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Vela J, Mora P, Montiel EE, Rico-Porras JM, Sanllorente O, Amoasii D, Lorite P, Palomeque T. Exploring horizontal transfer of mariner transposable elements among ants and aphids. Gene 2024; 899:148144. [PMID: 38195050 DOI: 10.1016/j.gene.2024.148144] [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: 07/21/2023] [Revised: 12/21/2023] [Accepted: 01/04/2024] [Indexed: 01/11/2024]
Abstract
Aphids and ants are mutualistic species with a close space-time relationship, which may facilitate the occurrence of horizontal transfer events between these insect groups. Myrmar-like mariner elements were previously isolated from two ant (Myrmica ruginodis and Tapinoma ibericum) and two aphid species (Aphis fabae and Aphis hederae). The aim of this work is to determine the presence of Myrmar-like mariner elements in new ant and aphid species, as well as to analyze the likelihood of horizontal transfer events between these taxa. To accomplish this, the Myrmar-like element has been isolated from five aphid species and six ant species. Among these new analyzed species, full-length Myrmar-like mariner elements with very high sequence similarity have been isolated from the aphids Aphis nerii, Aphis spiraecola, Brachycaudus cardui, and Rhopalosiphum maidis as well as from the ants Lasius grandis and Lasius niger, even though aphids and ants belong to two insect orders (Hemiptera and Hymenoptera) that have evolved independently for at least 300 million-years. Both Lasius species establish frequent mutualistic relationships with multiple aphid species, including A. nerii, A. spiraecola, and B. cardui. The study of the putative protein encoded by them and the phylogenetic analysis suggests that they could be active transposons shared by aphids and ants through horizontal transfer events. Additionally, mariner elements with internal deletion were found in several aphids and one ant species, showing a high degree of sequence similarity among them. The characteristics of these elements with internal deletion suggest a complex origin involving various evolutionary processes, possibly including also horizontal transfer events. Myrmar-like elements have also been isolated from the other ant species, although without similarity with the aphid mariner sequences. Myrmar-like elements are also present in phylogenetically distant insect species, as well as in one crustacean species. The phylogenetic study carried out with all Myrmar-like elements suggests the probable occurrence of horizontal transfer events.
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Affiliation(s)
- Jesús Vela
- Departamento de Biología Experimental, Área de Genética, Universidad de Jaén, 23071 Jaén, Spain.
| | - Pablo Mora
- Departamento de Biología Experimental, Área de Genética, Universidad de Jaén, 23071 Jaén, Spain.
| | - Eugenia E Montiel
- Departamento de Biología (Genética), Facultad de Ciencias, Universidad Autónoma de Madrid, 28049 Madrid, Spain; Centro de Investigación en Biodiversidad y Cambio Global (CIBC-UAM), Universidad Autónoma de Madrid, 28049 Madrid, Spain.
| | - José M Rico-Porras
- Departamento de Biología Experimental, Área de Genética, Universidad de Jaén, 23071 Jaén, Spain.
| | - Olivia Sanllorente
- Departamento de Zoología, Facultad de Ciencias, Universidad de Granada, 18071 Granada, Spain.
| | - Daniela Amoasii
- Departamento de Biología Experimental, Área de Genética, Universidad de Jaén, 23071 Jaén, Spain.
| | - Pedro Lorite
- Departamento de Biología Experimental, Área de Genética, Universidad de Jaén, 23071 Jaén, Spain.
| | - Teresa Palomeque
- Departamento de Biología Experimental, Área de Genética, Universidad de Jaén, 23071 Jaén, Spain.
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2
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Fan J, Yang S, Wennmann JT, Wang D, Jehle JA. The distribution and characteristic of two transposable elements in the genome of Cydia pomonella granulovirus and codling moth. Mol Phylogenet Evol 2023; 182:107745. [PMID: 36842732 DOI: 10.1016/j.ympev.2023.107745] [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: 02/23/2022] [Revised: 01/20/2023] [Accepted: 02/21/2023] [Indexed: 02/26/2023]
Abstract
Baculoviruses are capable to acquire insect host transposable elements (TEs) in their genomes and are hypothesized as possible vectors of insect transposons between Lepidopteran species. Here, we investigated the host origin of two TEs, namely the Tc1/mariner-like element TCp3.2 and a 0.7 kbp insertion sequence (IS07), found in the genome of different isolates of Cydia pomonella granulovirus (CpGV), a member of the Betabaculovirus genus. The sequences of both TEs were searched for in the full genome sequence database of codling moth (CM, Cydia pomonella L.). A total of eleven TCp3.2 TE copies and 76 copies of the IS07 fragments were identified in the CM genome. These TEs were distributed over the 22 autosomes and the Z chromosome (chr1) of CM, except chr6, chr12, chr16, chr23, chr27 and the W chromosome (chr29). TCp3.2 copies with two transposase genes in opposite direction, representing a novel feature, were identified on chr10 and chr18. The TCp3.2 transposase was characterized by DD41D motif of classic Tc1/mariner transposons, consisting of DNA-binding domain, catalytic domain and nuclear localization signal (NLS). Transcription analyses of uninfected and CpGV-infected CM larvae suggested a doubling of the TCp3.2 transposase transcription rate in virus infected larvae. Furthermore, IS07 insertion into the CpGV genome apparently added new transcription initiation sites to the viral genome. The global analysis of the distribution of two TEs in the genome of CM addressed the influx of mobile TEs from CM to CpGV, a genetic process that contributes to the population diversity of baculoviruses.
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Affiliation(s)
- Jiangbin Fan
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling 712100, China; Institute for Biological Control, Julius Kühn-Institut, Heinrichstraße. 243, 64287 Darmstadt, Germany
| | - Shili Yang
- Institute for Biological Control, Julius Kühn-Institut, Heinrichstraße. 243, 64287 Darmstadt, Germany
| | - Jörg T Wennmann
- Institute for Biological Control, Julius Kühn-Institut, Heinrichstraße. 243, 64287 Darmstadt, Germany
| | - Dun Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling 712100, China
| | - Johannes A Jehle
- Institute for Biological Control, Julius Kühn-Institut, Heinrichstraße. 243, 64287 Darmstadt, Germany.
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3
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Mobilome of the Rhus Gall Aphid Schlechtendalia chinensis Provides Insight into TE Insertion-Related Inactivation of Functional Genes. Int J Mol Sci 2022; 23:ijms232415967. [PMID: 36555609 PMCID: PMC9783078 DOI: 10.3390/ijms232415967] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 12/07/2022] [Accepted: 12/12/2022] [Indexed: 12/23/2022] Open
Abstract
Transposable elements (TEs) comprise a considerable proportion of insect genomic DNA; how they contribute to genome structure and organization is still poorly understood. Here, we present an analysis of the TE repertoire in the chromosome-level genome assembly of Rhus gall aphid Schlechtendalia chinensis. The TE fractions are composed of at least 32 different superfamilies and many TEs from different families were transcriptionally active in the S. chinensis genome. Furthermore, different types of transposase-derived proteins were also found in the S. chinensis genome. We also provide insight into the TEs related insertional inactivation, and exogenization of TEs in functional genes. We considered that the presence of TE fragments in the introns of functional genes could impact the activity of functional genes, and a large number of TE fragments in introns could lead to the indirect inactivation of functional genes. The present study will be beneficial in understanding the role and impact of TEs in genomic evolution of their hosts.
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4
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Nawae W, Sonthirod C, Yoocha T, Waiyamitra P, Soisook P, Tangphatsornruang S, Pootakham W. Genome assembly of the Pendlebury's roundleaf bat, Hipposideros pendleburyi, revealed the expansion of Tc1/Mariner DNA transposons in Rhinolophoidea. DNA Res 2022; 29:6754705. [PMID: 36214371 PMCID: PMC9549598 DOI: 10.1093/dnares/dsac026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Indexed: 11/16/2022] Open
Abstract
Bats (Chiroptera) constitute the second largest order of mammals and have several distinctive features, such as true self-powered flight and strong immunity. The Pendlebury's roundleaf bat, Hipposideros pendleburyi, is endemic to Thailand and listed as a vulnerable species. We employed the 10× Genomics linked-read technology to obtain a genome assembly of H. pendleburyi. The assembly size was 2.17 Gb with a scaffold N50 length of 15,398,518 bases. Our phylogenetic analysis placed H. pendleburyi within the rhinolophoid clade of the suborder Yinpterochiroptera. A synteny analysis showed that H. pendleburyi shared conserved chromosome segments (up to 105 Mb) with Rhinolophus ferrumequinum and Phyllostomus discolor albeit having different chromosome numbers and belonging different families. We found positive selection signals in genes involved in inflammation, spermatogenesis and Wnt signalling. The analyses of transposable elements suggested the contraction of short interspersed nuclear elements (SINEs) and the accumulation of young mariner DNA transposons in the analysed hipposiderids. Distinct mariners were likely horizontally transferred to hipposiderid genomes over the evolution of this family. The lineage-specific profiles of SINEs and mariners might involve in the evolution of hipposiderids and be associated with the phylogenetic separations of these bats from other bat families.
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Affiliation(s)
- Wanapinun Nawae
- National Omics Center (NOC), National Science and Technology Development Agency, Thailand Science Park, Pathum Thani, Thailand
| | - Chutima Sonthirod
- National Omics Center (NOC), National Science and Technology Development Agency, Thailand Science Park, Pathum Thani, Thailand
| | - Thippawan Yoocha
- National Omics Center (NOC), National Science and Technology Development Agency, Thailand Science Park, Pathum Thani, Thailand
| | - Pitchaporn Waiyamitra
- National Omics Center (NOC), National Science and Technology Development Agency, Thailand Science Park, Pathum Thani, Thailand
| | - Pipat Soisook
- Princess Maha Chakri Sirindhorn Natural History Museum, Prince of Songkla University, Hat Yai, Thailand
| | - Sithichoke Tangphatsornruang
- National Omics Center (NOC), National Science and Technology Development Agency, Thailand Science Park, Pathum Thani, Thailand
| | - Wirulda Pootakham
- To whom correspondence should be addressed. Tel: +66 2 5646700 Ext 71445. Fax: +66 2 5646707.
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Yokoi K, Kimura K, Bono H. Revealing Landscapes of Transposable Elements in Apis Species by Meta-Analysis. INSECTS 2022; 13:insects13080698. [PMID: 36005323 PMCID: PMC9408917 DOI: 10.3390/insects13080698] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 07/29/2022] [Accepted: 08/01/2022] [Indexed: 12/04/2022]
Abstract
Transposable elements (TEs) are grouped into several families with diverse sequences. Owing to their diversity, studies involving the detection, classification, and annotation of TEs are difficult tasks. Moreover, simple comparisons of TEs among different species with different methods can lead to misinterpretations. The genome data of several honey bee (Apis) species are available in public databases. Therefore, we conducted a meta-analysis of TEs, using 11 sets of genome data for Apis species, in order to establish data of “landscape of TEs”. Consensus TE sequences were constructed and their distributions in the Apis genomes were determined. Our results showed that TEs belonged to four to seven TE families among 13 and 15 families of TEs detected in classes I and II respectively mainly consisted of Apis TEs and that more DNA/TcMar-Mariner consensus sequences and copies were present in all Apis genomes tested. In addition, more consensus sequences and copy numbers of DNA/TcMar-Mariner were detected in Apis mellifera than in other Apis species. These results suggest that TcMar-Mariner might exert A. mellifera-specific effects on the host A. mellifera species. In conclusion, our unified approach enabled comparison of Apis genome sequences to determine the TE landscape, which provide novel evolutionary insights into Apis species.
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Affiliation(s)
- Kakeru Yokoi
- Insect Design Technology Group, Division of Insect Advanced Technology, Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), 1-2 Owashi, Tsukuba, Ibaraki 305-8634, Japan
- Correspondence: ; Tel.: +81-29-838-6129
| | - Kiyoshi Kimura
- Smart Livestock Facilities Group, Division of Advanced Feeding Technology Research, National Institute of Livestock and Grassland Science (NILGS), National Agriculture and Food Research Organization (NARO), Tsukuba, 2 Ikenodai, Tsukuba, Ibaraki 305-0901, Japan;
| | - Hidemasa Bono
- Laboratory of BioDX, Genome Editing Innovation Center, Hiroshima University, 3-10-23 Kagamiyama, Higashi-Hiroshima City, Hiroshima 739-0046, Japan;
- Laboratory of Genome Informatics, Graduate School of Integrated Sciences for Life, Hiroshima University, 3-10-23 Kagamiyama, Higashi-Hiroshima City, Hiroshima 739-0046, Japan
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6
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Ahmad A, Su X, Harris AJ, Ren Z. Closing the Gap: Horizontal Transfer of Mariner Transposons between Rhus Gall Aphids and Other Insects. BIOLOGY 2022; 11:731. [PMID: 35625459 PMCID: PMC9139091 DOI: 10.3390/biology11050731] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 05/05/2022] [Accepted: 05/06/2022] [Indexed: 11/17/2022]
Abstract
Horizontal transfer of transposons (HTT) is an essential source of genomic evolution in eukaryotes. The HTT dynamics are well characterized in eukaryotes, including insects; however, there is a considerable gap in knowledge about HTT regarding many eukaryotes' species. In this study, we analyzed the events of the HTT between Rhus gall aphids (Hemiptera) and other insects. We analyzed the Mariner-like transposable elements (MLEs) belonging to Rhus gall aphids for the possible HT events. The MLEs have a patchy distribution and high similarity over the entire element length with insect MLEs from different orders. We selected representative sequences from the Rhus gall MLEs and identified five events of HT between MLEs of Rhus gall aphids and other insects from five different orders. We also found multiple HTT events among the MLEs of insects from the five orders, demonstrating that these Mariner elements have been involved in recurrent HT between Rhus gall aphids and other insects. Our current study closed the knowledge gap surrounding HTT and reported the events between Rhus gall aphids and other insects for the first time. We believe that this study about HTT events will help us understand the evolution and spread of transposable elements in the genomes of Rhus gall aphids.
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Affiliation(s)
- Aftab Ahmad
- School of Life Science, Shanxi University, Taiyuan 030006, China;
| | - Xu Su
- Academy of Plateau Science and Sustainability, Qinghai Normal University, Xining 810016, China;
- School of Life Sciences, Qinghai Normal University, Xining 810008, China
| | - AJ Harris
- South China Botanical Garden, Chinese Academy of Sciences, Tianhe District, Guangzhou 510650, China;
| | - Zhumei Ren
- School of Life Science, Shanxi University, Taiyuan 030006, China;
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7
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Aphids and Ants, Mutualistic Species, Share a Mariner Element with an Unusual Location on Aphid Chromosomes. Genes (Basel) 2021; 12:genes12121966. [PMID: 34946915 PMCID: PMC8701394 DOI: 10.3390/genes12121966] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 12/07/2021] [Accepted: 12/07/2021] [Indexed: 12/20/2022] Open
Abstract
Aphids (Hemiptera, Aphididae) are small phytophagous insects. The aim of this study was to determine if the mariner elements found in the ant genomes are also present in Aphis fabae and Aphis hederae genomes and the possible existence of horizontal transfer events. Aphids maintain a relationship of mutualism with the ants. The close contact between these insects could favour horizontal transfer events of transposable elements. Myrmar mariner element isolated from Myrmica ruginodis and Tapinoma ibericum ants have also been found in the two Aphis species: A. fabae and A. hederae (Afabmar-Mr and Ahedmar-Mr elements). Besides, Afabmar-Mr could be an active transposon. Myrmar-like elements are also present in other insect species as well as in one Crustacean species. The phylogenetic study carried out with all Myrmar-like elements suggests the existence of horizontal transfer. Most aphids have 2n = 8 with a XX-X0 sex determination system. Their complicated life cycle is mostly parthenogenetic with sexual individuals only in autumn. The production of X0 males, originated by XX females which produce only spermatozoa with one X chromosome, must necessarily occur through specialized cytogenetic and molecular mechanisms which are not entirely known. In both aphid species, the mariner elements are located on all chromosomes, including the X chromosomes. However, on the two X chromosomes, no positive signals are detected in their small DAPI-negative telomere regions. The rDNA sites are located, as in the majority of Aphids species, on one of the telomere regions of each X chromosome. The hybridization patterns obtained by double FISH demonstrate that Afabmar-Mr and Ahedmar-Mr elements do not hybridize at the rDNA sites of their host species. Possible causes for the absence of these transposons in the rDNA genes are discussed, probably related with the X chromosome biology.
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8
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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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Ahmad A, Wallau GL, Ren Z. Characterization of Mariner transposons in seven species of Rhus gall aphids. Sci Rep 2021; 11:16349. [PMID: 34381125 PMCID: PMC8357937 DOI: 10.1038/s41598-021-95843-5] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 07/23/2021] [Indexed: 02/07/2023] Open
Abstract
Transposable elements (TEs), also known as jumping genes, are widely spread in the genomes of insects and play a considerable role in genomic evolution. Mariner/DD34D family belongs to class II transposable elements which is widely spread in the genomes of insects and have considerable role in genomic evolution. Mariner like elements (MLEs) were searched in the genomes of seven species of Rhus gall aphids belonging to six genera. In total, 121 MLEs were detected in the genomes of the seven investigated species of Rhus gall aphids, which showed a wide distribution in both close and distant related species. The sequences of MLEs ranged from 1 to 1.4 kb in length and the structural analysis of the MLEs showed that only five copies were potentially active with intact open reading frame (ORF) and terminal inverted repeats (TIRs). Phylogenetic analysis showed that all the 121 MLE sequences belonged to four subfamilies, i.e., Mauritiana, Drosophila, Vertumana and Irritans, among which Drosophila and Vertumana subfamilies were reported in aphids for the first time. Our present report revealed the diversity and distribution of MLEs in Rhus gall aphid genomes and expanded our understandings on the characterization of transposable elements in aphid genomes, which might be useful as genetic markers and tools and would play an important role in genomic evolution and adaptation of aphids.
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Affiliation(s)
- Aftab Ahmad
- School of Life Science, Shanxi University, 92 Wucheng Rd, Taiyuan, 030006, Shanxi, China
| | - Gabriel Luz Wallau
- Departamento de Entomologia e Núcleo de Bioinf Ormática, Instituto Aggeu Magalhães (IAM) - Fundação Oswaldo Cruz (FIOCRUZ), Recife, 50740-465, Brazil
| | - Zhumei Ren
- School of Life Science, Shanxi University, 92 Wucheng Rd, Taiyuan, 030006, Shanxi, China.
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10
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Shen D, Gao B, Miskey C, Chen C, Sang Y, Zong W, Wang S, Wang Y, Wang X, Ivics Z, Song C. Multiple Invasions of Visitor, a DD41D Family of Tc1/mariner Transposons, throughout the Evolution of Vertebrates. Genome Biol Evol 2021; 12:1060-1073. [PMID: 32602886 DOI: 10.1093/gbe/evaa135] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/23/2020] [Indexed: 12/13/2022] Open
Abstract
Although the DD41D (named as Visitor, VS) family of Tc1/mariner transposons was discovered in Arthropods and Mollusca, the evolution profile of this family is still largely unknown. We found that VS is widespread in the animal kingdom, including 140 species of 18 orders in invertebrates and 30 species of 12 orders in vertebrates, and one land plant species. Our data revealed multiple horizontal transfer events in both invertebrates and vertebrates and invasion into multiple lineages of mammals, including Chiroptera (seven species), Dasyuromorphia/Marsupialia (one species), Didelphimorphia/Marsupialia (one species), Diprotodontia/Marsupialia (two species), and Primates (one species). Phylogenetic analysis revealed a close relationship of VSs to DD37D/maT and DD34D/mariner and confirmed that VSs with the DD40D signature identified previously are not a distinct family but originated from DD41D/VS. Age analysis revealed that the most recent invasion of VSs was found in ray-finned fishes and a toad, followed by relatively young invasions in bats and marsupials, whereas VSs in mammals, jawless fishes, and lizards were mainly represented by ancient copies, suggesting old age. Phylogenetic analyses and comparison of pairwise distances between VSs and recombination-activating gene 1 (RAG1) support horizontal transfer events of VSs in vertebrates. The intact VSs from bats were nonfunctional as determined by the transposition activity assay. Some vertebrate lineages and species were identified as the hot hosts of Tc1/mariner transposons. Overall, our study presents the evolution profile of VSs and suggests that VSs play roles in diversifying and shaping the genomes of diverse animal lineages.
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Affiliation(s)
- Dan Shen
- College of Animal Science & Technology, Yangzhou University, China.,Division of Medical Biotechnology, Paul Ehrlich Institute, Langen, Germany
| | - Bo Gao
- College of Animal Science & Technology, Yangzhou University, China
| | - Csaba Miskey
- Division of Medical Biotechnology, Paul Ehrlich Institute, Langen, Germany
| | - Cai Chen
- College of Animal Science & Technology, Yangzhou University, China
| | - Yatong Sang
- College of Animal Science & Technology, Yangzhou University, China
| | - Wencheng Zong
- College of Animal Science & Technology, Yangzhou University, China
| | - Saisai Wang
- College of Animal Science & Technology, Yangzhou University, China
| | - Yali Wang
- College of Animal Science & Technology, Yangzhou University, China
| | - Xiaoyan Wang
- College of Animal Science & Technology, Yangzhou University, China
| | - Zoltán Ivics
- Division of Medical Biotechnology, Paul Ehrlich Institute, Langen, Germany
| | - Chengyi Song
- College of Animal Science & Technology, Yangzhou University, China
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11
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Puzakov MV, Puzakova LV, Cheresiz SV, Sang Y. The IS630/Tc1/mariner transposons in three ctenophore genomes. Mol Phylogenet Evol 2021; 163:107231. [PMID: 34133948 DOI: 10.1016/j.ympev.2021.107231] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 05/31/2021] [Accepted: 06/11/2021] [Indexed: 10/21/2022]
Abstract
Transposable elements (TEs) exert a significant effect on the structure and functioning of the genomes and also serve as a source of the new genes. The study of the TE diversity and evolution in different taxa is indispensable for the fundamental understanding of their roles in the genomes. IS630/Tc1/mariner (ITm) transposable elements represent the most prevalent and diverse group of DNA transposons. In this work, we studied the diversity, evolutionary dynamics and the phylogenetic relationships of the ITm transposons found in three ctenophore species: Mnemiopsis leidyi, Pleurobrachia bachei, Beroe ovata. We identified 29 ITm transposons, seven of which possess the terminal inverted repeats (TIRs) and an intact transposase, and, thus, are, presumably, active. Four other ITm transposons have the features of domesticated TEs. According to the results of the phylogenetic analysis, the ITm transposons of the ctenophores represent five groups - MLE/DD34D, TLE/DD34-38E, mosquito/DD37E, Visiror/DD41D and pogo/DDxD. Pogo/DDxD superfamily turnes out to be the most diverse and prevalent, since it accounts for more than 40% of the TEs identified. The data obtained in this research will fill the gap of knowledge of the diversity and evolution of the ITm transposons in the multicellular genomes and will lay the ground for the study of the TE effects on the evolution of the ctenophores.
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Affiliation(s)
- Mikhail V Puzakov
- A.O. Kovalevsky Institute of Biology of the Southern Seas of RAS, Nakhimov av., 2, Sevastopol 299011, Russia.
| | - Ludmila V Puzakova
- A.O. Kovalevsky Institute of Biology of the Southern Seas of RAS, Nakhimov av., 2, Sevastopol 299011, Russia
| | - Sergey V Cheresiz
- V. Zelman Institute for Medicine and Psychology, Novosibirsk State University, Pirogova st., 1, Novosibirsk 630090, Russia; State Scientific Research Institute of Physiology and Basic Medicine, P.O. Box 237, Novosibirsk 630117, Russia
| | - Yatong Sang
- College of Animal Science & Technology, Yangzhou University, Yangzhou, Jiangsu 225009, China
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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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Gao B, Zong W, Miskey C, Ullah N, Diaby M, Chen C, Wang X, Ivics Z, Song C. Intruder (DD38E), a recently evolved sibling family of DD34E/Tc1 transposons in animals. Mob DNA 2020; 11:32. [PMID: 33303022 PMCID: PMC7731502 DOI: 10.1186/s13100-020-00227-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 11/30/2020] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND A family of Tc1/mariner transposons with a characteristic DD38E triad of catalytic amino acid residues, named Intruder (IT), was previously discovered in sturgeon genomes, but their evolutionary landscapes remain largely unknown. RESULTS Here, we comprehensively investigated the evolutionary profiles of ITs, and evaluated their cut-and-paste activities in cells. ITs exhibited a narrow taxonomic distribution pattern in the animal kingdom, with invasions into two invertebrate phyla (Arthropoda and Cnidaria) and three vertebrate lineages (Actinopterygii, Agnatha, and Anura): very similar to that of the DD36E/IC family. Some animal orders and species seem to be more hospitable to Tc1/mariner transposons, one order of Amphibia and seven Actinopterygian orders are the most common orders with horizontal transfer events and have been invaded by all four families (DD38E/IT, DD35E/TR, DD36E/IC and DD37E/TRT) of Tc1/mariner transposons, and eight Actinopterygii species were identified as the major hosts of these families. Intact ITs have a total length of 1.5-1.7 kb containing a transposase gene flanked by terminal inverted repeats (TIRs). The phylogenetic tree and sequence identity showed that IT transposases were most closely related to DD34E/Tc1. ITs have been involved in multiple events of horizontal transfer in vertebrates and have invaded most lineages recently (< 5 million years ago) based on insertion age analysis. Accordingly, ITs presented high average sequence identity (86-95%) across most vertebrate species, suggesting that some are putatively active. ITs can transpose in human HeLa cells, and the transposition efficiency of consensus TIRs was higher than that of the TIRs of natural isolates. CONCLUSIONS We conclude that DD38E/IT originated from DD34E/Tc1 and can be detected in two invertebrate phyla (Arthropoda and Cnidaria), and in three vertebrate lineages (Actinopterygii, Agnatha and Anura). IT has experienced multiple HT events in animals, dominated by recent amplifications in most species and has high identity among vertebrate taxa. Our reconstructed IT transposon vector designed according to the sequence from the "cat" genome showed high cut-and-paste activity. The data suggest that IT has been acquired recently and is active in many species. This study is meaningful for understanding the evolution of the Tc1/mariner superfamily members and their hosts.
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Affiliation(s)
- Bo Gao
- College of Animal Science & Technology, Yangzhou University, 48 Wenhui East Road, Yangzhou, 225009, Jiangsu, China.,Division of Medical Biotechnology, Paul Ehrlich Institute, 63225, Langen, Germany
| | - Wencheng Zong
- College of Animal Science & Technology, Yangzhou University, 48 Wenhui East Road, Yangzhou, 225009, Jiangsu, China
| | - Csaba Miskey
- Division of Medical Biotechnology, Paul Ehrlich Institute, 63225, Langen, Germany
| | - Numan Ullah
- College of Animal Science & Technology, Yangzhou University, 48 Wenhui East Road, Yangzhou, 225009, Jiangsu, China
| | - Mohamed Diaby
- College of Animal Science & Technology, Yangzhou University, 48 Wenhui East Road, Yangzhou, 225009, Jiangsu, China
| | - Cai Chen
- College of Animal Science & Technology, Yangzhou University, 48 Wenhui East Road, Yangzhou, 225009, Jiangsu, China
| | - Xiaoyan Wang
- College of Animal Science & Technology, Yangzhou University, 48 Wenhui East Road, Yangzhou, 225009, Jiangsu, China
| | - Zoltán Ivics
- Division of Medical Biotechnology, Paul Ehrlich Institute, 63225, Langen, Germany
| | - Chengyi Song
- College of Animal Science & Technology, Yangzhou University, 48 Wenhui East Road, Yangzhou, 225009, Jiangsu, China.
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Gao B, Wang Y, Diaby M, Zong W, Shen D, Wang S, Chen C, Wang X, Song C. Evolution of pogo, a separate superfamily of IS630-Tc1-mariner transposons, revealing recurrent domestication events in vertebrates. Mob DNA 2020; 11:25. [PMID: 32742312 PMCID: PMC7386202 DOI: 10.1186/s13100-020-00220-0] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 06/26/2020] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Tc1/mariner and Zator, as two superfamilies of IS630-Tc1-mariner (ITm) group, have been well-defined. However, the molecular evolution and domestication of pogo transposons, once designated as an important family of the Tc1/mariner superfamily, are still poorly understood. RESULTS Here, phylogenetic analysis show that pogo transposases, together with Tc1/mariner, DD34E/Gambol, and Zator transposases form four distinct monophyletic clades with high bootstrap supports (> = 74%), suggesting that they are separate superfamilies of ITm group. The pogo superfamily represents high diversity with six distinct families (Passer, Tigger, pogoR, Lemi, Mover, and Fot/Fot-like) and wide distribution with an expansion spanning across all the kingdoms of eukaryotes. It shows widespread occurrences in animals and fungi, but restricted taxonomic distribution in land plants. It has invaded almost all lineages of animals-even mammals-and has been domesticated repeatedly in vertebrates, with 12 genes, including centromere-associated protein B (CENPB), CENPB DNA-binding domain containing 1 (CENPBD1), Jrk helix-turn-helix protein (JRK), JRK like (JRKL), pogo transposable element derived with KRAB domain (POGK), and with ZNF domain (POGZ), and Tigger transposable element-derived 2 to 7 (TIGD2-7), deduced as originating from this superfamily. Two of them (JRKL and TIGD2) seem to have been co-domesticated, and the others represent independent domestication events. Four genes (TIGD3, TIGD4, TIGD5, and POGZ) tend to represent ancient domestications in vertebrates, while the others only emerge in mammals and seem to be domesticated recently. Significant structural variations including target site duplication (TSD) types and the DDE triad signatures (DD29-56D) were observed for pogo transposons. Most domesticated genes are derived from the complete transposase genes; but CENPB, POGK, and POGZ are chimeric genes fused with additional functional domains. CONCLUSIONS This is the first report to systematically reveal the evolutionary profiles of the pogo transposons, suggesting that pogo and Tc1/Mariner are two separate superfamilies of ITm group, and demonstrating the repeated domestications of pogo in vertebrates. These data indicate that pogo transposons have played important roles in shaping the genome and gene evolution of fungi and animals. This study expands our understanding of the diversity of pogo transposons and updates the classification of ITm group.
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Affiliation(s)
- Bo Gao
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009 Jiangsu China
| | - Yali Wang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009 Jiangsu China
| | - Mohamed Diaby
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009 Jiangsu China
| | - Wencheng Zong
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009 Jiangsu China
| | - Dan Shen
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009 Jiangsu China
| | - Saisai Wang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009 Jiangsu China
| | - Cai Chen
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009 Jiangsu China
| | - Xiaoyan Wang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009 Jiangsu China
| | - Chengyi Song
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009 Jiangsu China
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Dupeyron M, Baril T, Bass C, Hayward A. Phylogenetic analysis of the Tc1/mariner superfamily reveals the unexplored diversity of pogo-like elements. Mob DNA 2020; 11:21. [PMID: 32612713 PMCID: PMC7325037 DOI: 10.1186/s13100-020-00212-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Accepted: 04/08/2020] [Indexed: 01/18/2023] Open
Abstract
Background Tc1/mariner transposons are widespread DNA transposable elements (TEs) that have made important contributions to the evolution of host genomic complexity in metazoans. However, the evolution and diversity of the Tc1/mariner superfamily remains poorly understood. Following recent developments in genome sequencing and the availability of a wealth of new genomes, Tc1/mariner TEs have been identified in many new taxa across the eukaryotic tree of life. To date, the majority of studies focussing on Tc1/mariner elements have considered only a single host lineage or just a small number of host lineages. Thus, much remains to be learnt about the evolution of Tc1/mariner TEs by performing analyses that consider elements that originate from across host diversity. Results We mined the non-redundant database of NCBI using BLASTp searches, with transposase sequences from a diverse set of reference Tc1/mariner elements as queries. A total of 5158 Tc1/mariner elements were retrieved and used to reconstruct evolutionary relationships within the superfamily. The resulting phylogeny is well resolved and includes several new groups of Tc1/mariner elements. In particular, we identify a new family of plant-genome restricted Tc1/mariner elements, which we call PlantMar. We also show that the pogo family is much larger and more diverse than previously appreciated, and we review evidence for a potential revision of its status to become a separate superfamily. Conclusions Our study provides an overview of Tc1-mariner phylogeny and summarises the impressive diversity of Tc1-mariner TEs among sequenced eukaryotes. Tc1/mariner TEs are successful in a wide range of eukaryotes, especially unikonts (the taxonomic supergroup containing Amoebozoa, Opisthokonta, Breviatea, and Apusomonadida). In particular, ecdysozoa, and especially arthropods, emerge as important hosts for Tc1/mariner elements (except the PlantMar family). Meanwhile, the pogo family, which is by far the largest Tc1/mariner family, also includes many elements from fungal and chordate genomes. Moreover, there is evidence of the repeated exaptation of pogo elements in vertebrates, including humans, in addition to the well-known example of CENP-B. Collectively, our findings provide a considerable advancement in understanding of Tc1/mariner elements, and more generally they suggest that much work remains to improve understanding of the diversity and evolution of DNA TEs.
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Affiliation(s)
- Mathilde Dupeyron
- Centre for Ecology and Conservation, University of Exeter, Penryn Campus, Penryn, Cornwall, TR10 9FE UK
| | - Tobias Baril
- Centre for Ecology and Conservation, University of Exeter, Penryn Campus, Penryn, Cornwall, TR10 9FE UK
| | - Chris Bass
- Centre for Ecology and Conservation, University of Exeter, Penryn Campus, Penryn, Cornwall, TR10 9FE UK
| | - Alexander Hayward
- Centre for Ecology and Conservation, University of Exeter, Penryn Campus, Penryn, Cornwall, TR10 9FE UK
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Ustyantsev K, Biryukov M, Sukhikh I, Shatskaya NV, Fet V, Blinov A, Konopatskaia I. Diversity of <i>mariner</i>-like elements in Orthoptera. Vavilovskii Zhurnal Genet Selektsii 2020. [DOI: 10.18699/vj19.581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Mariner-like elements (MLEs) are among the most widespread DNA transposable elements in eukaryotes. Insects were the first organisms in which MLEs were identified, however the diversity of MLEs in the insect order Orthoptera has not yet been addressed. In the present study, we explore the diversity of MLEs elements in 16 species of Orthoptera belonging to three infraorders, Acridoidea (Caelifera), Grylloidea (Ensifera), and Tettigoniidea (Ensifera) by combining data mined from computational analysis of sequenced degenerative PCR MLE amplicons and available Orthoptera genomic scaffolds. In total, 75 MLE lineages (Ortmar) were identified in all the studied genomes. Automatic phylogeny-based classification suggested that the current known variability of MLEs can be assigned to seven statistically well-supported phylogenetic clusters (I–VII), and the identified Orthoptera lineages were distributed among all of them. The majority of the lineages (36 out of 75) belong to cluster I; 20 belong to cluster VI; and seven, six, four, one and one lineages belong to clusters II, IV, VII, III, and V, respectively. Two of the clusters (II and IV) were composed of a single Orthoptera MLE lineage each (Ortmar37 and Ortmar45, respectively) which were distributed in the vast majority of the studied Orthoptera genomes. Finally, for 16 Orthoptera MLE lineages, horizontal transfer from the distantly related taxa belonging to other insect orders may have occurred. We believe that our study can serve as a basis for future researches on the diversity, distribution, and evolution of MLEs in species of other taxa that are still lacking the sequenced genomes.
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Affiliation(s)
| | | | - I. Sukhikh
- Institute of Cytology and Genetics, SB RAS
| | | | | | - A. Blinov
- Institute of Cytology and Genetics, SB RAS; Institute of Molecular and Cellular Biology, SB RAS
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Puzakov MV, Puzakova LV. leidyi Is a New Group of DD41D Transposons in Mnemiopsis leidyi Genome. RUSS J GENET+ 2019. [DOI: 10.1134/s1022795419070123] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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18
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Petersen M, Armisén D, Gibbs RA, Hering L, Khila A, Mayer G, Richards S, Niehuis O, Misof B. Diversity and evolution of the transposable element repertoire in arthropods with particular reference to insects. BMC Evol Biol 2019; 19:11. [PMID: 30626321 PMCID: PMC6327564 DOI: 10.1186/s12862-018-1324-9] [Citation(s) in RCA: 91] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 12/11/2018] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Transposable elements (TEs) are a major component of metazoan genomes and are associated with a variety of mechanisms that shape genome architecture and evolution. Despite the ever-growing number of insect genomes sequenced to date, our understanding of the diversity and evolution of insect TEs remains poor. RESULTS Here, we present a standardized characterization and an order-level comparison of arthropod TE repertoires, encompassing 62 insect and 11 outgroup species. The insect TE repertoire contains TEs of almost every class previously described, and in some cases even TEs previously reported only from vertebrates and plants. Additionally, we identified a large fraction of unclassifiable TEs. We found high variation in TE content, ranging from less than 6% in the antarctic midge (Diptera), the honey bee and the turnip sawfly (Hymenoptera) to more than 58% in the malaria mosquito (Diptera) and the migratory locust (Orthoptera), and a possible relationship between the content and diversity of TEs and the genome size. CONCLUSION While most insect orders exhibit a characteristic TE composition, we also observed intraordinal differences, e.g., in Diptera, Hymenoptera, and Hemiptera. Our findings shed light on common patterns and reveal lineage-specific differences in content and evolution of TEs in insects. We anticipate our study to provide the basis for future comparative research on the insect TE repertoire.
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Affiliation(s)
- Malte Petersen
- University of Bonn, Bonn, Germany
- Zoological Research Museum Alexander Koenig, Center for Molecular Biodiversity Research, Adenauerallee 160, Bonn, 53113 Germany
- Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, Frankfurt, 60325 Germany
| | - David Armisén
- Université de Lyon, Institut de Génomique Fonctionnelle de Lyon, CNRS UMR 5242, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, 46 allée d’Italie, Lyon, 69364 France
| | - Richard A. Gibbs
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, Houston, 77030 TX USA
| | - Lars Hering
- Department of Zoology, Institute of Biology, University of Kassel, Heinrich-Plett-Str. 40, Kassel, 34132 Germany
| | - Abderrahman Khila
- Université de Lyon, Institut de Génomique Fonctionnelle de Lyon, CNRS UMR 5242, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, 46 allée d’Italie, Lyon, 69364 France
| | - Georg Mayer
- Department of Zoology, Institute of Biology, University of Kassel, Heinrich-Plett-Str. 40, Kassel, 34132 Germany
| | - Stephen Richards
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, Houston, 77030 TX USA
| | - Oliver Niehuis
- Department of Evolutionary Biology and Ecology, Institute for Biology I (Zoology), University of Freiburg, Freiburg (Brsg.), 79104 Germany
| | - Bernhard Misof
- Zoological Research Museum Alexander Koenig, Center for Molecular Biodiversity Research, Adenauerallee 160, Bonn, 53113 Germany
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An Analysis of IS630/Tc1/mariner Transposons in the Genome of a Pacific Oyster, Crassostrea gigas. J Mol Evol 2018; 86:566-580. [PMID: 30283979 DOI: 10.1007/s00239-018-9868-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Accepted: 09/28/2018] [Indexed: 10/28/2022]
Abstract
Transposable elements represent the DNA fragments capable of increasing their copy number and moving within the genome. Class II mobile elements represents the DNA transposons, which transpose via excision and the subsequent reinsertion at random genomic loci. The increase of their copy number occurs only when the transposition event is coupled with the replication. IS630/Tc1/mariner DNA transposon superfamily is one of the largest and widely distributed among the Class II elements. In this work, we provide a detailed analysis of IS630/Tc1/mariner DNA transposons from the Pacific oyster, Crassostrea gigas. IS630/Tc1/mariner transposons represented in the genome of the Pacific oyster belong to four families, Tc1 (DD34E), mariner (DD34D), pogo (DDxD), and rosa (DD41D). More than a half of IS630/Tc1/mariner elements from C. gigas belong to Tc1 family. Furthermore, Mariner-31_CGi element was shown to represent a new and previously unknown family with DD37E signature. We also discovered the full-size transcripts of eight elements from Tc1, mariner, and pogo families, three of which can, presumably, retain their transposition activity.
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