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Tian J, Tong D, Li Z, Wang E, Yu Y, Lv H, Hu Z, Sun F, Wang G, He M, Xia T. Mage transposon: a novel gene delivery system for mammalian cells. Nucleic Acids Res 2024; 52:2724-2739. [PMID: 38300794 PMCID: PMC10954464 DOI: 10.1093/nar/gkae048] [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: 09/14/2023] [Revised: 01/10/2024] [Accepted: 01/22/2024] [Indexed: 02/03/2024] Open
Abstract
Transposons, as non-viral integration vectors, provide a secure and efficient method for stable gene delivery. In this study, we have discovered Mage (MG), a novel member of the piggyBac(PB) family, which exhibits strong transposability in a variety of mammalian cells and primary T cells. The wild-type MG showed a weaker insertion preference for near genes, transcription start sites (TSS), CpG islands, and DNaseI hypersensitive sites in comparison to PB, approaching the random insertion pattern. Utilizing in silico virtual screening and feasible combinatorial mutagenesis in vitro, we effectively produced the hyperactive MG transposase (hyMagease). This variant boasts a transposition rate 60% greater than its native counterpart without significantly altering its insertion pattern. Furthermore, we applied the hyMagease to efficiently deliver chimeric antigen receptor (CAR) into T cells, leading to stable high-level expression and inducing significant anti-tumor effects both in vitro and in xenograft mice models. These findings provide a compelling tool for gene transfer research, emphasizing its potential and prospects in the domains of genetic engineering and gene therapy.
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Affiliation(s)
- Jinghan Tian
- Institute of Pathology, Department of Pathology, School of Basic Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
| | - Doudou Tong
- Institute of Pathology, Department of Pathology, School of Basic Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
| | | | - Erqiang Wang
- Institute of Pathology, Department of Pathology, School of Basic Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
| | - Yifei Yu
- Elongevity Inc, Wuhan, Hubei 430000, China
| | - Hangya Lv
- Elongevity Inc, Wuhan, Hubei 430000, China
| | - Zhendan Hu
- Elongevity Inc, Wuhan, Hubei 430000, China
| | - Fang Sun
- Elongevity Inc, Wuhan, Hubei 430000, China
| | - Guoping Wang
- Institute of Pathology, Department of Pathology, School of Basic Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
| | - Min He
- Elongevity Inc, Wuhan, Hubei 430000, China
| | - Tian Xia
- Institute of Pathology, Department of Pathology, School of Basic Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
- School of Artificial Intelligence and Automation, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
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Li X, Guan Z, Wang F, Wang Y, Asare E, Shi S, Lin Z, Ji T, Gao B, Song C. Evolution of piggyBac Transposons in Apoidea. INSECTS 2023; 14:402. [PMID: 37103217 PMCID: PMC10140906 DOI: 10.3390/insects14040402] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Revised: 04/15/2023] [Accepted: 04/19/2023] [Indexed: 06/19/2023]
Abstract
In this study, we investigated the presence of piggyBac (PB) transposons in 44 bee genomes from the Apoidea order, which is a superfamily within the Hymenoptera, which includes a large number of bee species crucial for pollination. We annotated the PB transposons in these 44 bee genomes and examined their evolution profiles, including structural characteristics, distribution, diversity, activity, and abundance. The mined PB transposons were divided into three clades, with uneven distribution in each genus of PB transposons in Apoidea. The complete PB transposons we discovered are around 2.23-3.52 kb in length and encode transposases of approximately 580 aa, with terminal inverted repeats (TIRs) of about 14 bp and 4 bp (TTAA) target-site duplications. Long TIRs (200 bp, 201 bp, and 493 bp) were also detected in some species of bees. The DDD domains of the three transposon types were more conserved, while the other protein domains were less conserved. Generally, most PB transposons showed low abundance in the genomes of Apoidea. Divergent evolution dynamics of PB were observed in the genomes of Apoidea. PB transposons in some identified species were relatively young, whiles others were older and with some either active or inactive. In addition, multiple invasions of PB were also detected in some genomes of Apoidea. Our findings highlight the contribution of PB transposons to genomic variation in these species and suggest their potential as candidates for future gene transfer tools.
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3
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Wachtl G, Schád É, Huszár K, Palazzo A, Ivics Z, Tantos Á, Orbán TI. Functional Characterization of the N-Terminal Disordered Region of the piggyBac Transposase. Int J Mol Sci 2022; 23:10317. [PMID: 36142241 PMCID: PMC9499001 DOI: 10.3390/ijms231810317] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 08/22/2022] [Accepted: 09/03/2022] [Indexed: 01/15/2023] Open
Abstract
The piggyBac DNA transposon is an active element initially isolated from the cabbage looper moth, but members of this superfamily are also present in most eukaryotic evolutionary lineages. The functionally important regions of the transposase are well described. There is an RNase H-like fold containing the DDD motif responsible for the catalytic DNA cleavage and joining reactions and a C-terminal cysteine-rich domain important for interaction with the transposon DNA. However, the protein also contains a ~100 amino acid long N-terminal disordered region (NTDR) whose function is currently unknown. Here we show that deletion of the NTDR significantly impairs piggyBac transposition, although the extent of decrease is strongly cell-type specific. Moreover, replacing the NTDR with scrambled but similarly disordered sequences did not rescue transposase activity, indicating the importance of sequence conservation. Cell-based transposon excision and integration assays reveal that the excision step is more severely affected by NTDR deletion. Finally, bioinformatic analyses indicated that the NTDR is specific for the piggyBac superfamily and is also present in domesticated, transposase-derived proteins incapable of catalyzing transposition. Our results indicate an essential role of the NTDR in the "fine-tuning" of transposition and its significance in the functions of piggyBac-originated co-opted genes.
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Affiliation(s)
- Gerda Wachtl
- Institute of Enzymology, Research Centre for Natural Sciences, Eötvös Loránd Research Network, 1117 Budapest, Hungary
- Doctoral School of Biology, Institute of Biology, ELTE Eötvös Loránd University, 1117 Budapest, Hungary
| | - Éva Schád
- Institute of Enzymology, Research Centre for Natural Sciences, Eötvös Loránd Research Network, 1117 Budapest, Hungary
| | - Krisztina Huszár
- Institute of Enzymology, Research Centre for Natural Sciences, Eötvös Loránd Research Network, 1117 Budapest, Hungary
| | - Antonio Palazzo
- Department of Biology, University of Bari “Aldo Moro”, 70125 Bari, Italy
| | - Zoltán Ivics
- Transposition and Genome Engineering, Division of Medical Biotechnology, Paul Ehrlich Institute, 63225 Langen, Germany
| | - Ágnes Tantos
- Institute of Enzymology, Research Centre for Natural Sciences, Eötvös Loránd Research Network, 1117 Budapest, Hungary
| | - Tamás I. Orbán
- Institute of Enzymology, Research Centre for Natural Sciences, Eötvös Loránd Research Network, 1117 Budapest, Hungary
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Kolacsek O, Wachtl G, Fóthi Á, Schamberger A, Sándor S, Pergel E, Varga N, Raskó T, Izsvák Z, Apáti Á, Orbán TI. Functional indications for transposase domestications - Characterization of the human piggyBac transposase derived (PGBD) activities. Gene 2022; 834:146609. [PMID: 35609796 DOI: 10.1016/j.gene.2022.146609] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 05/17/2022] [Accepted: 05/18/2022] [Indexed: 12/13/2022]
Abstract
Transposable elements are widespread in all living organisms. In addition to self-reproduction, they are a major source of genetic variation that drives genome evolution but our knowledge of the functions of human genes derived from transposases is limited. There are examples of transposon-derived, domesticated human genes that lost (SETMAR) or retained (THAP9) their transposase activity, however, several remnants in the human genome have not been thoroughly investigated yet. These include the five human piggyBac-derived sequences (PGBD1-5) which share ancestry with the Trichoplusia ni originated piggyBac (PB) transposase. Since PB is widely used in gene delivery applications, the potential activities of endogenous PGBDs are important to address. However, previous data is controversial, especially with the claimed transposition activity of PGBD5, it awaits further investigations. Here, we aimed to systematically analyze all five human PGBD proteins from several aspects, including phylogenetic conservation, potential transposase activity, expression pattern and their regulation in different stress conditions. Among PGBDs, PGBD5 is under the highest purifying selection, and exhibits the most cell type specific expression pattern. In a two-component vector system, none of the human PGBDs could mobilize either the insect PB transposon or the endogenous human PB-like MER75 and MER85 elements with intact terminal sequences. When cells were exposed to various stress conditions, including hypoxia, oxidative or UV stress, the expression profiles of all PGBDs showed different, often cell type specific responses; however, the pattern of PGBD5 in most cases had the opposite tendency than that of the other piggyBac-derived elements. Taken together, our results indicate that human PGBD elements did not retain their mobilizing activity, but their cell type specific, and cellular stress related expression profiles point toward distinct domesticated functions that require further characterization.
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Affiliation(s)
- Orsolya Kolacsek
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
| | - Gerda Wachtl
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary; Doctoral School of Biology, Institute of Biology, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Ábel Fóthi
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
| | - Anita Schamberger
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
| | - Sára Sándor
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
| | - Enikő Pergel
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
| | - Nóra Varga
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
| | - Tamás Raskó
- Max Delbrück Center for Molecular Medicine in the Helmholtz Society, Berlin, Germany
| | - Zsuzsanna Izsvák
- Max Delbrück Center for Molecular Medicine in the Helmholtz Society, Berlin, Germany
| | - Ágota Apáti
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
| | - Tamás I Orbán
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary.
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Zong W, Gao B, Diaby M, Shen D, Wang S, Wang Y, Sang Y, Chen C, Wang X, Song C. Traveler, a New DD35E Family of Tc1/Mariner Transposons, Invaded Vertebrates Very Recently. Genome Biol Evol 2021; 12:66-76. [PMID: 32068835 PMCID: PMC7093834 DOI: 10.1093/gbe/evaa034] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/13/2020] [Indexed: 02/06/2023] Open
Abstract
The discovery of new members of the Tc1/mariner superfamily of transposons is expected based on the increasing availability of genome sequencing data. Here, we identified a new DD35E family termed Traveler (TR). Phylogenetic analyses of its DDE domain and full-length transposase showed that, although TR formed a monophyletic clade, it exhibited the highest sequence identity and closest phylogenetic relationship with DD34E/Tc1. This family displayed a very restricted taxonomic distribution in the animal kingdom and was only detected in ray-finned fish, anura, and squamata, including 91 vertebrate species. The structural organization of TRs was highly conserved across different classes of animals. Most intact TR transposons had a length of ∼1.5 kb (range 1,072-2,191 bp) and harbored a single open reading frame encoding a transposase of ∼340 aa (range 304-350 aa) flanked by two short-terminal inverted repeats (13-68 bp). Several conserved motifs, including two helix-turn-helix motifs, a GRPR motif, a nuclear localization sequence, and a DDE domain, were also identified in TR transposases. This study also demonstrated the presence of horizontal transfer events of TRs in vertebrates, whereas the average sequence identities and the evolutionary dynamics of TR elements across species and clusters strongly indicated that the TR family invaded the vertebrate lineage very recently and that some of these elements may be currently active, combining the intact TR copies in multiple lineages of vertebrates. These data will contribute to the understanding of the evolutionary history of Tc1/mariner transposons and that of their hosts.
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Affiliation(s)
- Wencheng Zong
- College of Animal Science & Technology, Yangzhou University, Jiangsu, China
| | - Bo Gao
- College of Animal Science & Technology, Yangzhou University, Jiangsu, China
| | - Mohamed Diaby
- College of Animal Science & Technology, Yangzhou University, Jiangsu, China
| | - Dan Shen
- College of Animal Science & Technology, Yangzhou University, Jiangsu, China
| | - Saisai Wang
- College of Animal Science & Technology, Yangzhou University, Jiangsu, China
| | - Yali Wang
- College of Animal Science & Technology, Yangzhou University, Jiangsu, China
| | - Yatong Sang
- College of Animal Science & Technology, Yangzhou University, Jiangsu, China
| | - Cai Chen
- College of Animal Science & Technology, Yangzhou University, Jiangsu, China
| | - Xiaoyan Wang
- College of Animal Science & Technology, Yangzhou University, Jiangsu, China
| | - Chengyi Song
- College of Animal Science & Technology, Yangzhou University, Jiangsu, China
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Luchetti A, Lomiento M, Mantovani B. Riding the Wave: The SINE-Specific V Highly-Conserved Domain Spread into Mammalian Genomes Exploiting the Replication Burst of the MER6 DNA Transposon. Int J Mol Sci 2019; 20:ijms20225607. [PMID: 31717545 PMCID: PMC6887750 DOI: 10.3390/ijms20225607] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 11/05/2019] [Accepted: 11/06/2019] [Indexed: 02/06/2023] Open
Abstract
Transposable elements are widely distributed within genomes where they may significantly impact their evolution and cell functions. Short interspersed elements (SINEs) are non-autonomous, fast-evolving elements, but some of them carry a highly conserved domain (HCD), whose sequence remained substantially unchanged throughout the metazoan evolution. SINEs carrying the HCD called V are absent in amniote genomes, but V-like sequences were found within the miniature inverted-repeat transposable element (MITE) MER6 in Homo sapiens. In the present work, the genomic distribution and evolution of MER6 are investigated, in order to reconstruct the origin of human V domain and to envisage its possible functional role. The analysis of 85 tetrapod genomes revealed that MER6 and its variant MER6A are found in primates, while only the MER6A variant was found in bats and eulipotyphlans. These MITEs appeared no longer active, in line with literature data on mammalian DNA transposons. Moreover, they appeared to have originated from a Mariner element found in turtles and from a V-SINE from bony fishes. MER6 insertions were found within genes and conserved in mRNAs: in line with previous hypothesis on functional role of HCDs, the MER6 V domain may be important for cell function also in mammals.
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Affiliation(s)
- Andrea Luchetti
- Department of Biological, Geological and Environmental Sciences, University of Bologna, 40126 Bologna, Italy;
- Correspondence: ; Tel.: +39-051-209-4165
| | - Mariana Lomiento
- Sant’Orsola Malpighi Hospital, University of Bologna, 40138 Bologna Italy;
| | - Barbara Mantovani
- Department of Biological, Geological and Environmental Sciences, University of Bologna, 40126 Bologna, Italy;
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7
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Platt RN, Faircloth BC, Sullivan KAM, Kieran TJ, Glenn TC, Vandewege MW, Lee TE, Baker RJ, Stevens RD, Ray DA. Conflicting Evolutionary Histories of the Mitochondrial and Nuclear Genomes in New World Myotis Bats. Syst Biol 2018; 67:236-249. [PMID: 28945862 PMCID: PMC5837689 DOI: 10.1093/sysbio/syx070] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Revised: 07/31/2017] [Accepted: 08/15/2017] [Indexed: 01/05/2023] Open
Abstract
The rapid diversification of Myotis bats into more than 100 species is one of the most extensive mammalian radiations available for study. Efforts to understand relationships within Myotis have primarily utilized mitochondrial markers and trees inferred from nuclear markers lacked resolution. Our current understanding of relationships within Myotis is therefore biased towards a set of phylogenetic markers that may not reflect the history of the nuclear genome. To resolve this, we sequenced the full mitochondrial genomes of 37 representative Myotis, primarily from the New World, in conjunction with targeted sequencing of 3648 ultraconserved elements (UCEs). We inferred the phylogeny and explored the effects of concatenation and summary phylogenetic methods, as well as combinations of markers based on informativeness or levels of missing data, on our results. Of the 294 phylogenies generated from the nuclear UCE data, all are significantly different from phylogenies inferred using mitochondrial genomes. Even within the nuclear data, quartet frequencies indicate that around half of all UCE loci conflict with the estimated species tree. Several factors can drive such conflict, including incomplete lineage sorting, introgressive hybridization, or even phylogenetic error. Despite the degree of discordance between nuclear UCE loci and the mitochondrial genome and among UCE loci themselves, the most common nuclear topology is recovered in one quarter of all analyses with strong nodal support. Based on these results, we re-examine the evolutionary history of Myotis to better understand the phenomena driving their unique nuclear, mitochondrial, and biogeographic histories.
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Affiliation(s)
- Roy N Platt
- Department of Biological Sciences, Texas Tech University, 2901 Main St, Lubbock, TX, USA
| | - Brant C Faircloth
- Department of Biological Sciences and Museum of Natural Science, Louisiana State University, 202 Life Science Building, Baton Rouge, LA, USA
| | - Kevin A M Sullivan
- Department of Biological Sciences, Texas Tech University, 2901 Main St, Lubbock, TX, USA
| | - Troy J Kieran
- Department of Environmental Health Science, University of Georgia, 206 Environmental Health Sciences Building, Athens, GA, USA
| | - Travis C Glenn
- Department of Environmental Health Science, University of Georgia, 206 Environmental Health Sciences Building, Athens, GA, USA
| | - Michael W Vandewege
- Department of Biological Sciences, Texas Tech University, 2901 Main St, Lubbock, TX, USA
| | - Thomas E Lee
- Department of Biology, Abilene Christian University, 1600 Campus Ct. Abilene, TX, USA
| | - Robert J Baker
- Department of Biological Sciences, Texas Tech University, 2901 Main St, Lubbock, TX, USA
| | - Richard D Stevens
- Natural Resource Management, Texas Tech University, 2901 Main St, Lubbock, TX, USA
| | - David A Ray
- Department of Biological Sciences, Texas Tech University, 2901 Main St, Lubbock, TX, USA
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Platt RN, Vandewege MW, Ray DA. Mammalian transposable elements and their impacts on genome evolution. Chromosome Res 2018; 26:25-43. [PMID: 29392473 PMCID: PMC5857283 DOI: 10.1007/s10577-017-9570-z] [Citation(s) in RCA: 141] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Revised: 12/12/2017] [Accepted: 12/28/2017] [Indexed: 12/22/2022]
Abstract
Transposable elements (TEs) are genetic elements with the ability to mobilize and replicate themselves in a genome. Mammalian genomes are dominated by TEs, which can reach copy numbers in the hundreds of thousands. As a result, TEs have had significant impacts on mammalian evolution. Here we summarize the current understanding of TE content in mammal genomes and find that, with a few exceptions, most fall within a predictable range of observations. First, one third to one half of the genome is derived from TEs. Second, most mammalian genomes are dominated by LINE and SINE retrotransposons, more limited LTR retrotransposons, and minimal DNA transposon accumulation. Third, most mammal genome contains at least one family of actively accumulating retrotransposon. Finally, horizontal transfer of TEs among lineages is rare. TE exaptation events are being recognized with increasing frequency. Despite these beneficial aspects of TE content and activity, the majority of TE insertions are neutral or deleterious. To limit the deleterious effects of TE proliferation, the genome has evolved several defense mechanisms that act at the epigenetic, transcriptional, and post-transcriptional levels. The interaction between TEs and these defense mechanisms has led to an evolutionary arms race where TEs are suppressed, evolve to escape suppression, then are suppressed again as the defense mechanisms undergo compensatory change. The result is complex and constantly evolving interactions between TEs and host genomes.
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Affiliation(s)
- Roy N Platt
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, USA.
| | | | - David A Ray
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, USA
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9
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Wallau GL, Vieira C, Loreto ÉLS. Genetic exchange in eukaryotes through horizontal transfer: connected by the mobilome. Mob DNA 2018; 9:6. [PMID: 29422954 PMCID: PMC5791352 DOI: 10.1186/s13100-018-0112-9] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Accepted: 01/24/2018] [Indexed: 12/11/2022] Open
Abstract
Background All living species contain genetic information that was once shared by their common ancestor. DNA is being inherited through generations by vertical transmission (VT) from parents to offspring and from ancestor to descendant species. This process was considered the sole pathway by which biological entities exchange inheritable information. However, Horizontal Transfer (HT), the exchange of genetic information by other means than parents to offspring, was discovered in prokaryotes along with strong evidence showing that it is a very important process by which prokaryotes acquire new genes. Main body For some time now, it has been a scientific consensus that HT events were rare and non-relevant for evolution of eukaryotic species, but there is growing evidence supporting that HT is an important and frequent phenomenon in eukaryotes as well. Conclusion Here, we will discuss the latest findings regarding HT among eukaryotes, mainly HT of transposons (HTT), establishing HTT once and for all as an important phenomenon that should be taken into consideration to fully understand eukaryotes genome evolution. In addition, we will discuss the latest development methods to detect such events in a broader scale and highlight the new approaches which should be pursued by researchers to fill the knowledge gaps regarding HTT among eukaryotes.
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Affiliation(s)
- Gabriel Luz Wallau
- 1Entomology Department, Aggeu Magalhães Institute, Oswaldo Cruz Foundation, Recife, PE Brazil
| | - Cristina Vieira
- 2Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive, UMR5558, F-69622 Villeurbanne, France
| | - Élgion Lúcio Silva Loreto
- 3Department of Biochemistry and Molecular Biology, Federal University of Santa Maria, Santa Maria, RS Brazil
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Bouallègue M, Rouault JD, Hua-Van A, Makni M, Capy P. Molecular Evolution of piggyBac Superfamily: From Selfishness to Domestication. Genome Biol Evol 2017; 9:323-339. [PMID: 28082605 PMCID: PMC5381638 DOI: 10.1093/gbe/evw292] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/13/2016] [Indexed: 12/19/2022] Open
Abstract
The piggyBac transposable element was originally isolated from the cabbage looper moth, Trichoplusia ni, in the 1980s. Despite its early discovery and specificity compared to the other Class II elements, the diversity and evolution of this superfamily have been only partially analyzed. Two main types of elements can be distinguished: the piggyBac-like elements (PBLE) with terminal inverted repeats, untranslated region, and an open reading frame encoding a transposase, and the piggyBac-derived sequences (PGBD), containing a sequence derived from a piggyBac transposase, and which correspond to domesticated elements. To define the distribution, their structural diversity and phylogenetic relationships, analyses were conducted using known PBLE and PGBD sequences to scan databases. From this data mining, numerous new sequences were characterized (50 for PBLE and 396 for PGBD). Structural analyses suggest that four groups of PBLE can be defined according to the presence/absence of sub-terminal repeats. The transposase is characterized by highly variable catalytic domain and C-terminal region. There is no relationship between the structural groups and the phylogeny of these PBLE elements. The PGBD are clearly structured into nine main groups. A new group of domesticated elements is suspected in Neopterygii and the remaining eight previously described elements have been investigated in more detail. In all cases, these sequences are no longer transposable elements, the catalytic domain of the ancestral transposase is not always conserved, but they are under strong purifying selection. The phylogeny of both PBLE and PGBD suggests multiple and independent domestication events of PGBD from different PBLE ancestors.
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Affiliation(s)
- Maryem Bouallègue
- Laboratoire Evolution, Génomes, Comportement, Ecologie CNRS, Univ. Paris-Sud, IRD, Université Paris-Saclay, Gif-sur-Yvette, France
- Université de Tunis El Manar, Faculté des Sciences de Tunis, UR11ES10 Génomique des Insectes Ravageurs de Cultures, Tunis, Tunisie
| | - Jacques-Deric Rouault
- Laboratoire Evolution, Génomes, Comportement, Ecologie CNRS, Univ. Paris-Sud, IRD, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Aurélie Hua-Van
- Laboratoire Evolution, Génomes, Comportement, Ecologie CNRS, Univ. Paris-Sud, IRD, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Mohamed Makni
- Université de Tunis El Manar, Faculté des Sciences de Tunis, UR11ES10 Génomique des Insectes Ravageurs de Cultures, Tunis, Tunisie
| | - Pierre Capy
- Laboratoire Evolution, Génomes, Comportement, Ecologie CNRS, Univ. Paris-Sud, IRD, Université Paris-Saclay, Gif-sur-Yvette, France
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11
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Venner S, Miele V, Terzian C, Biémont C, Daubin V, Feschotte C, Pontier D. Ecological networks to unravel the routes to horizontal transposon transfers. PLoS Biol 2017; 15:e2001536. [PMID: 28199335 PMCID: PMC5331948 DOI: 10.1371/journal.pbio.2001536] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Transposable elements (TEs) represent the single largest component of numerous eukaryotic genomes, and their activity and dispersal constitute an important force fostering evolutionary innovation. The horizontal transfer of TEs (HTT) between eukaryotic species is a common and widespread phenomenon that has had a profound impact on TE dynamics and, consequently, on the evolutionary trajectory of many species' lineages. However, the mechanisms promoting HTT remain largely unknown. In this article, we argue that network theory combined with functional ecology provides a robust conceptual framework and tools to delineate how complex interactions between diverse organisms may act in synergy to promote HTTs.
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Affiliation(s)
- Samuel Venner
- Laboratoire de Biométrie et Biologie Evolutive UMR5558-CNRS, Université de Lyon, Université Claude Bernard Lyon 1, Villeurbanne, Lyon, France
- LabEx ECOFECT (Eco-Evolutionary Dynamics of Infectious Diseases), Université Claude Bernard Lyon 1, Villeurbanne, Lyon, France
| | - Vincent Miele
- Laboratoire de Biométrie et Biologie Evolutive UMR5558-CNRS, Université de Lyon, Université Claude Bernard Lyon 1, Villeurbanne, Lyon, France
| | - Christophe Terzian
- LabEx ECOFECT (Eco-Evolutionary Dynamics of Infectious Diseases), Université Claude Bernard Lyon 1, Villeurbanne, Lyon, France
- UMR754 INRA, Université Claude Bernard Lyon 1, Lyon, France
- Ecole Pratique des Hautes Etudes, Paris, France
| | - Christian Biémont
- Laboratoire de Biométrie et Biologie Evolutive UMR5558-CNRS, Université de Lyon, Université Claude Bernard Lyon 1, Villeurbanne, Lyon, France
| | - Vincent Daubin
- Laboratoire de Biométrie et Biologie Evolutive UMR5558-CNRS, Université de Lyon, Université Claude Bernard Lyon 1, Villeurbanne, Lyon, France
- LabEx ECOFECT (Eco-Evolutionary Dynamics of Infectious Diseases), Université Claude Bernard Lyon 1, Villeurbanne, Lyon, France
| | - Cédric Feschotte
- Department of Human Genetics, University of Utah, School of Medicine, Salt Lake City, Utah, United States of America
| | - Dominique Pontier
- Laboratoire de Biométrie et Biologie Evolutive UMR5558-CNRS, Université de Lyon, Université Claude Bernard Lyon 1, Villeurbanne, Lyon, France
- LabEx ECOFECT (Eco-Evolutionary Dynamics of Infectious Diseases), Université Claude Bernard Lyon 1, Villeurbanne, Lyon, France
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12
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Sotero-Caio CG, Platt RN, Suh A, Ray DA. Evolution and Diversity of Transposable Elements in Vertebrate Genomes. Genome Biol Evol 2017; 9:161-177. [PMID: 28158585 PMCID: PMC5381603 DOI: 10.1093/gbe/evw264] [Citation(s) in RCA: 159] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/06/2016] [Indexed: 12/21/2022] Open
Abstract
Transposable elements (TEs) are selfish genetic elements that mobilize in genomes via transposition or retrotransposition and often make up large fractions of vertebrate genomes. Here, we review the current understanding of vertebrate TE diversity and evolution in the context of recent advances in genome sequencing and assembly techniques. TEs make up 4-60% of assembled vertebrate genomes, and deeply branching lineages such as ray-finned fishes and amphibians generally exhibit a higher TE diversity than the more recent radiations of birds and mammals. Furthermore, the list of taxa with exceptional TE landscapes is growing. We emphasize that the current bottleneck in genome analyses lies in the proper annotation of TEs and provide examples where superficial analyses led to misleading conclusions about genome evolution. Finally, recent advances in long-read sequencing will soon permit access to TE-rich genomic regions that previously resisted assembly including the gigantic, TE-rich genomes of salamanders and lungfishes.
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Affiliation(s)
| | - Roy N. Platt
- Department of Biological Sciences, Texas Tech University, Lubbock, TX
| | - Alexander Suh
- Department of Evolutionary Biology (EBC), Uppsala University, Uppsala, Sweden
| | - David A. Ray
- Department of Biological Sciences, Texas Tech University, Lubbock, TX
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13
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Evsikov AV, Marín de Evsikova C. Friend or Foe: Epigenetic Regulation of Retrotransposons in Mammalian Oogenesis and Early Development. THE YALE JOURNAL OF BIOLOGY AND MEDICINE 2016; 89:487-497. [PMID: 28018140 PMCID: PMC5168827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Epigenetics is the study of phenotypic variation arising from developmental and environmental factors regulating gene transcription at molecular, cellular, and physiological levels. A naturally occurring biological process driven by epigenetics is the egg-to-embryo developmental transition when two fully differentiated adult cells - egg and sperm - revert to an early stem cell type with totipotency but subsequently differentiates into pluripotent embryonic stem cells that give rise to any cell type. Transposable elements (TEs) are active in mammalian oocytes and early embryos, and this activity, albeit counterintuitive because TEs can lead to genomic instability in somatic cells, correlates to successful development. TEs bridge genetic and epigenetic landscapes because TEs are genetic elements whose silencing and de-repression are regulated by epigenetic mechanisms that are sensitive to environmental factors. Ultimately, transposition events can change size, content, and function of mammalian genomes. Thus, TEs act beyond mutagenic agents reshuffling the genomes, and epigenetic regulation of TEs may act as a proximate mechanism by which evolutionary forces increase a species' hidden reserve of epigenetic and phenotypic variability facilitating the adaptation of genomes to their environment.
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Affiliation(s)
- Alexei V. Evsikov
- To whom all correspondence should be addressed: Caralina Marín de Evsikova, Alexei V. Evsikov, Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, 12901 Bruce B Downs Blvd., MDC07, Tampa, FL 33612, CMdE: ; (813) 974 2248; AVE: ; (813) 974 6922, Fax: 813-974-7357
| | - Caralina Marín de Evsikova
- To whom all correspondence should be addressed: Caralina Marín de Evsikova, Alexei V. Evsikov, Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, 12901 Bruce B Downs Blvd., MDC07, Tampa, FL 33612, CMdE: ; (813) 974 2248; AVE: ; (813) 974 6922, Fax: 813-974-7357
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14
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Platt RN, Mangum SF, Ray DA. Pinpointing the vesper bat transposon revolution using the Miniopterus natalensis genome. Mob DNA 2016; 7:12. [PMID: 27489570 PMCID: PMC4971623 DOI: 10.1186/s13100-016-0071-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Accepted: 07/13/2016] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Around 40 million years ago DNA transposons began accumulating in an ancestor of bats in the family Vespertilionidae. Since that time, Class II transposons have been continuously reinvading and accumulating in vespertilionid genomes at a rate that is unprecedented in mammals. Miniopterus (Miniopteridae), a genus of long-fingered bats that was recently elevated from Vespertilionidae, is the sister taxon to the vespertilionids and is often used as an outgroup when studying transposable elements in vesper bats. Previous wet-lab techniques failed to identify Helitrons, TcMariners, or hAT transposons in Miniopterus. Limitations of those methods and ambiguous results regarding the distribution of piggyBac transposons left some questions as to the distribution of Class II elements in this group. The recent release of the Miniopterus natalensis genome allows for transposable element discovery with a higher degree of precision. RESULTS Here we analyze the transposable element content of M. natalensis to pinpoint with greater accuracy the taxonomic distribution of Class II transposable elements in bats. These efforts demonstrate that, compared to the vespertilionids, Class II TEs are highly mutated and comprise only a small portion of the M. natalensis genome. Despite the limited Class II content, M. natalensis possesses a limited number of lineage-specific, low copy number piggyBacs and shares several TcMariner families with vespertilionid bats. Multiple efforts to identify Helitrons, one of the major TE components of vesper bat genomes, using de novo repeat identification and structural based searches failed. CONCLUSIONS These observations combined with previous results inform our understanding of the events leading to the unique Class II element acquisition that characterizes vespertilionids. While it appears that a small number of TcMariner and piggyBac elements were deposited in the ancestral Miniopterus + vespertilionid genome, these elements are not present in M. natalensis genome at high copy number. Instead, this work indicates that the vesper bats alone experienced the expansion of TEs ranging from Helitrons to piggyBacs to hATs.
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Affiliation(s)
- Roy N Platt
- Department of Biological Sciences, Texas Tech University, Box 43131, Lubbock, TX 79409-3131 USA
| | - Sarah F Mangum
- Department of Biological Sciences, Texas Tech University, Box 43131, Lubbock, TX 79409-3131 USA
| | - David A Ray
- Department of Biological Sciences, Texas Tech University, Box 43131, Lubbock, TX 79409-3131 USA
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15
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Smeds L, Warmuth V, Bolivar P, Uebbing S, Burri R, Suh A, Nater A, Bureš S, Garamszegi LZ, Hogner S, Moreno J, Qvarnström A, Ružić M, Sæther SA, Sætre GP, Török J, Ellegren H. Evolutionary analysis of the female-specific avian W chromosome. Nat Commun 2015; 6:7330. [PMID: 26040272 PMCID: PMC4468903 DOI: 10.1038/ncomms8330] [Citation(s) in RCA: 92] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Accepted: 04/28/2015] [Indexed: 02/07/2023] Open
Abstract
The typically repetitive nature of the sex-limited chromosome means that it is often excluded from or poorly covered in genome assemblies, hindering studies of evolutionary and population genomic processes in non-recombining chromosomes. Here, we present a draft assembly of the non-recombining region of the collared flycatcher W chromosome, containing 46 genes without evidence of female-specific functional differentiation. Survival of genes during W chromosome degeneration has been highly non-random and expression data suggest that this can be attributed to selection for maintaining gene dose and ancestral expression levels of essential genes. Re-sequencing of large population samples revealed dramatically reduced levels of within-species diversity and elevated rates of between-species differentiation (lineage sorting), consistent with low effective population size. Concordance between W chromosome and mitochondrial DNA phylogenetic trees demonstrates evolutionary stable matrilineal inheritance of this nuclear–cytonuclear pair of chromosomes. Our results show both commonalities and differences between W chromosome and Y chromosome evolution. The evolution of non-recombining chromosomes is poorly understood. Here, the authors sequence the collared flycatcher female-specific W chromosome and show nonrandom survival of genes during W chromosome degeneration which is due to selection for maintaining gene dose and expression levels of essential genes.
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Affiliation(s)
- Linnéa Smeds
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala, Sweden
| | - Vera Warmuth
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala, Sweden
| | - Paulina Bolivar
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala, Sweden
| | - Severin Uebbing
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala, Sweden
| | - Reto Burri
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala, Sweden
| | - Alexander Suh
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala, Sweden
| | - Alexander Nater
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala, Sweden
| | - Stanislav Bureš
- Laboratory of Ornithology, Department of Zoology, Palacky University, 77146 Olomouc, Czech Republic
| | - Laszlo Z Garamszegi
- Department of Evolutionary Ecology, Estación Biológica de Doñana-CSIC, 41092 Seville, Spain
| | - Silje Hogner
- 1] Department of Biosciences, Centre for Ecological and Evolutionary Synthesis, University of Oslo, 0316 Oslo, Norway [2] Natural History Museum, University of Oslo, 0318 Oslo, Norway
| | - Juan Moreno
- Museo Nacional de Ciencias Naturales-CSIC, 28006 Madrid, Spain
| | - Anna Qvarnström
- Department of Animal Ecology, Evolutionary Biology Centre, Uppsala University, 75236 Uppsala, Sweden
| | - Milan Ružić
- Bird Protection and Study Society of Serbia, Radnička 20a, 21000 Novi Sad, Serbia
| | - Stein-Are Sæther
- 1] Department of Biosciences, Centre for Ecological and Evolutionary Synthesis, University of Oslo, 0316 Oslo, Norway [2] Norwegian Institute for Nature Research (NINA), 7034 Trondheim, Norway
| | - Glenn-Peter Sætre
- Department of Biosciences, Centre for Ecological and Evolutionary Synthesis, University of Oslo, 0316 Oslo, Norway
| | - Janos Török
- Behavioural Ecology Group, Department of Systematic Zoology and Ecology, Eötvös Loránd University, 1117 Budapest, Hungary
| | - Hans Ellegren
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala, Sweden
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16
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Ray DA, Pagan HJ, Platt RN, Kroll AR, Schaack S, Stevens RD. Differential SINE evolution in vesper and non-vesper bats. Mob DNA 2015; 6:10. [PMID: 25991928 PMCID: PMC4436864 DOI: 10.1186/s13100-015-0038-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Accepted: 04/15/2015] [Indexed: 12/31/2022] Open
Abstract
Background Short interspersed elements (SINEs) have a powerful influence on genome evolution and can be useful markers for phylogenetic inference and population genetic analyses. In this study, we examined survey sequence and whole genome data to determine the evolutionary dynamics of Ves SINEs in the genomes of 11 bats, nine from Vespertilionidae. Results We identified 41 subfamilies of Ves and linked several to specific lineages. We also revealed substantial differences among lineages including the observation that Ves accumulation and Ves subfamily diversity is significantly higher in vesper as opposed to non-vesper bats. This is especially interesting when one considers the increased transposable element diversity of vesper bats in general. Conclusions Our data suggest that survey sequencing and genome mining are valuable tools to investigate SINE evolution among related lineages and can provide substantial information about the ability of SINEs to proliferate in diverse genomes. This method would also be a useful first step in determining which subfamilies would be the best to target when developing SINEs as markers for phylogenetic and population genetic analyses. Electronic supplementary material The online version of this article (doi:10.1186/s13100-015-0038-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- David A Ray
- Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409 USA
| | - Heidi Jt Pagan
- Harbor Branch Oceanographic Institute, Florida Atlantic University, Fort Pierce, FL USA
| | - Roy N Platt
- Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409 USA
| | - Ashley R Kroll
- Department of Biology, Reed College, Portland, OR 97202 USA
| | - Sarah Schaack
- Department of Biology, Reed College, Portland, OR 97202 USA
| | - Richard D Stevens
- Department of Natural Resources Management and the Museum, Texas Tech University, Lubbock, TX 79409 USA
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17
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Suh A, Churakov G, Ramakodi MP, Platt RN, Jurka J, Kojima KK, Caballero J, Smit AF, Vliet KA, Hoffmann FG, Brosius J, Green RE, Braun EL, Ray DA, Schmitz J. Multiple lineages of ancient CR1 retroposons shaped the early genome evolution of amniotes. Genome Biol Evol 2014; 7:205-17. [PMID: 25503085 PMCID: PMC4316615 DOI: 10.1093/gbe/evu256] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Chicken repeat 1 (CR1) retroposons are long interspersed elements (LINEs) that are ubiquitous within amniote genomes and constitute the most abundant family of transposed elements in birds, crocodilians, turtles, and snakes. They are also present in mammalian genomes, where they reside as numerous relics of ancient retroposition events. Yet, despite their relevance for understanding amniote genome evolution, the diversity and evolution of CR1 elements has never been studied on an amniote-wide level. We reconstruct the temporal and quantitative activity of CR1 subfamilies via presence/absence analyses across crocodilian phylogeny and comparative analyses of 12 crocodilian genomes, revealing relative genomic stasis of retroposition during genome evolution of extant Crocodylia. Our large-scale phylogenetic analysis of amniote CR1 subfamilies suggests the presence of at least seven ancient CR1 lineages in the amniote ancestor; and amniote-wide analyses of CR1 successions and quantities reveal differential retention (presence of ancient relics or recent activity) of these CR1 lineages across amniote genome evolution. Interestingly, birds and lepidosaurs retained the fewest ancient CR1 lineages among amniotes and also exhibit smaller genome sizes. Our study is the first to analyze CR1 evolution in a genome-wide and amniote-wide context and the data strongly suggest that the ancestral amniote genome contained myriad CR1 elements from multiple ancient lineages, and remnants of these are still detectable in the relatively stable genomes of crocodilians and turtles. Early mammalian genome evolution was thus characterized by a drastic shift from CR1 prevalence to dominance and hyperactivity of L2 LINEs in monotremes and L1 LINEs in therians.
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Affiliation(s)
- Alexander Suh
- Institute of Experimental Pathology (ZMBE), University of Münster, Germany Department of Evolutionary Biology (EBC), Uppsala University, Sweden
| | - Gennady Churakov
- Institute of Experimental Pathology (ZMBE), University of Münster, Germany
| | - Meganathan P Ramakodi
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University Present address: Cancer Prevention and Control Program, Fox Chase Cancer Center, Philadelphia, PA Present address: Department of Biology, Temple University, Philadelphia, PA
| | - Roy N Platt
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University Department of Biological Sciences, Texas Tech University
| | - Jerzy Jurka
- Genetic Information Research Institute, Mountain View, California
| | - Kenji K Kojima
- Genetic Information Research Institute, Mountain View, California
| | | | - Arian F Smit
- Institute for Systems Biology, Seattle, Washington
| | | | - Federico G Hoffmann
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University
| | - Jürgen Brosius
- Institute of Experimental Pathology (ZMBE), University of Münster, Germany
| | - Richard E Green
- Department of Biomolecular Engineering, University of California
| | - Edward L Braun
- Department of Biology and Genetics Institute, University of Florida
| | - David A Ray
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University Department of Biological Sciences, Texas Tech University
| | - Jürgen Schmitz
- Institute of Experimental Pathology (ZMBE), University of Münster, Germany
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18
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Thomas J, Phillips CD, Baker RJ, Pritham EJ. Rolling-circle transposons catalyze genomic innovation in a mammalian lineage. Genome Biol Evol 2014; 6:2595-610. [PMID: 25223768 PMCID: PMC4224331 DOI: 10.1093/gbe/evu204] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Rolling-circle transposons (Helitrons) are a newly discovered group of mobile DNA widespread in plant and invertebrate genomes but limited to the bat family Vespertilionidae among mammals. Little is known about the long-term impact of Helitron activity because the genomes where Helitron activity has been extensively studied are predominated by young families. Here, we report a comprehensive catalog of vetted Helitrons from the 7× Myotis lucifugus genome assembly. To estimate the timing of transposition, we scored presence/absence across related vespertilionid genome sequences with estimated divergence times. This analysis revealed that the Helibat family has been a persistent source of genomic innovation throughout the vespertilionid diversification from approximately 30–36 Ma to as recently as approximately 1.8–6 Ma. This is the first report of persistent Helitron transposition over an extended evolutionary timeframe. These findings illustrate that the pattern of Helitron activity is akin to the vertical persistence of LINE retrotransposons in primates and other mammalian lineages. Like retrotransposition in primates, rolling-circle transposition has generated lineage-specific variation and accounts for approximately 110 Mb, approximately 6% of the genome of M. lucifugus. The Helitrons carry a heterogeneous assortment of host sequence including retroposed messenger RNAs, retrotransposons, DNA transposons, as well as introns, exons and regulatory regions (promoters, 5′-untranslated regions [UTRs], and 3′-UTRs) of which some are evolving in a pattern suggestive of purifying selection. Evidence that Helitrons have contributed putative promoters, exons, splice sites, polyadenylation sites, and microRNA-binding sites to transcripts otherwise conserved across mammals is presented, and the implication of Helitron activity to innovation in these unique mammals is discussed.
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Affiliation(s)
- Jainy Thomas
- Department of Human Genetics, University of Utah
| | - Caleb D Phillips
- Department of Biological Sciences and Museum, Texas Tech University
| | - Robert J Baker
- Department of Biological Sciences and Museum, Texas Tech University
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19
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Zhang HH, Feschotte C, Han MJ, Zhang Z. Recurrent horizontal transfers of Chapaev transposons in diverse invertebrate and vertebrate animals. Genome Biol Evol 2014; 6:1375-86. [PMID: 24868016 PMCID: PMC4079192 DOI: 10.1093/gbe/evu112] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/21/2014] [Indexed: 01/08/2023] Open
Abstract
Horizontal transfer (HT) of a transposable element (TE) into a new genome is regarded as an important force to drive genome variation and biological innovation. In addition, HT also plays an important role in the persistence of TEs in eukaryotic genomes. Here, we provide the first documented example for the repeated HT of three families of Chapaev transposons in a wide range of animal species, including mammals, reptiles, jawed fishes, lampreys, insects, and in an insect bracovirus. Multiple alignments of the Chapaev transposons identified in these species revealed extremely high levels of nucleotide sequence identity (79-99%), which are inconsistent with vertical evolution given the deep divergence time separating these host species. Rather, the discontinuous distribution amongst species and lack of purifying selection acting on these transposons strongly suggest that they were independently and horizontally transferred into these species lineages. The detection of Chapaev transposons in an insect bracovirus indicated that these viruses might act as a possible vector for the horizontal spread of Chapaev transposons. One of the Chapaev families was also shared by lampreys and some of their common hosts (such as sturgeon and paddlefish), which suggested that parasite-host interaction might facilitate HTs.
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Affiliation(s)
- Hua-Hao Zhang
- School of Life Sciences, Chongqing University, ChinaCollege of Pharmacy and Life Science, Jiujiang University, China
| | - Cédric Feschotte
- Department of Human Genetics, University of Utah School of Medicine
| | - Min-Jin Han
- School of Life Sciences, Chongqing University, China
| | - Ze Zhang
- School of Life Sciences, Chongqing University, China
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20
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Large Numbers of Novel miRNAs Originate from DNA Transposons and Are Coincident with a Large Species Radiation in Bats. Mol Biol Evol 2014; 31:1536-45. [DOI: 10.1093/molbev/msu112] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
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21
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Pavelitz T, Gray LT, Padilla SL, Bailey AD, Weiner AM. PGBD5: a neural-specific intron-containing piggyBac transposase domesticated over 500 million years ago and conserved from cephalochordates to humans. Mob DNA 2013; 4:23. [PMID: 24180413 PMCID: PMC3902484 DOI: 10.1186/1759-8753-4-23] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2013] [Accepted: 10/04/2013] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND piggyBac domain (PGBD) transposons are found in organisms ranging from fungi to humans. Three domesticated piggyBac elements have been described. In the ciliates Paramecium tetraurelia and Tetrahymena thermophila, homologs known as piggyMacs excise internal eliminated sequences from germline micronuclear DNA during regeneration of the new somatic macronucleus. In primates, a PGBD3 element inserted into the Cockayne syndrome group B (CSB) gene over 43 Mya serves as an alternative 3' terminal exon, enabling the CSB gene to generate both full length CSB and a conserved CSB-PGBD3 fusion protein that joins an N-terminal CSB domain to the C-terminal transposase domain. RESULTS We describe a fourth domesticated piggyBac element called PGBD5. We show that i) PGBD5 was first domesticated in the common ancestor of the cephalochordate Branchiostoma floridae (aka lancelet or amphioxus) and vertebrates, and is conserved in all vertebrates including lamprey but cannot be found in more basal urochordates, hemichordates, or echinoderms; ii) the lancelet, lamprey, and human PGBD5 genes are syntenic and orthologous; iii) no potentially mobile ancestral PGBD5 elements can be identified in other more deeply rooted organisms; iv) although derived from an IS4-related transposase of the RNase H clan, PGBD5 protein is unlikely to retain enzymatic activity because the catalytic DDD(D) motif is not conserved; v) PGBD5 is preferentially expressed in certain granule cell lineages of the brain and in the central nervous system based on available mouse and human in situ hybridization data, and the tissue-specificity of documented mammalian EST and mRNA clones; vi) the human PGBD5 promoter and gene region is rich in bound regulatory factors including the neuron-restrictive silencer factors NRSF/REST and CoREST, as well as SIN3, KAP1, STAT3, and CTCF; and vii) despite preferential localization within the nucleus, PGBD5 protein is unlikely to bind DNA or chromatin as neither DNase I digestion nor high salt extraction release PGBD5 from fractionated mouse brain nuclei. CONCLUSIONS We speculate that the neural-specific PGBD5 transposase was domesticated >500 My after cephalochordates and vertebrates split from urochordates, and that PGBD5 may have played a role in the evolution of a primitive deuterostome neural network into a centralized nervous system.
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Affiliation(s)
| | | | | | | | - Alan M Weiner
- Department of Biochemistry, School of Medicine, University of Washington, Seattle, WA 98195-7350, USA.
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22
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Lavoie CA, Platt RN, Novick PA, Counterman BA, Ray DA. Transposable element evolution in Heliconius suggests genome diversity within Lepidoptera. Mob DNA 2013; 4:21. [PMID: 24088337 PMCID: PMC4016481 DOI: 10.1186/1759-8753-4-21] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2013] [Accepted: 09/27/2013] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND Transposable elements (TEs) have the potential to impact genome structure, function and evolution in profound ways. In order to understand the contribution of transposable elements (TEs) to Heliconius melpomene, we queried the H. melpomene draft sequence to identify repetitive sequences. RESULTS We determined that TEs comprise ~25% of the genome. The predominant class of TEs (~12% of the genome) was the non-long terminal repeat (non-LTR) retrotransposons, including a novel SINE family. However, this was only slightly higher than content derived from DNA transposons, which are diverse, with several families having mobilized in the recent past. Compared to the only other well-studied lepidopteran genome, Bombyx mori, H. melpomene exhibits a higher DNA transposon content and a distinct repertoire of retrotransposons. We also found that H. melpomene exhibits a high rate of TE turnover with few older elements accumulating in the genome. CONCLUSIONS Our analysis represents the first complete, de novo characterization of TE content in a butterfly genome and suggests that, while TEs are able to invade and multiply, TEs have an overall deleterious effect and/or that maintaining a small genome is advantageous. Our results also hint that analysis of additional lepidopteran genomes will reveal substantial TE diversity within the group.
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Affiliation(s)
- Christine A Lavoie
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State, MS 39762, USA
- Institute for Genomics, Biocomputing and Biotechnology, Mississippi, MS 39762, USA
| | - Roy N Platt
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State, MS 39762, USA
- Institute for Genomics, Biocomputing and Biotechnology, Mississippi, MS 39762, USA
| | - Peter A Novick
- Department of Biological Sciences and Geology, Queensborough Community College, Bayside, New York, NY 11364, USA
| | | | - David A Ray
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State, MS 39762, USA
- Institute for Genomics, Biocomputing and Biotechnology, Mississippi, MS 39762, USA
- Current Address: Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409, USA
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23
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Palavesam A, Esnault C, O’Brochta DA. Post-integration silencing of piggyBac transposable elements in Aedes aegypti. PLoS One 2013; 8:e68454. [PMID: 23861905 PMCID: PMC3701635 DOI: 10.1371/journal.pone.0068454] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2013] [Accepted: 05/30/2013] [Indexed: 12/04/2022] Open
Abstract
The piggyBac transposon, originating in the genome of the Lepidoptera Trichoplusia ni, has a broad host range, making it useful for the development of a number of transposon-based functional genomic technologies including gene vectors, enhancer-, gene- and protein-traps. While capable of being used as a vector for the creation of transgenic insects and insect cell lines, piggyBac has very limited mobility once integrated into the genome of the yellow fever mosquito, Aedes aegypti. A transgenic Aedes aegypti cell line (AagPB8) was created containing three integrated piggyBac elements and the remobilization potential of the elements was tested. The integrated piggyBac elements in AagPB8 were transpositionally silent in the presence of functional transposase, which was shown to be capable of catalyzing the movement of plasmid-borne piggyBac elements in the same cells. The structural integrity of one of the integrated elements along with the quality of element-flanking DNA, which is known to influence transposition rates, were tested in D. melanogaster. The element was found to be structurally intact, capable of transposition and excision in the soma and germ-line of Drosophila melanogaster, and in a DNA sequence context highly conducive to element movement in Drosophila melanogaster. These data show that transpositional silencing of integrated piggyBac elements in the genome of Aedes aegypti appears to be a function of higher scale genome organization or perhaps epigenetic factors, and not due to structural defects or suboptimal integration sites.
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Affiliation(s)
- Azhahianambi Palavesam
- Department of Entomology, The Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, Maryland, United States of America
| | - Caroline Esnault
- Department of Entomology, The Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, Maryland, United States of America
| | - David A. O’Brochta
- Department of Entomology, The Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, Maryland, United States of America
- Institute for Bioscience and Biotechnology Research, Rockville, Maryland, United States of America
- * E-mail:
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Platt II RN, Ray DA. A non-LTR retroelement extinction in Spermophilus tridecemlineatus. Gene 2012; 500:47-53. [DOI: 10.1016/j.gene.2012.03.051] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2012] [Revised: 03/08/2012] [Accepted: 03/09/2012] [Indexed: 10/28/2022]
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Pagán HJT, Macas J, Novák P, McCulloch ES, Stevens RD, Ray DA. Survey sequencing reveals elevated DNA transposon activity, novel elements, and variation in repetitive landscapes among vesper bats. Genome Biol Evol 2012; 4:575-85. [PMID: 22491057 PMCID: PMC3342881 DOI: 10.1093/gbe/evs038] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The repetitive landscapes of mammalian genomes typically display high Class I (retrotransposon) transposable element (TE) content, which usually comprises around half of the genome. In contrast, the Class II (DNA transposon) contribution is typically small (<3% in model mammals). Most mammalian genomes exhibit a precipitous decline in Class II activity beginning roughly 40 Ma. The first signs of more recently active mammalian Class II TEs were obtained from the little brown bat, Myotis lucifugus, and are reflected by higher genome content (∼5%). To aid in determining taxonomic limits and potential impacts of this elevated Class II activity, we performed 454 survey sequencing of a second Myotis species as well as four additional taxa within the family Vespertilionidae and an outgroup species from Phyllostomidae. Graph-based clustering methods were used to reconstruct the major repeat families present in each species and novel elements were identified in several taxa. Retrotransposons remained the dominant group with regard to overall genome mass. Elevated Class II TE composition (3–4%) was observed in all five vesper bats, while less than 0.5% of the phyllostomid reads were identified as Class II derived. Differences in satellite DNA and Class I TE content are also described among vespertilionid taxa. These analyses present the first cohesive description of TE evolution across closely related mammalian species, revealing genome-scale differences in TE content within a single family.
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Affiliation(s)
- Heidi J T Pagán
- Department of Biochemistry, Molecular Biology, Entomology, and Plant Pathology, Mississippi State University, MS, USA
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Smith A, Rutherford K, Benkel B. Characterization of a Tigger1 element from the genome of the American mink (Neovison vison). Gene 2012; 498:164-8. [PMID: 22387302 DOI: 10.1016/j.gene.2012.02.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2011] [Revised: 01/31/2012] [Accepted: 02/07/2012] [Indexed: 11/28/2022]
Abstract
Tigger elements belong to the Tc1/Mariner family of DNA transposons which is remarkably widespread in nature with homologs present in organisms as diverse as fungi, plants and animals. In this report, we present the nucleotide sequence of a defragmented Tigger1 element from the genome of the American mink. The element is 2,274 bp long, carries 13 bp terminal inverted repeats (TIRs) and contains the vestiges of two open reading frames (ORFs), one of which is similar to the centromere associated protein CENP B. In addition, we estimate that the genome of the American mink contains approximately 1000 Tigger1 elements, but find no evidence for the transcription of extant elements in the mink.
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Affiliation(s)
- Amanda Smith
- Nova Scotia Agricultural College, Department of Plant and Animal Sciences, PO Box 550, Truro, Nova Scotia, Canada B2N 5E3
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Gilbert C, Hernandez SS, Flores-Benabib J, Smith EN, Feschotte C. Rampant horizontal transfer of SPIN transposons in squamate reptiles. Mol Biol Evol 2011; 29:503-15. [PMID: 21771716 DOI: 10.1093/molbev/msr181] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Transposable elements (TEs) are highly abundant in the genome and capable of mobility, two properties that make them particularly prone to transfer horizontally between organisms. Although the impact of horizontal transfer (HT) of TEs is well recognized in prokaryotes, the frequency of this phenomenon and its contribution to genome evolution in eukaryotes remain poorly appreciated. Here, we provide evidence that a DNA transposon called SPIN has colonized the genome of 17 species of reptiles representing nearly every major lineage of squamates, including 14 families of lizards, snakes, and amphisbaenians. Slot blot analyses indicate that SPIN has amplified to high copy numbers in most of these species, ranging from 2,000-28,000 copies per haploid genome. In contrast, we could not detect the presence of SPIN in any of the turtles (seven species from seven families) and crocodiles (four species) examined. Genetic distances between SPIN sequences from species belonging to different squamate families are consistently very low (average = 0.1), considering the deep evolutionary divergence of the families investigated (most are >100 My diverged). Furthermore, these distances fall below interfamilial distances calculated for two genes known to have evolved under strong functional constraint in vertebrates (RAG1, average = 0.24 and C-mos, average = 0.27). These data, combined with phylogenetic analyses, indicate that the widespread distribution of SPIN among squamates is the result of at least 13 independent events of HTs. Molecular dating and paleobiogeographical data suggest that these transfers took place during the last 50 My on at least three different continents (North America, South America and, Africa). Together, these results triple the number of known SPIN transfer events among tetrapods, provide evidence for a previously hypothesized transoceanic movement of SPIN transposons during the Cenozoic, and further underscore the role of HT in the evolution of vertebrate genomes.
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28
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The limited distribution of Helitrons to vesper bats supports horizontal transfer. Gene 2010; 474:52-8. [PMID: 21193022 DOI: 10.1016/j.gene.2010.12.007] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2010] [Accepted: 12/20/2010] [Indexed: 11/21/2022]
Abstract
Transposable elements (TEs) have the unique ability to move and replicate within the genome and therefore engender dramatic changes to genome architecture. Among different types of TEs, rolling-circle transposons (Helitrons) are well known for their ability to capture and amplify host gene fragments. Bioinformatic analysis revealed that Helitrons constitute ~3% of the Myotis lucifugus, (little brown bat) genome, while no Helitrons were found in any of the other 44+ sequenced mammalian genomes. Recently horizontal transfer has been implicated for some of the M. lucifugus Helitrons, in part explaining this disparate distribution among mammals. The purpose of this work is to determine both the distribution of Helitrons among bats and to estimate the number of independent invasions. We employed a combination of in silico, PCR and hybridization based techniques to identify Helitrons from diverse bat species belonging to ten different families. This work reveals that Helitrons invaded the vesper bat lineage, at least once. Indeed, Helitrons were not identified in the sister taxa 'Miniopterus', which suggests that the amplification of Helibat occurred (30-36 mya) only in the vesper bat lineage. The estimated age of amplification of the Helibats and the rapid radiation of vesper bats are roughly coincidental and suggest that the invasion and amplification of these elements might have influenced their evolutionary trajectory potentially contributing to phenotypic and genotypic diversity.
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Novick PA, Smith JD, Floumanhaft M, Ray DA, Boissinot S. The evolution and diversity of DNA transposons in the genome of the Lizard Anolis carolinensis. Genome Biol Evol 2010; 3:1-14. [PMID: 21127169 PMCID: PMC3014272 DOI: 10.1093/gbe/evq080] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/26/2010] [Indexed: 01/19/2023] Open
Abstract
DNA transposons have considerably affected the size and structure of eukaryotic genomes and have been an important source of evolutionary novelties. In vertebrates, DNA transposons are discontinuously distributed due to the frequent extinction and recolonization of these genomes by active elements. We performed a detailed analysis of the DNA transposons in the genome of the lizard Anolis carolinensis, the first non-avian reptile to have its genome sequenced. Elements belonging to six of the previously recognized superfamilies of elements (hAT, Tc1/Mariner, Helitron, PIF/Harbinger, Polinton/Maverick, and Chapaev) were identified. However, only four (hAT, Tc1/Mariner, Helitron, and Chapaev) of these superfamilies have successfully amplified in the anole genome, producing 67 distinct families. The majority (57/67) are nonautonomous and demonstrate an extraordinary diversity of structure, resulting from frequent interelement recombination and incorporation of extraneous DNA sequences. The age distribution of transposon families differs among superfamilies and reveals different dynamics of amplification. Chapaev is the only superfamily to be extinct and is represented only by old copies. The hAT, Tc1/Mariner, and Helitron superfamilies show different pattern of amplification, yet they are predominantly represented by young families, whereas divergent families are exceedingly rare. Although it is likely that some elements, in particular long ones, are subjected to purifying selection and do not reach fixation, the majority of families are neutral and accumulate in the anole genome in large numbers. We propose that the scarcity of old copies in the anole genome results from the rapid decay of elements, caused by a high rate of DNA loss.
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Affiliation(s)
- Peter A. Novick
- Department of Biology, Queens College, the City University of New York
- Graduate School and University Center, the City University of New York
| | - Jeremy D. Smith
- Department of Biochemistry and Molecular Biology, Mississippi State University
| | - Mark Floumanhaft
- Department of Biology, Queens College, the City University of New York
| | - David A. Ray
- Department of Biochemistry and Molecular Biology, Mississippi State University
| | - Stéphane Boissinot
- Department of Biology, Queens College, the City University of New York
- Graduate School and University Center, the City University of New York
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