Münster, Germany
| | - Nicolas Altemose
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
| | - Arang Rhie
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Leighton J. Core
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA
- Institute for Systems Genomics, University of Connecticut, Storrs, CT, USA
| | | | - Wojciech Makalowski
- Institute of Bioinformatics, Faculty of Medicine, University of Münster, Münster, Germany
| | - Daniel Olson
- Department of Computer Science, University of Montana, Missoula, MT, USA
| | - Jeb Rosen
- Institute for Systems Biology, Seattle, WA, USA
| | | | | | - Mitchell R. Vollger
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Travis J. Wheeler
- Department of Computer Science, University of Montana, Missoula, MT, USA
| | - Michael C. Schatz
- Department of Computer Science and Department of Biology, Johns Hopkins University, Baltimore, MD, USA
| | - Evan E. Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
| | - Adam M. Phillippy
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Winston Timp
- Department of Molecular Biology and Genetics, Johns Hopkins University, Baltimore, MD, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Karen H. Miga
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Rachel J. O’Neill
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA
- Institute for Systems Genomics, University of Connecticut, Storrs, CT, USA
- Department of Genetics and Genome Sciences, UConn Health, Farmington, CT, USA
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20
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Goubert C, Craig RJ, Bilat AF, Peona V, Vogan AA, Protasio AV. A beginner's guide to manual curation of transposable elements. Mob DNA 2022; 13:7. [PMID: 35354491 PMCID: PMC8969392 DOI: 10.1186/s13100-021-00259-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 12/17/2021] [Indexed: 12/11/2022] Open
Abstract
Background In the study of transposable elements (TEs), the generation of a high confidence set of consensus sequences that represent the diversity of TEs found in a given genome is a key step in the path to investigate these fascinating genomic elements. Many algorithms and pipelines are available to automatically identify putative TE families present in a genome. Despite the availability of these valuable resources, producing a library of high-quality full-length TE consensus sequences largely remains a process of manual curation. This know-how is often passed on from mentor-to-mentee within research groups, making it difficult for those outside the field to access this highly specialised skill. Results Our manuscript attempts to fill this gap by providing a set of detailed computer protocols, software recommendations and video tutorials for those aiming to manually curate TEs. Detailed step-by-step protocols, aimed at the complete beginner, are presented in the Supplementary Methods. Conclusions The proposed set of programs and tools presented here will make the process of manual curation achievable and amenable to all researchers and in special to those new to the field of TEs. Supplementary Information The online version contains supplementary material available at 10.1186/s13100-021-00259-7.
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Affiliation(s)
- Clement Goubert
- Canadian Center for Computational Genomics, McGill University, Montreal, Québec, Canada.,Department of Human Genetics, McGill University, Montreal, Québec, Canada
| | - Rory J Craig
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, EH9 3FL, UK
| | - Agustin F Bilat
- Departamento de Genética, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Valentina Peona
- Department of Organismal Biology, Uppsala University, Norbyvägen 18D, 752 36, Uppsala, Sweden
| | - Aaron A Vogan
- Department of Organismal Biology, Uppsala University, Norbyvägen 18D, 752 36, Uppsala, Sweden
| | - Anna V Protasio
- Department of Pathology, Tennis Court Road, Cambridge, CB1 2PQ, UK. .,Christ's College, St Andrews Street, Cambridge, CB2 3BU, UK.
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21
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Timmons CM, Shazib SUA, Katz LA. Epigenetic influences of mobile genetic elements on ciliate genome architecture and evolution. J Eukaryot Microbiol 2022; 69:e12891. [PMID: 35100457 DOI: 10.1111/jeu.12891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 01/20/2022] [Accepted: 01/22/2022] [Indexed: 11/27/2022]
Abstract
Mobile genetic elements (MGEs) are transient genetic material that can move either within a single organism's genome or between individuals or species. While historically considered 'junk' DNA (i.e. deleterious or at best neutral), more recent studies reveal the adaptive advantages MGEs provide in lineages across the tree of life. Ciliates, a group of single-celled microbial eukaryotes characterized by nuclear dimorphism, exemplify how epigenetic influences from MGEs shape genome architecture and patterns of molecular evolution. Ciliate nuclear dimorphism may have evolved as a response to transposon invasion and ciliates have since co-opted transposons to carry out programmed DNA deletion. Another example of the effect of MGEs is in providing mechanisms for lateral gene transfer from bacteria, which introduces genetic diversity and, in several cases, drives ecological specialization in ciliates. As a third example, the integration of viral DNA, likely through transduction, provides new genetic material and can change the way host cells defend themselves against other viral pathogens. We argue that the acquisition of MGEs through non-Mendelian patterns of inheritance, coupled with their effects on ciliate genome architecture and expression and persistence throughout evolutionary history, exemplify how the transmission of mobile elements should be considered a mechanism of transgenerational epigenetic inheritance.
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Affiliation(s)
- Caitlin M Timmons
- Department of Biological Sciences, Smith College, Northampton, Massachusetts, 01063, USA
| | - Shahed U A Shazib
- Department of Biological Sciences, Smith College, Northampton, Massachusetts, 01063, USA
| | - Laura A Katz
- Department of Biological Sciences, Smith College, Northampton, Massachusetts, 01063, USA
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22
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inPOSE: A Flexible Toolbox for Chromosomal Cloning and Amplification of Bacterial Transgenes. Microorganisms 2022; 10:microorganisms10020236. [PMID: 35208691 PMCID: PMC8875745 DOI: 10.3390/microorganisms10020236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 01/14/2022] [Accepted: 01/18/2022] [Indexed: 12/10/2022] Open
Abstract
Cloning the genes and operons encoding heterologous functions in bacterial hosts is now almost exclusively carried out using plasmid vectors. This has multiple drawbacks, including the need for constant selection and variation in copy numbers. The chromosomal integration of transgenes has always offered a viable alternative; however, to date, it has been of limited use due to its tedious nature and often being limited to a single copy. We introduce here a strategy that uses bacterial insertion sequences, which are the simplest autonomous transposable elements to insert and amplify genetic cargo into a bacterial chromosome. Transgene insertion can take place either as transposition or homologous recombination, and copy number amplification is achieved using controlled copy-paste transposition. We display the successful use of IS1 and IS3 for this purpose in Escherichia coli cells using various selection markers. We demonstrate the insertion of selectable genes, an unselectable gene and a five-gene operon in up to two copies in a single step. We continue with the amplification of the inserted cassette to double-digit copy numbers within two rounds of transposase induction and selection. Finally, we analyze the stability of the cloned genetic constructs in the lack of selection and find it to be superior to all investigated plasmid-based systems. Due to the ubiquitous nature of transposable elements, we believe that with proper design, this strategy can be adapted to numerous other bacterial species.
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Zidi M, Denis F, Klai K, Chénais B, Caruso A, Djebbi S, Mezghani M, Casse N. Genome-wide characterization of Mariner-like transposons and their derived MITEs in the Whitefly Bemisia tabaci (Hemiptera: Aleyrodidae). G3 (BETHESDA, MD.) 2021; 11:jkab287. [PMID: 34849769 PMCID: PMC8664452 DOI: 10.1093/g3journal/jkab287] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 07/28/2021] [Indexed: 12/02/2022]
Abstract
The whitefly, Bemisia tabaci is a hemipteran pest of vegetable crops vectoring a broad category of viruses. Currently, this insect pest showed a high adaptability and resistance to almost all the chemical compounds commonly used for its control. In many cases, transposable elements (TEs) contributed to the evolution of host genomic plasticity. This study focuses on the annotation of Mariner-like elements (MLEs) and their derived Miniature Inverted repeat Transposable Elements (MITEs) in the genome of B. tabaci. Two full-length MLEs belonging to mauritiana and irritans subfamilies were detected and named Btmar1.1 and Btmar2.1, respectively. Additionally, 548 defective MLE sequences clustering mainly into 19 different Mariner lineages of mauritiana and irritans subfamilies were identified. Each subfamily showed a significant variation in MLE copy number and size. Furthermore, 71 MITEs were identified as MLEs derivatives that could be mobilized via the potentially active transposases encoded by Btmar 1.1 and Btmar2.1. The vast majority of sequences detected in the whitefly genome present unusual terminal inverted repeats (TIRs) of up to 400 bp in length. However, some exceptions are sequences without TIRs. This feature of the MLEs and their derived MITEs in B. tabaci genome that distinguishes them from all the other MLEs so far described in insects, which have TIRs size ranging from 20 to 40 bp. Overall, our study provides an overview of MLEs, especially those with large TIRs, and their related MITEs, as well as diversity of their families, which will provide a better understanding of the evolution and adaptation of the whitefly genome.
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Affiliation(s)
- Marwa Zidi
- Laboratory of Biochemistry and Biotechnology (LR01ES05), Faculty of Sciences of Tunis, University of Tunis El Manar, 2092 Tunis, Tunisia
- Biologie des Organismes, Stress, Santé, Environnement, Le Mans Université, F-72085 Le Mans, France
| | - Françoise Denis
- Biologie des Organismes, Stress, Santé, Environnement, Le Mans Université, F-72085 Le Mans, France
- Laboratoire BOREA MNHN, CNRS FRE 2030, SU, IRD 207, UCN, UA, 75231 Paris, France
| | - Khouloud Klai
- Laboratory of Biochemistry and Biotechnology (LR01ES05), Faculty of Sciences of Tunis, University of Tunis El Manar, 2092 Tunis, Tunisia
- Biologie des Organismes, Stress, Santé, Environnement, Le Mans Université, F-72085 Le Mans, France
| | - Benoît Chénais
- Biologie des Organismes, Stress, Santé, Environnement, Le Mans Université, F-72085 Le Mans, France
| | - Aurore Caruso
- Biologie des Organismes, Stress, Santé, Environnement, Le Mans Université, F-72085 Le Mans, France
| | - Salma Djebbi
- Laboratory of Biochemistry and Biotechnology (LR01ES05), Faculty of Sciences of Tunis, University of Tunis El Manar, 2092 Tunis, Tunisia
| | - Maha Mezghani
- Laboratory of Biochemistry and Biotechnology (LR01ES05), Faculty of Sciences of Tunis, University of Tunis El Manar, 2092 Tunis, Tunisia
| | - Nathalie Casse
- Biologie des Organismes, Stress, Santé, Environnement, Le Mans Université, F-72085 Le Mans, France
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24
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Merkerova MD, Krejcik Z. Transposable elements and Piwi‑interacting RNAs in hemato‑oncology with a focus on myelodysplastic syndrome (Review). Int J Oncol 2021; 59:105. [PMID: 34779490 DOI: 10.3892/ijo.2021.5285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 10/12/2021] [Indexed: 11/06/2022] Open
Abstract
Our current understanding of hematopoietic stem cell differentiation and the abnormalities that lead to leukemogenesis originates from the accumulation of knowledge regarding protein‑coding genes. However, the possible impact of transposable element (TE) mobilization and the expression of P‑element‑induced WImpy testis‑interacting RNAs (piRNAs) on leukemogenesis has been beyond the scope of scientific interest to date. The expression profiles of these molecules and their importance for human health have only been characterized recently due to the rapid progress of high‑throughput sequencing technology development. In the present review, current knowledge on the expression profile and function of TEs and piRNAs was summarized, with specific focus on their reported involvement in leukemogenesis and pathogenesis of myelodysplastic syndrome.
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Affiliation(s)
| | - Zdenek Krejcik
- Institute of Hematology and Blood Transfusion, 128 20 Prague, Czech Republic
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25
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Ho EKH, Bellis ES, Calkins J, Adrion JR, Latta IV LC, Schaack S. Engines of change: Transposable element mutation rates are high and variable within Daphnia magna. PLoS Genet 2021; 17:e1009827. [PMID: 34723969 PMCID: PMC8594854 DOI: 10.1371/journal.pgen.1009827] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 11/16/2021] [Accepted: 09/16/2021] [Indexed: 12/22/2022] Open
Abstract
Transposable elements (TEs) represent a major portion of most eukaryotic genomes, yet little is known about their mutation rates or how their activity is shaped by other evolutionary forces. Here, we compare short- and long-term patterns of genome-wide mutation accumulation (MA) of TEs among 9 genotypes from three populations of Daphnia magna from across a latitudinal gradient. While the overall proportion of the genome comprised of TEs is highly similar among genotypes from Finland, Germany, and Israel, populations are distinguishable based on patterns of insertion site polymorphism. Our direct rate estimates indicate TE movement is highly variable (net rates ranging from -11.98 to 12.79 x 10-5 per copy per generation among genotypes), differing both among populations and TE families. Although gains outnumber losses when selection is minimized, both types of events appear to be highly deleterious based on their low frequency in control lines where propagation is not limited to random, single-progeny descent. With rate estimates 4 orders of magnitude higher than base substitutions, TEs clearly represent a highly mutagenic force in the genome. Quantifying patterns of intra- and interspecific variation in TE mobility with and without selection provides insight into a powerful mechanism generating genetic variation in the genome.
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Affiliation(s)
- Eddie K. H. Ho
- Department of Biology, Reed College, Portland, Oregon, United States of America
| | - Emily S. Bellis
- Department of Biology, Reed College, Portland, Oregon, United States of America
- Department of Computer Science, Arkansas State University, Jonesboro, Arkansas, United States of America
| | - Jaclyn Calkins
- Department of Biology, Reed College, Portland, Oregon, United States of America
- College of Human Medicine, Michigan State University, East Lansing, Michigan, United States of America
| | - Jeffrey R. Adrion
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, United States of America
| | - Leigh C. Latta IV
- Department of Biology, Reed College, Portland, Oregon, United States of America
- Lewis-Clark State College, Lewiston, Idaho, United States of America
| | - Sarah Schaack
- Department of Biology, Reed College, Portland, Oregon, United States of America
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26
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The Dynamism of Transposon Methylation for Plant Development and Stress Adaptation. Int J Mol Sci 2021; 22:ijms222111387. [PMID: 34768817 PMCID: PMC8583499 DOI: 10.3390/ijms222111387] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 10/13/2021] [Accepted: 10/19/2021] [Indexed: 02/06/2023] Open
Abstract
Plant development processes are regulated by epigenetic alterations that shape nuclear structure, gene expression, and phenotypic plasticity; these alterations can provide the plant with protection from environmental stresses. During plant growth and development, these processes play a significant role in regulating gene expression to remodel chromatin structure. These epigenetic alterations are mainly regulated by transposable elements (TEs) whose abundance in plant genomes results in their interaction with genomes. Thus, TEs are the main source of epigenetic changes and form a substantial part of the plant genome. Furthermore, TEs can be activated under stress conditions, and activated elements cause mutagenic effects and substantial genetic variability. This introduces novel gene functions and structural variation in the insertion sites and primarily contributes to epigenetic modifications. Altogether, these modifications indirectly or directly provide the ability to withstand environmental stresses. In recent years, many studies have shown that TE methylation plays a major role in the evolution of the plant genome through epigenetic process that regulate gene imprinting, thereby upholding genome stability. The induced genetic rearrangements and insertions of mobile genetic elements in regions of active euchromatin contribute to genome alteration, leading to genomic stress. These TE-mediated epigenetic modifications lead to phenotypic diversity, genetic variation, and environmental stress tolerance. Thus, TE methylation is essential for plant evolution and stress adaptation, and TEs hold a relevant military position in the plant genome. High-throughput techniques have greatly advanced the understanding of TE-mediated gene expression and its associations with genome methylation and suggest that controlled mobilization of TEs could be used for crop breeding. However, development application in this area has been limited, and an integrated view of TE function and subsequent processes is lacking. In this review, we explore the enormous diversity and likely functions of the TE repertoire in adaptive evolution and discuss some recent examples of how TEs impact gene expression in plant development and stress adaptation.
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27
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Stitzer MC, Anderson SN, Springer NM, Ross-Ibarra J. The genomic ecosystem of transposable elements in maize. PLoS Genet 2021; 17:e1009768. [PMID: 34648488 PMCID: PMC8547701 DOI: 10.1371/journal.pgen.1009768] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 10/26/2021] [Accepted: 08/10/2021] [Indexed: 12/16/2022] Open
Abstract
Transposable elements (TEs) constitute the majority of flowering plant DNA, reflecting their tremendous success in subverting, avoiding, and surviving the defenses of their host genomes to ensure their selfish replication. More than 85% of the sequence of the maize genome can be ascribed to past transposition, providing a major contribution to the structure of the genome. Evidence from individual loci has informed our understanding of how transposition has shaped the genome, and a number of individual TE insertions have been causally linked to dramatic phenotypic changes. Genome-wide analyses in maize and other taxa have frequently represented TEs as a relatively homogeneous class of fragmentary relics of past transposition, obscuring their evolutionary history and interaction with their host genome. Using an updated annotation of structurally intact TEs in the maize reference genome, we investigate the family-level dynamics of TEs in maize. Integrating a variety of data, from descriptors of individual TEs like coding capacity, expression, and methylation, as well as similar features of the sequence they inserted into, we model the relationship between attributes of the genomic environment and the survival of TE copies and families. In contrast to the wholesale relegation of all TEs to a single category of junk DNA, these differences reveal a diversity of survival strategies of TE families. Together these generate a rich ecology of the genome, with each TE family representing the evolution of a distinct ecological niche. We conclude that while the impact of transposition is highly family- and context-dependent, a family-level understanding of the ecology of TEs in the genome can refine our ability to predict the role of TEs in generating genetic and phenotypic diversity.
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Affiliation(s)
- Michelle C. Stitzer
- Center for Population Biology and Department of Evolution and Ecology, University of California, Davis, California, United States of America
| | - Sarah N. Anderson
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, Minnesota, United States of America
| | - Nathan M. Springer
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, Minnesota, United States of America
| | - Jeffrey Ross-Ibarra
- Center for Population Biology and Department of Evolution and Ecology, University of California, Davis, California, United States of America
- Genome Center, University of California, Davis, California, United States of America
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28
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Torres DE, Thomma BPHJ, Seidl MF. Transposable Elements Contribute to Genome Dynamics and Gene Expression Variation in the Fungal Plant Pathogen Verticillium dahliae. Genome Biol Evol 2021; 13:evab135. [PMID: 34100895 PMCID: PMC8290119 DOI: 10.1093/gbe/evab135] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/04/2021] [Indexed: 12/12/2022] Open
Abstract
Transposable elements (TEs) are a major source of genetic and regulatory variation in their host genome and are consequently thought to play important roles in evolution. Many fungal and oomycete plant pathogens have evolved dynamic and TE-rich genomic regions containing genes that are implicated in host colonization and adaptation. TEs embedded in these regions have typically been thought to accelerate the evolution of these genomic compartments, but little is known about their dynamics in strains that harbor them. Here, we used whole-genome sequencing data of 42 strains of the fungal plant pathogen Verticillium dahliae to systematically identify polymorphic TEs that may be implicated in genomic as well as in gene expression variation. We identified 2,523 TE polymorphisms and characterize a subset of 8% of the TEs as polymorphic elements that are evolutionary younger, less methylated, and more highly expressed when compared with the remaining 92% of the total TE complement. As expected, the polyrmorphic TEs are enriched in the adaptive genomic regions. Besides, we observed an association of polymorphic TEs with pathogenicity-related genes that localize nearby and that display high expression levels. Collectively, our analyses demonstrate that TE dynamics in V. dahliae contributes to genomic variation, correlates with expression of pathogenicity-related genes, and potentially impacts the evolution of adaptive genomic regions.
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Affiliation(s)
- David E Torres
- Theoretical Biology and Bioinformatics Group, Department of Biology, Utrecht University, The Netherlands
- Laboratory of Phytopathology, Wageningen University and Research, The Netherlands
| | - Bart P H J Thomma
- Laboratory of Phytopathology, Wageningen University and Research, The Netherlands
- Cluster of Excellence on Plant Sciences (CEPLAS), Institute for Plant Sciences, University of Cologne, Germany
| | - Michael F Seidl
- Theoretical Biology and Bioinformatics Group, Department of Biology, Utrecht University, The Netherlands
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29
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Elliott TA, Heitkam T, Hubley R, Quesneville H, Suh A, Wheeler TJ. TE Hub: A community-oriented space for sharing and connecting tools, data, resources, and methods for transposable element annotation. Mob DNA 2021; 12:16. [PMID: 34154643 PMCID: PMC8215825 DOI: 10.1186/s13100-021-00244-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 06/03/2021] [Indexed: 12/16/2022] Open
Abstract
Transposable elements (TEs) play powerful and varied evolutionary and functional roles, and are widespread in most eukaryotic genomes. Research into their unique biology has driven the creation of a large collection of databases, software, classification systems, and annotation guidelines. The diversity of available TE-related methods and resources raises compatibility concerns and can be overwhelming to researchers and communicators seeking straightforward guidance or materials. To address these challenges, we have initiated a new resource, TE Hub, that provides a space where members of the TE community can collaborate to document and create resources and methods. The space consists of (1) a website organized with an open wiki framework, https://tehub.org , (2) a conversation framework via a Twitter account and a Slack channel, and (3) bi-monthly Hub Update video chats on the platform's development. In addition to serving as a centralized repository and communication platform, TE Hub lays the foundation for improved integration, standardization, and effectiveness of diverse tools and protocols. We invite the TE community, both novices and experts in TE identification and analysis, to join us in expanding our community-oriented resource.
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Affiliation(s)
| | - Tyler A. Elliott
- grid.34429.380000 0004 1936 8198Centre for Biodiversity Genomics, University of Guelph, Guelph, ON Canada
| | - Tony Heitkam
- grid.4488.00000 0001 2111 7257Faculty of Biology, Technische Universität Dresden, 01069 Dresden, Germany
| | - Robert Hubley
- grid.64212.330000 0004 0463 2320Institute for Systems Biology, Seattle, WA USA
| | - Hadi Quesneville
- grid.507621.7Université Paris-Saclay, INRAE, URGI, 78026 Versailles, France
| | - Alexander Suh
- grid.8273.e0000 0001 1092 7967School of Biological Sciences, University of East Anglia, Norwich, UK ,grid.8993.b0000 0004 1936 9457Department of Organismal Biology, Uppsala University, Uppsala, Sweden
| | - Travis J. Wheeler
- grid.253613.00000 0001 2192 5772Department of Computer Science, University of Montana, Missoula, MT USA
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30
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Choi IS, Wojciechowski MF, Ruhlman TA, Jansen RK. In and out: Evolution of viral sequences in the mitochondrial genomes of legumes (Fabaceae). Mol Phylogenet Evol 2021; 163:107236. [PMID: 34147655 DOI: 10.1016/j.ympev.2021.107236] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 06/11/2021] [Accepted: 06/14/2021] [Indexed: 10/21/2022]
Abstract
Plant specific mitoviruses in the 'genus' Mitovirus (Narnaviridae) and their integrated sequences (non-retroviral endogenous RNA viral elements or NERVEs) have been recently identified in various plant lineages. However, the sparse phylogenetic coverage of complete plant mitochondrial genome (mitogenome) sequences and the non-conserved nature of mitochondrial intergenic regions have hindered comparative studies on mitovirus NERVEs in plants. In this study, 10 new mitogenomes were sequenced from legumes (Fabaceae). Based on comparative genomic analysis of 27 total mitogenomes, we identified mitovirus NERVEs and transposable elements across the family. All legume mitogenomes included NERVEs and total NERVE length varied from ca. 2 kb in the papilionoid Trifolium to 35 kb in the mimosoid Acacia. Most of the NERVE integration sites were in highly variable intergenic regions, however, some were positioned in six cis-spliced mitochondrial introns. In the Acacia mitogenome, there were L1-like transposon sequences including an almost full-length copy with target site duplications (TSDs). The integration sites of NERVEs in four introns showed evidence of L1-like retrotransposition events. Phylogenetic analysis revealed that there were multiple instances of precise deletion of NERVEs between TSDs. This study provides clear evidence that a L1-like retrotransposition mechanism has a long history of contributing to the integration of viral RNA into plant mitogenomes while microhomology-mediated deletion can restore the integration site.
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Affiliation(s)
- In-Su Choi
- Department of Integrative Biology, University of Texas at Austin, Austin, TX 78712, USA; School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA.
| | | | - Tracey A Ruhlman
- Department of Integrative Biology, University of Texas at Austin, Austin, TX 78712, USA.
| | - Robert K Jansen
- Department of Integrative Biology, University of Texas at Austin, Austin, TX 78712, USA; Centre of Excellence in Bionanoscience Research, Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia.
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31
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Storer JM, Hubley R, Rosen J, Smit AFA. Curation Guidelines for de novo Generated Transposable Element Families. Curr Protoc 2021; 1:e154. [PMID: 34138525 DOI: 10.1002/cpz1.154] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Transposable elements (TEs) have the ability to alter individual genomic landscapes and shape the course of evolution for species in which they reside. Such profound changes can be understood by studying the biology of the organism and the interplay of the TEs it hosts. Characterizing and curating TEs across a wide range of species is a fundamental first step in this endeavor. This protocol employs techniques honed while developing TE libraries for a wide range of organisms and specifically addresses: (1) the extension of truncated de novo results into full-length TE families; (2) the iterative refinement of TE multiple sequence alignments; and (3) the use of alignment visualization to assess model completeness and subfamily structure. © 2021 Wiley Periodicals LLC. Basic Protocol: Extension and edge polishing of consensi and seed alignments derived from de novo repeat finders Support Protocol: Generating seed alignments using a library of consensi and a genome assembly.
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Affiliation(s)
| | | | - Jeb Rosen
- Institute for Systems Biology, Seattle, Washington
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32
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Expression Quantitative Trait Loci (eQTLs) Associated with Retrotransposons Demonstrate their Modulatory Effect on the Transcriptome. Int J Mol Sci 2021; 22:ijms22126319. [PMID: 34204806 PMCID: PMC8231655 DOI: 10.3390/ijms22126319] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Revised: 06/03/2021] [Accepted: 06/10/2021] [Indexed: 12/26/2022] Open
Abstract
Transposable elements (TEs) are repetitive elements that belong to a variety of functional classes and have an important role in shaping genome evolution. Around 50% of the human genome contains TEs, and they have been termed the "dark matter" of the genome because relatively little is known about their function. While TEs have been shown to participate in aberrant gene regulation and the pathogenesis of diseases, only a few studies have explored the systemic effect of TEs on gene expression. In the present study, we analysed whole genome sequences and blood whole transcriptome data from 570 individuals within the Parkinson's Progressive Markers Initiative (PPMI) cohort to identify expression quantitative trait loci (eQTL) regulating genome-wide gene expression associated with TEs. We identified 2132 reference TEs that were polymorphic for their presence or absence in our study cohort. The presence or absence of the TE element could change the expression of the gene or gene clusters from zero to tens of thousands of copies of RNA. The main finding is that many TEs possess very strong regulatory effects, and they have the potential to modulate large genetic networks with hundreds of target genes over the genome. We illustrate the plethora of regulatory mechanisms using examples of their action at the HLA gene cluster and data showing different TEs' convergence to modulate WFS1 gene expression. In conclusion, the presence or absence of polymorphisms of TEs has an eminent genome-wide regulatory function with large effect size at the level of the whole transcriptome. The role of TEs in explaining, in part, the missing heritability for complex traits is convincing and should be considered.
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33
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Antoine-Lorquin A, Arensburger P, Arnaoty A, Asgari S, Batailler M, Beauclair L, Belleannée C, Buisine N, Coustham V, Guyetant S, Helou L, Lecomte T, Pitard B, Stévant I, Bigot Y. Two repeated motifs enriched within some enhancers and origins of replication are bound by SETMAR isoforms in human colon cells. Genomics 2021; 113:1589-1604. [PMID: 33812898 DOI: 10.1016/j.ygeno.2021.03.032] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 03/25/2021] [Accepted: 03/30/2021] [Indexed: 11/15/2022]
Abstract
Setmar is a gene specific to simian genomes. The function(s) of its isoforms are poorly understood and their existence in healthy tissues remains to be validated. Here we profiled SETMAR expression and its genome-wide binding landscape in colon tissue. We found isoforms V3 and V6 in healthy and tumour colon tissues as well as incell lines. In two colorectal cell lines SETMAR binds to several thousand Hsmar1 and MADE1 terminal ends, transposons mostly located in non-genic regions of active chromatin including in enhancers. It also binds to a 12-bp motifs similar to an inner motif in Hsmar1 and MADE1 terminal ends. This motif is interspersed throughout the genome and is enriched in GC-rich regions as well as in CpG islands that contain constitutive replication origins. It is also found in enhancers other than those associated with Hsmar1 and MADE1. The role of SETMAR in the expression of genes, DNA replication and in DNA repair are discussed.
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Affiliation(s)
| | - Peter Arensburger
- Biological Sciences Department, California State Polytechnic University, Pomona, CA 91768, - United States
| | - Ahmed Arnaoty
- EA GICC, 7501, CHRU de Tours, 37044 TOURS, Cedex 09, France
| | - Sassan Asgari
- School of Biological Sciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Martine Batailler
- PRC, UMR INRA 0085, CNRS 7247, Centre INRA Val de Loire, 37380 Nouzilly, France
| | - Linda Beauclair
- PRC, UMR INRA 0085, CNRS 7247, Centre INRA Val de Loire, 37380 Nouzilly, France
| | | | - Nicolas Buisine
- UMR CNRS 7221, Muséum National d'Histoire Naturelle, 75005 Paris, France
| | | | - Serge Guyetant
- Tumorothèque du CHRU de Tours, 37044 Tours, Cedex, France
| | - Laura Helou
- PRC, UMR INRA 0085, CNRS 7247, Centre INRA Val de Loire, 37380 Nouzilly, France
| | | | - Bruno Pitard
- Université de Nantes, CNRS ERL6001, Inserm 1232, CRCINA, F-44000 Nantes, France
| | - Isabelle Stévant
- Institut de Génomique Fonctionnelle de Lyon, Univ Lyon, CNRS UMR 5242, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon, 1, 46 allée d'Italie, 69364 Lyon, France
| | - Yves Bigot
- PRC, UMR INRA 0085, CNRS 7247, Centre INRA Val de Loire, 37380 Nouzilly, France.
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34
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Retrotransposable Elements: DNA Fingerprinting and the Assessment of Genetic Diversity. Methods Mol Biol 2021; 2222:263-286. [PMID: 33301099 DOI: 10.1007/978-1-0716-0997-2_15] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Retrotransposable elements (RTEs) are highly common mobile genetic elements that are composed of several classes and make up the majority of eukaryotic genomes. The "copy-out and paste-in" life cycle of replicative transposition in these dispersive and ubiquitous RTEs leads to new genome insertions without excision of the original element. RTEs are important drivers of species diversity; they exhibit great variety in structure, size, and mechanisms of transposition, making them important putative components in genome evolution. Accordingly, various applications have been developed to explore the polymorphisms in RTE insertion patterns. These applications include conventional or anchored polymerase chain reaction (PCR) and quantitative or digital PCR with primers designed for the 5' or 3' junction. Marker systems exploiting these PCR methods can be easily developed and are inexpensively used in the absence of extensive genome sequence data. The main inter-repeat amplification polymorphism techniques include inter-retrotransposon amplified polymorphism (IRAP), retrotransposon microsatellite amplified polymorphism (REMAP), and Inter-Primer Binding Site (iPBS) for PCR amplification with a single or two primers.
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Collens AB, Katz LA. Opinion: Genetic Conflict With Mobile Elements Drives Eukaryotic Genome Evolution, and Perhaps Also Eukaryogenesis. J Hered 2021; 112:140-144. [PMID: 33538295 PMCID: PMC7953837 DOI: 10.1093/jhered/esaa060] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 12/17/2020] [Indexed: 12/13/2022] Open
Abstract
Through analyses of diverse microeukaryotes, we have previously argued that eukaryotic genomes are dynamic systems that rely on epigenetic mechanisms to distinguish germline (i.e., DNA to be inherited) from soma (i.e., DNA that undergoes polyploidization, genome rearrangement, etc.), even in the context of a single nucleus. Here, we extend these arguments by including two well-documented observations: (1) eukaryotic genomes interact frequently with mobile genetic elements (MGEs) like viruses and transposable elements (TEs), creating genetic conflict, and (2) epigenetic mechanisms regulate MGEs. Synthesis of these ideas leads to the hypothesis that genetic conflict with MGEs contributed to the evolution of a dynamic eukaryotic genome in the last eukaryotic common ancestor (LECA), and may have contributed to eukaryogenesis (i.e., may have been a driver in the evolution of FECA, the first eukaryotic common ancestor). Sex (i.e., meiosis) may have evolved within the context of the development of germline-soma distinctions in LECA, as this process resets the germline genome by regulating/eliminating somatic (i.e., polyploid, rearranged) genetic material. Our synthesis of these ideas expands on hypotheses of the origin of eukaryotes by integrating the roles of MGEs and epigenetics.
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Affiliation(s)
- Adena B Collens
- Department of Biological Sciences, Smith College, Northampton, MA
| | - Laura A Katz
- Department of Biological Sciences, Smith College, Northampton, MA
- Program in Organismic and Evolutionary Biology, University of Massachusetts, Amherst, MA
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Palazzo A, Escuder E, D'Addabbo P, Lovero D, Marsano RM. A genomic survey of Tc1-mariner transposons in nematodes suggests extensive horizontal transposon transfer events. Mol Phylogenet Evol 2021; 158:107090. [PMID: 33545274 DOI: 10.1016/j.ympev.2021.107090] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 01/27/2021] [Accepted: 01/27/2021] [Indexed: 01/24/2023]
Abstract
The number of reports concerning horizontal transposon transfers (HTT) in metazoan species is considerably increased, alongside with the exponential growth of genomic sequence data However, our understanding of the mechanisms of such phenomenon is still at an early stage. Nematodes constitute an animal phylum successfully adapted to almost every ecosystem and for this reason could potentially contribute to spreading the genetic information through horizontal transfer. To date, few studies describe HTT of nematode retrotransposons. This is due to the lack of annotation of transposable elements in the sequenced nematode genomes, especially DNA transposons, which are acknowledged as the best horizontal travelers among mobile sequences. We have therefore started a survey of DNA transposons and their possible involvement in HTT in sequenced nematode genomes. Here, we describe 83 new Tc1/mariner elements distributed in 17 nematode species. Among them, nine families were possibly horizontally transferred between nematodes and the most diverse animal species, including ants as preferred partner of HTT. The results obtained suggest that HTT events involving nematodes Tc1/mariner elements are not uncommon, and that nematodes could have a possible role as transposon reservoir that, in turn, can be redistributed among animal genomes. Overall, this could be relevant to understand how the inter-species genetic flows shape the landscape of genetic variation of organisms inhabiting specific environmental communities.
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Affiliation(s)
- Antonio Palazzo
- Dipartimento di Biologia, Università degli Studi di Bari "Aldo Moro", Bari, Italy
| | - Elsa Escuder
- Dipartimento di Biologia, Università degli Studi di Bari "Aldo Moro", Bari, Italy
| | - Pietro D'Addabbo
- Dipartimento di Biologia, Università degli Studi di Bari "Aldo Moro", Bari, Italy
| | - Domenica Lovero
- Dipartimento di Scienze Biomediche ed Oncologia Umana (DIMO), Università degli Studi di Bari "Aldo Moro", Bari, Italy
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Helou L, Beauclair L, Dardente H, Piégu B, Tsakou-Ngouafo L, Lecomte T, Kentsis A, Pontarotti P, Bigot Y. The piggyBac-derived protein 5 (PGBD5) transposes both the closely and the distantly related piggyBac-like elements Tcr-pble and Ifp2. J Mol Biol 2021; 433:166839. [PMID: 33539889 DOI: 10.1016/j.jmb.2021.166839] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 12/21/2020] [Accepted: 01/14/2021] [Indexed: 12/16/2022]
Abstract
The vertebrate piggyBac derived transposase 5 (PGBD5) encodes a domesticated transposase, which is active and able to transpose its distantly related piggyBac-like element (pble), Ifp2. This raised the question whether PGBD5 would be more effective at mobilizing a phylogenetically closely related pble element. We aimed to identify the pble most closely related to the pgbd5 gene. We updated the landscape of vertebrate pgbd genes to develop efficient filters and identify the most closely related pble to each of these genes. We found that Tcr-pble is phylogenetically the closest pble to the pgbd5 gene. Furthermore, we evaluated the capacity of two murine and human PGBD5 isoforms, Mm523 and Hs524, to transpose both Tcr-pble and Ifp2 elements. We found that both pbles could be transposed by Mm523 with similar efficiency. However, integrations of both pbles occurred through both proper transposition and improper PGBD5-dependent recombination. This suggested that the ability of PGBD5 to bind both pbles may not be based on the primary sequence of element ends, but may involve recognition of inner DNA motifs, possibly related to palindromic repeats. In agreement with this hypothesis, we identified internal palindromic repeats near the end of 24 pble sequences, which display distinct sequences.
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Affiliation(s)
- Laura Helou
- UMR INRAE 0085, CNRS 7247, Physiologie de la Reproduction et des Comportements, Centre INRA Val de Loire, 37380 Nouzilly, France
| | - Linda Beauclair
- UMR INRAE 0085, CNRS 7247, Physiologie de la Reproduction et des Comportements, Centre INRA Val de Loire, 37380 Nouzilly, France
| | - Hugues Dardente
- UMR INRAE 0085, CNRS 7247, Physiologie de la Reproduction et des Comportements, Centre INRA Val de Loire, 37380 Nouzilly, France
| | - Benoît Piégu
- UMR INRAE 0085, CNRS 7247, Physiologie de la Reproduction et des Comportements, Centre INRA Val de Loire, 37380 Nouzilly, France
| | - Louis Tsakou-Ngouafo
- UMR MEPHI D-258, I, IRD, Aix Marseille Université, 19-21 Boulevard Jean Moulin, 13005 Marseille, France; CNRS SNC 5039, 13005 Marseille, France
| | | | - Alex Kentsis
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Weill Cornell Medical College, Cornell University, New York, NY, USA; Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Pierre Pontarotti
- UMR INRAE 0085, CNRS 7247, Physiologie de la Reproduction et des Comportements, Centre INRA Val de Loire, 37380 Nouzilly, France; CNRS SNC 5039, 13005 Marseille, France
| | - Yves Bigot
- UMR INRAE 0085, CNRS 7247, Physiologie de la Reproduction et des Comportements, Centre INRA Val de Loire, 37380 Nouzilly, France.
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Helou L, Beauclair L, Dardente H, Arensburger P, Buisine N, Jaszczyszyn Y, Guillou F, Lecomte T, Kentsis A, Bigot Y. The C-terminal Domain of piggyBac Transposase Is Not Required for DNA Transposition. J Mol Biol 2021; 433:166805. [PMID: 33450253 DOI: 10.1016/j.jmb.2020.166805] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 12/29/2020] [Indexed: 12/21/2022]
Abstract
PiggyBac(PB)-like elements (pble) are members of a eukaryotic DNA transposon family. This family is of interest to evolutionary genomics because pble transposases have been domesticated at least 9 times in vertebrates. The amino acid sequence of pble transposases can be split into three regions: an acidic N-terminal domain (~100 aa), a central domain (~400 aa) containing a DD[D/E] catalytic triad, and a cysteine-rich domain (CRD; ~90 aa). Two recent reports suggested that a functional CRD is required for pble transposase activity. Here we found that two CRD-deficient pble transposases, a PB variant and an isoform encoded by the domesticated PB-derived vertebrate transposase gene 5 (pgbd5) trigger transposition of the Ifp2 pble. When overexpressed in HeLa cells, these CRD-deficient transposases can insert Ifp2 elements with proper and improper transposon ends, associated with deleterious effects on cells. Finally, we found that mouse CRD-deficient transposase Pgbd5, as well as PB, do not insert pbles at random into chromosomes. Transposition events occurred more often in genic regions, in the neighbourhood of the transcription start sites and were often found in genes predominantly expressed in the human central nervous system.
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Affiliation(s)
- Laura Helou
- PRC, UMR INRAE 0085, CNRS 7247, Centre INRAE Val de Loire, 37380 Nouzilly, France
| | - Linda Beauclair
- PRC, UMR INRAE 0085, CNRS 7247, Centre INRAE Val de Loire, 37380 Nouzilly, France
| | - Hugues Dardente
- PRC, UMR INRAE 0085, CNRS 7247, Centre INRAE Val de Loire, 37380 Nouzilly, France
| | - Peter Arensburger
- Biological Sciences Department, California State Polytechnic University, Pomona, CA 91768, USA
| | - Nicolas Buisine
- UMR CNRS 7221, Muséum National d'Histoire Naturelle, 75005 Paris, France
| | - Yan Jaszczyszyn
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Florian Guillou
- PRC, UMR INRAE 0085, CNRS 7247, Centre INRAE Val de Loire, 37380 Nouzilly, France
| | | | - Alex Kentsis
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Weill Cornell Medical College, Cornell University, New York, NY, USA; Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yves Bigot
- PRC, UMR INRAE 0085, CNRS 7247, Centre INRAE Val de Loire, 37380 Nouzilly, France.
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Storer J, Hubley R, Rosen J, Wheeler TJ, Smit AF. The Dfam community resource of transposable element families, sequence models, and genome annotations. Mob DNA 2021; 12:2. [PMID: 33436076 PMCID: PMC7805219 DOI: 10.1186/s13100-020-00230-y] [Citation(s) in RCA: 224] [Impact Index Per Article: 74.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 12/28/2020] [Indexed: 02/02/2023] Open
Abstract
Dfam is an open access database of repetitive DNA families, sequence models, and genome annotations. The 3.0-3.3 releases of Dfam ( https://dfam.org ) represent an evolution from a proof-of-principle collection of transposable element families in model organisms into a community resource for a broad range of species, and for both curated and uncurated datasets. In addition, releases since Dfam 3.0 provide auxiliary consensus sequence models, transposable element protein alignments, and a formalized classification system to support the growing diversity of organisms represented in the resource. The latest release includes 266,740 new de novo generated transposable element families from 336 species contributed by the EBI. This expansion demonstrates the utility of many of Dfam's new features and provides insight into the long term challenges ahead for improving de novo generated transposable element datasets.
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Affiliation(s)
| | - Robert Hubley
- Institute for Systems Biology, Seattle, WA, 98109, USA.
| | - Jeb Rosen
- Institute for Systems Biology, Seattle, WA, 98109, USA
| | | | - Arian F Smit
- Institute for Systems Biology, Seattle, WA, 98109, USA.
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40
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Genome wide annotation and characterization of young, intact long terminal repeat retrotransposons (In-LTR-RTs) of seven legume species. Genetica 2020; 148:253-268. [PMID: 32949338 DOI: 10.1007/s10709-020-00103-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Accepted: 09/02/2020] [Indexed: 10/23/2022]
Abstract
Availability of genome sequence of different legume species has provided an opportunity to characterize the abundance, distribution, and divergence of canonical intact long terminal retrotransposons (In-LTR-RT) superfamilies. Among seven legume species, Arachis ipaensis (Aip) showed the highest number of full-length canonical In-LTR-RTs (3325), followed by Glycine max (Gma, 2328), Vigna angularis (Van, 1625), Arachis durensis (Adu, 1348), Lotus japonicus (Lja, 1294), Medicago truncatula (Mtr, 788), and Circer arietinum (Car, 124). Divergence time analysis demonstrated that the amplification timeframe of LTR-RTs dramatically varied in different families. The average insertion time of Copia element varied from 0.51 (Van) to 1.37 million years ago (Mya) (Adu, and Aip), whereas that of Gypsy was between 0.22 (Mtr) and 1.82 Mya (Adu). Bayesian phylogenetic tree analysis suggested that the 1397 and 1917 reverse transcriptase (RT) domains of Copia and Gypsy families of the seven legume species were clustered into 7 and 14 major groups, respectively. The highest proportion (approximately 94.79-100%) of transposable element (TE)-associated genes assigned to pathways was mapped to metabolism-related pathways in all species. The results enabled the structural understanding of full-length In-LTR-RTs and will be valuable resource for the further study of the impact of TEs on gene structure and expression in legume species.
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Lanciano S, Cristofari G. Measuring and interpreting transposable element expression. Nat Rev Genet 2020; 21:721-736. [PMID: 32576954 DOI: 10.1038/s41576-020-0251-y] [Citation(s) in RCA: 164] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/19/2020] [Indexed: 12/21/2022]
Abstract
Transposable elements (TEs) are insertional mutagens that contribute greatly to the plasticity of eukaryotic genomes, influencing the evolution and adaptation of species as well as physiology or disease in individuals. Measuring TE expression helps to understand not only when and where TE mobilization can occur but also how this process alters gene expression, chromatin accessibility or cellular signalling pathways. Although genome-wide gene expression assays such as RNA sequencing include transposon-derived transcripts, most computational analytical tools discard or misinterpret TE-derived reads. Emerging approaches are improving the identification of expressed TE loci and helping to discriminate TE transcripts that permit TE mobilization from chimeric gene-TE transcripts or pervasive transcription. Here we review the main challenges associated with the detection of TE expression, including mappability, insertional and internal sequence polymorphisms, and the diversity of the TE transcriptional landscape, as well as the different experimental and computational strategies to solve them.
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42
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Flynn JM, Hubley R, Goubert C, Rosen J, Clark AG, Feschotte C, Smit AF. RepeatModeler2 for automated genomic discovery of transposable element families. Proc Natl Acad Sci U S A 2020; 117:9451-9457. [PMID: 32300014 PMCID: PMC7196820 DOI: 10.1073/pnas.1921046117] [Citation(s) in RCA: 1170] [Impact Index Per Article: 292.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The accelerating pace of genome sequencing throughout the tree of life is driving the need for improved unsupervised annotation of genome components such as transposable elements (TEs). Because the types and sequences of TEs are highly variable across species, automated TE discovery and annotation are challenging and time-consuming tasks. A critical first step is the de novo identification and accurate compilation of sequence models representing all of the unique TE families dispersed in the genome. Here we introduce RepeatModeler2, a pipeline that greatly facilitates this process. This program brings substantial improvements over the original version of RepeatModeler, one of the most widely used tools for TE discovery. In particular, this version incorporates a module for structural discovery of complete long terminal repeat (LTR) retroelements, which are widespread in eukaryotic genomes but recalcitrant to automated identification because of their size and sequence complexity. We benchmarked RepeatModeler2 on three model species with diverse TE landscapes and high-quality, manually curated TE libraries: Drosophila melanogaster (fruit fly), Danio rerio (zebrafish), and Oryza sativa (rice). In these three species, RepeatModeler2 identified approximately 3 times more consensus sequences matching with >95% sequence identity and sequence coverage to the manually curated sequences than the original RepeatModeler. As expected, the greatest improvement is for LTR retroelements. Thus, RepeatModeler2 represents a valuable addition to the genome annotation toolkit that will enhance the identification and study of TEs in eukaryotic genome sequences. RepeatModeler2 is available as source code or a containerized package under an open license (https://github.com/Dfam-consortium/RepeatModeler, http://www.repeatmasker.org/RepeatModeler/).
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Affiliation(s)
- Jullien M Flynn
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853
| | | | - Clément Goubert
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853
| | - Jeb Rosen
- Institute for Systems Biology, Seattle, WA 98109
| | - Andrew G Clark
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853;
| | - Cédric Feschotte
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853;
| | - Arian F Smit
- Institute for Systems Biology, Seattle, WA 98109
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Ebrahimzadegan R, Houben A, Mirzaghaderi G. Repetitive DNA landscape in essential A and supernumerary B chromosomes of Festuca pratensis Huds. Sci Rep 2019; 9:19989. [PMID: 31882680 PMCID: PMC6934454 DOI: 10.1038/s41598-019-56383-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 12/11/2019] [Indexed: 11/09/2022] Open
Abstract
Here, we characterized the basic properties of repetitive sequences in essential A and supernumerary B chromosomes of Festuca pratensis Huds. This was performed by comparative analysis of low-pass Illumina sequence reads of B chromosome lacking (-B) and B chromosome containing (+B) individuals of F. pratensis. 61% of the nuclear genome is composed of repetitive sequences. 43.1% of the genome are transposons of which DNA transposons and retrotransposons made up 2.3% and 40.8%, respectively. LTR retrotransposons are the most abundant mobile elements and contribute to 40.7% of the genome and divided into Ty3-gypsy and Ty1-copia super families with 32.97% and 7.78% of the genome, respectively. Eighteen different satellite repeats were identified making up 3.9% of the genome. Five satellite repeats were used as cytological markers for chromosome identification and genome analysis in the genus Festuca. Four satellite repeats were identified on B chromosomes among which Fp-Sat48 and Fp-Sat253 were specific to the B chromosome of F. pratensis.
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Affiliation(s)
- Rahman Ebrahimzadegan
- Department of Agronomy and Plant Breeding, Faculty of Agriculture, University of Kurdistan, 6617715175, Sanandaj, Iran
| | - Andreas Houben
- Leibniz-Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK) Gatersleben, Corrensstrasse 3, 06466, Stadt Seeland, Germany
| | - Ghader Mirzaghaderi
- Department of Agronomy and Plant Breeding, Faculty of Agriculture, University of Kurdistan, 6617715175, Sanandaj, Iran.
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Orozco-Arias S, Isaza G, Guyot R, Tabares-Soto R. A systematic review of the application of machine learning in the detection and classification of transposable elements. PeerJ 2019; 7:e8311. [PMID: 31976169 PMCID: PMC6967008 DOI: 10.7717/peerj.8311] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Accepted: 11/28/2019] [Indexed: 12/16/2022] Open
Abstract
Background Transposable elements (TEs) constitute the most common repeated sequences in eukaryotic genomes. Recent studies demonstrated their deep impact on species diversity, adaptation to the environment and diseases. Although there are many conventional bioinformatics algorithms for detecting and classifying TEs, none have achieved reliable results on different types of TEs. Machine learning (ML) techniques can automatically extract hidden patterns and novel information from labeled or non-labeled data and have been applied to solving several scientific problems. Methodology We followed the Systematic Literature Review (SLR) process, applying the six stages of the review protocol from it, but added a previous stage, which aims to detect the need for a review. Then search equations were formulated and executed in several literature databases. Relevant publications were scanned and used to extract evidence to answer research questions. Results Several ML approaches have already been tested on other bioinformatics problems with promising results, yet there are few algorithms and architectures available in literature focused specifically on TEs, despite representing the majority of the nuclear DNA of many organisms. Only 35 articles were found and categorized as relevant in TE or related fields. Conclusions ML is a powerful tool that can be used to address many problems. Although ML techniques have been used widely in other biological tasks, their utilization in TE analyses is still limited. Following the SLR, it was possible to notice that the use of ML for TE analyses (detection and classification) is an open problem, and this new field of research is growing in interest.
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Affiliation(s)
- Simon Orozco-Arias
- Department of Computer Science, Universidad Autónoma de Manizales, Manizales, Caldas, Colombia.,Department of Systems and Informatics, Universidad de Caldas, Manizales, Caldas, Colombia
| | - Gustavo Isaza
- Department of Systems and Informatics, Universidad de Caldas, Manizales, Caldas, Colombia
| | - Romain Guyot
- Institut de Recherche pour le Développement, CIRAD, University of Montpellier, Montpellier, France.,Department of Electronics and Automation, Universidad Autónoma de Manizales, Manizales, Caldas, Colombia
| | - Reinel Tabares-Soto
- Department of Electronics and Automation, Universidad Autónoma de Manizales, Manizales, Caldas, Colombia
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Kojima KK. Structural and sequence diversity of eukaryotic transposable elements. Genes Genet Syst 2019; 94:233-252. [DOI: 10.1266/ggs.18-00024] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Affiliation(s)
- Kenji K. Kojima
- Genetic Information Research Institute
- Department of Life Sciences, National Cheng Kung University
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46
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Macko-Podgórni A, Stelmach K, Kwolek K, Grzebelus D. Stowaway miniature inverted repeat transposable elements are important agents driving recent genomic diversity in wild and cultivated carrot. Mob DNA 2019; 10:47. [PMID: 31798695 PMCID: PMC6881990 DOI: 10.1186/s13100-019-0190-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Accepted: 11/21/2019] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND Miniature inverted repeat transposable elements (MITEs) are small non-autonomous DNA transposons that are ubiquitous in plant genomes, and are mobilised by their autonomous relatives. Stowaway MITEs are derived from and mobilised by elements from the mariner superfamily. Those elements constitute a significant portion of the carrot genome; however the variation caused by Daucus carota Stowaway MITEs (DcStos), their association with genes and their putative impact on genome evolution has not been comprehensively analysed. RESULTS Fourteen families of Stowaway elements DcStos occupy about 0.5% of the carrot genome. We systematically analysed 31 genomes of wild and cultivated Daucus carota, yielding 18.5 thousand copies of these elements, showing remarkable insertion site polymorphism. DcSto element demography differed based on the origin of the host populations, and corresponded with the four major groups of D. carota, wild European, wild Asian, eastern cultivated and western cultivated. The DcStos elements were associated with genes, and most frequently occurred in 5' and 3' untranslated regions (UTRs). Individual families differed in their propensity to reside in particular segments of genes. Most importantly, DcSto copies in the 2 kb regions up- and downstream of genes were more frequently associated with open reading frames encoding transcription factors, suggesting their possible functional impact. More than 1.5% of all DcSto insertion sites in different host genomes contained different copies in exactly the same position, indicating the existence of insertional hotspots. The DcSto7b family was much more polymorphic than the other families in cultivated carrot. A line of evidence pointed at its activity in the course of carrot domestication, and identified Dcmar1 as an active carrot mariner element and a possible source of the transposition machinery for DcSto7b. CONCLUSION Stowaway MITEs have made a substantial contribution to the structural and functional variability of the carrot genome.
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Affiliation(s)
- Alicja Macko-Podgórni
- Institute of Plant Biology and Biotechnology, Faculty of Biotechnology and Horticulture, University of Agriculture in Krakow, 31425 Krakow, Poland
| | - Katarzyna Stelmach
- Institute of Plant Biology and Biotechnology, Faculty of Biotechnology and Horticulture, University of Agriculture in Krakow, 31425 Krakow, Poland
| | - Kornelia Kwolek
- Institute of Plant Biology and Biotechnology, Faculty of Biotechnology and Horticulture, University of Agriculture in Krakow, 31425 Krakow, Poland
| | - Dariusz Grzebelus
- Institute of Plant Biology and Biotechnology, Faculty of Biotechnology and Horticulture, University of Agriculture in Krakow, 31425 Krakow, Poland
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Cordeiro J, Carvalho TL, Valente VLDS, Robe LJ. Evolutionary history and classification of Micropia retroelements in Drosophilidae species. PLoS One 2019; 14:e0220539. [PMID: 31622354 PMCID: PMC6797199 DOI: 10.1371/journal.pone.0220539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 10/04/2019] [Indexed: 11/19/2022] Open
Abstract
Transposable elements (TEs) have the main role in shaping the evolution of genomes and host species, contributing to the creation of new genes and promoting rearrangements frequently associated with new regulatory networks. Support for these hypotheses frequently results from studies with model species, and Drosophila provides a great model organism to the study of TEs. Micropia belongs to the Ty3/Gypsy group of long terminal repeats (LTR) retroelements and comprises one of the least studied Drosophila transposable elements. In this study, we assessed the evolutionary history of Micropia within Drosophilidae, while trying to assist in the classification of this TE. At first, we performed searches of Micropia presence in the genome of natural populations from several species. Then, based on searches within online genomic databases, we retrieved Micropia-like sequences from the genomes of distinct Drosophilidae species. We expanded the knowledge of Micropia distribution within Drosophila species. The Micropia retroelements we detected consist of an array of divergent sequences, which we subdivided into 20 subfamilies. Even so, a patchy distribution of Micropia sequences within the Drosophilidae phylogeny could be identified, with incongruences between the species phylogeny and the Micropia phylogeny. Comparing the pairwise synonymous distance (dS) values between Micropia and three host nuclear sequences, we found several cases of unexpectedly high levels of similarity between Micropia sequences in divergent species. All these findings provide a hypothesis to the evolution of Micropia within Drosophilidae, which include several events of vertical and horizontal transposon transmission, associated with ancestral polymorphisms and recurrent Micropia sequences diversification.
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Affiliation(s)
- Juliana Cordeiro
- Departamento de Ecologia, Zoologia e Genética, Instituto de Biologia, Universidade Federal de Pelotas, Pelotas, RS, Brazil
| | - Tuane Letícia Carvalho
- Programa de Pós-Graduação em Biodiversidade Animal, Universidade Federal de Santa Maria, Santa Maria, RS, Brazil
| | - Vera Lúcia da Silva Valente
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre; Rio Grande do Sul; Brazil
| | - Lizandra Jaqueline Robe
- Programa de Pós-Graduação em Biodiversidade Animal, Universidade Federal de Santa Maria, Santa Maria, RS, Brazil
- Departamento de Ecologia e Evolução, Centro de Ciências Naturais e Exatas, Universidade Federal de Santa Maria, Santa Maria, RS, Brazil
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48
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Bernardo LP, Mombach DM, Loreto ELS. Characterization of Herves-like transposable elements (hATs) in Drosophila species and their evolutionary scenario. INSECT MOLECULAR BIOLOGY 2019; 28:616-627. [PMID: 30793407 DOI: 10.1111/imb.12577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
A monophyletic group of Drosophila hAT transposable elements, referred to as Herves-like, was characterized and found to be present in 46% of 57 screened Drosophila species. A remarkable characteristic of these elements is the presence of a long array of minisatellite repeats (MnRs) in both subterminal extremities of the elements. The copy number of these minisatellites was highly variable between and within populations. Twenty-three strains of Drosophila willistoni, covering its geographic distribution, were screened for polymorphism in the copy number of 5' MnRs, showing a variation from 7 to 20 repeat copies. These MnRs are well conserved among Drosophila species and probably function as transposase binding sequences, as provided by short subterminal repeats in other hAT elements. Miniature inverted repeat transposable elements were found in 27% of species carrying Herves-like elements. Phylogenetic analysis showed incongruences between transposable elements and species phylogenies, suggesting that at least four horizontal transfer events have occurred.
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Affiliation(s)
- L P Bernardo
- PPG Biodiverdade Animal, Universidade Federal de Santa Maria (UFSM), Santa Maria, Brazil
| | - D M Mombach
- Department of Biochemistry and Molecular Biology, CCNE, Univeridade Federal de Santa Maria, Santa Maria, Brazil
| | - E L S Loreto
- Department of Biochemistry and Molecular Biology, CCNE, Univeridade Federal de Santa Maria, Santa Maria, Brazil
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Orozco-Arias S, Isaza G, Guyot R. Retrotransposons in Plant Genomes: Structure, Identification, and Classification through Bioinformatics and Machine Learning. Int J Mol Sci 2019; 20:E3837. [PMID: 31390781 PMCID: PMC6696364 DOI: 10.3390/ijms20153837] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 07/31/2019] [Accepted: 08/02/2019] [Indexed: 01/26/2023] Open
Abstract
Transposable elements (TEs) are genomic units able to move within the genome of virtually all organisms. Due to their natural repetitive numbers and their high structural diversity, the identification and classification of TEs remain a challenge in sequenced genomes. Although TEs were initially regarded as "junk DNA", it has been demonstrated that they play key roles in chromosome structures, gene expression, and regulation, as well as adaptation and evolution. A highly reliable annotation of these elements is, therefore, crucial to better understand genome functions and their evolution. To date, much bioinformatics software has been developed to address TE detection and classification processes, but many problematic aspects remain, such as the reliability, precision, and speed of the analyses. Machine learning and deep learning are algorithms that can make automatic predictions and decisions in a wide variety of scientific applications. They have been tested in bioinformatics and, more specifically for TEs, classification with encouraging results. In this review, we will discuss important aspects of TEs, such as their structure, importance in the evolution and architecture of the host, and their current classifications and nomenclatures. We will also address current methods and their limitations in identifying and classifying TEs.
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Affiliation(s)
- Simon Orozco-Arias
- Department of Computer Science, Universidad Autónoma de Manizales, Manizales 170001, Colombia
- Department of Systems and Informatics, Universidad de Caldas, Manizales 170001, Colombia
| | - Gustavo Isaza
- Department of Systems and Informatics, Universidad de Caldas, Manizales 170001, Colombia
| | - Romain Guyot
- Department of Electronics and Automatization, Universidad Autónoma de Manizales, Manizales 170001, Colombia.
- Institut de Recherche pour le Développement, CIRAD, University Montpellier, 34000 Montpellier, France.
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50
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Transposable Elements Adaptive Role in Genome Plasticity, Pathogenicity and Evolution in Fungal Phytopathogens. Int J Mol Sci 2019; 20:ijms20143597. [PMID: 31340492 PMCID: PMC6679389 DOI: 10.3390/ijms20143597] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 06/18/2019] [Accepted: 06/25/2019] [Indexed: 01/08/2023] Open
Abstract
Transposable elements (TEs) are agents of genetic variability in phytopathogens as they are a source of adaptive evolution through genome diversification. Although many studies have uncovered information on TEs, the exact mechanism behind TE-induced changes within the genome remains poorly understood. Furthermore, convergent trends towards bigger genomes, emergence of novel genes and gain or loss of genes implicate a TE-regulated genome plasticity of fungal phytopathogens. TEs are able to alter gene expression by revamping the cis-regulatory elements or recruiting epigenetic control. Recent findings show that TEs recruit epigenetic control on the expression of effector genes as part of the coordinated infection strategy. In addition to genome plasticity and diversity, fungal pathogenicity is an area of economic concern. A survey of TE distribution suggests that their proximity to pathogenicity genes TEs may act as sites for emergence of novel pathogenicity factors via nucleotide changes and expansion or reduction of the gene family. Through a systematic survey of literature, we were able to conclude that the role of TEs in fungi is wide: ranging from genome plasticity, pathogenicity to adaptive behavior in evolution. This review also identifies the gaps in knowledge that requires further elucidation for a better understanding of TEs' contribution to genome architecture and versatility.
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