1
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Antoniolli HR, Pita S, Deprá M, Valente VL. Horizontal transfer and the widespread presence of Galileo transposons in Drosophilidae (Insecta: Diptera). Genet Mol Biol 2024; 46:e20230143. [PMID: 38569056 PMCID: PMC10990002 DOI: 10.1590/1678-4685-gmb-2023-0143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 01/30/2024] [Indexed: 04/05/2024] Open
Abstract
Galileo is a transposon notoriously involved with inversions in Drosophila buzzatii by ectopic recombination. Although widespread in Drosophila, little is known about this transposon in other lineages of Drosophilidae. Here, the abundance of the canonical Galileo and its evolutionary history in Drosophilidae genomes was estimated and reconstructed across genera within its two subfamilies. Sequences of this transposon were masked in these genomes and their transposase sequences were recovered using BLASTn. Phylogenetic analyses were employed to reconstruct their evolutionary history and compare it to that of host genomes. Galileo was found in nearly all 163 species, however, only 37 harbored nearly complete transposase sequences. In the remaining, Galileo was found highly fragmented. Copies from related species were clustered, however horizontal transfer events were detected between the melanogaster and montium groups of Drosophila, and between the latter and the Lordiphosa genus. The similarity of sequences found in the virilis and willistoni groups of Drosophila was found to be a consequence of lineage sorting. Therefore, the evolution of Galileo is primarily marked by vertical transmission and long-term inactivation, mainly through the deletion of open reading frames. The latter has the potential to lead copies of this transposon to become miniature inverted-repeat transposable elements.
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Affiliation(s)
- Henrique R.M. Antoniolli
- Universidade Federal do Rio Grande do Sul (UFRGS), Laboratório de
Drosophila, Programa de Pós-Graduação em Genética e Biologia Molecular, Porto
Alegre, RS, Brazil
| | - Sebastián Pita
- Universidad de la República (UdelaR), Facultad de Ciencias, Sección
Genética Evolutiva, Montevideo, Uruguay
| | - Maríndia Deprá
- Universidade Federal do Rio Grande do Sul (UFRGS), Laboratório de
Drosophila, Programa de Pós-Graduação em Genética e Biologia Molecular, Porto
Alegre, RS, Brazil
| | - Vera L.S. Valente
- Universidade Federal do Rio Grande do Sul (UFRGS), Laboratório de
Drosophila, Programa de Pós-Graduação em Genética e Biologia Molecular, Porto
Alegre, RS, Brazil
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2
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Gao D. Introduction of Plant Transposon Annotation for Beginners. BIOLOGY 2023; 12:1468. [PMID: 38132293 PMCID: PMC10741241 DOI: 10.3390/biology12121468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 11/21/2023] [Accepted: 11/23/2023] [Indexed: 12/23/2023]
Abstract
Transposons are mobile DNA sequences that contribute large fractions of many plant genomes. They provide exclusive resources for tracking gene and genome evolution and for developing molecular tools for basic and applied research. Despite extensive efforts, it is still challenging to accurately annotate transposons, especially for beginners, as transposon prediction requires necessary expertise in both transposon biology and bioinformatics. Moreover, the complexity of plant genomes and the dynamic evolution of transposons also bring difficulties for genome-wide transposon discovery. This review summarizes the three major strategies for transposon detection including repeat-based, structure-based, and homology-based annotation, and introduces the transposon superfamilies identified in plants thus far, and some related bioinformatics resources for detecting plant transposons. Furthermore, it describes transposon classification and explains why the terms 'autonomous' and 'non-autonomous' cannot be used to classify the superfamilies of transposons. Lastly, this review also discusses how to identify misannotated transposons and improve the quality of the transposon database. This review provides helpful information about plant transposons and a beginner's guide on annotating these repetitive sequences.
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Affiliation(s)
- Dongying Gao
- Small Grains and Potato Germplasm Research Unit, USDA-ARS, Aberdeen, ID 83210, USA
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3
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Zattera ML, Bruschi DP. Transposable Elements as a Source of Novel Repetitive DNA in the Eukaryote Genome. Cells 2022; 11:cells11213373. [PMID: 36359770 PMCID: PMC9659126 DOI: 10.3390/cells11213373] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 09/23/2022] [Accepted: 09/26/2022] [Indexed: 12/02/2022] Open
Abstract
The impact of transposable elements (TEs) on the evolution of the eukaryote genome has been observed in a number of biological processes, such as the recruitment of the host’s gene expression network or the rearrangement of genome structure. However, TEs may also provide a substrate for the emergence of novel repetitive elements, which contribute to the generation of new genomic components during the course of the evolutionary process. In this review, we examine published descriptions of TEs that give rise to tandem sequences in an attempt to comprehend the relationship between TEs and the emergence of de novo satellite DNA families in eukaryotic organisms. We evaluated the intragenomic behavior of the TEs, the role of their molecular structure, and the chromosomal distribution of the paralogous copies that generate arrays of repeats as a substrate for the emergence of new repetitive elements in the genome. We highlight the involvement and importance of TEs in the eukaryote genome and its remodeling processes.
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Affiliation(s)
- Michelle Louise Zattera
- Departamento de Genética, Programa de Pós-Graduação em Genética, Setor de Ciências Biológicas, Universidade Federal do Paraná, Curitiba 81530-000, PR, Brazil
| | - Daniel Pacheco Bruschi
- Departamento de Genética, Laboratorio de Citogenética Evolutiva e Conservação Animal, Setor de Ciências Biológicas, Universidade Federal do Paraná, Curitiba 81530-000, PR, Brazil
- Correspondence:
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4
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Lata D, Coates BS, Walden KKO, Robertson HM, Miller NJ. Genome size evolution in the beetle genus Diabrotica. G3 (BETHESDA, MD.) 2022; 12:jkac052. [PMID: 35234880 PMCID: PMC8982398 DOI: 10.1093/g3journal/jkac052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 02/22/2022] [Indexed: 11/20/2022]
Abstract
Diabrocite corn rootworms are one of the most economically significant pests of maize in the United States and Europe and an emerging model for insect-plant interactions. Genome sizes of several species in the genus Diabrotica were estimated using flow cytometry along with that of Acalymma vittatum as an outgroup. Genome sizes ranged between 1.56 and 1.64 gigabase pairs and between 2.26 and 2.59 Gb, respectively, for the Diabrotica subgroups fucata and virgifera; the Acalymma vittatum genome size was around 1.65 Gb. This result indicated that a substantial increase in genome size occurred in the ancestor of the virgifera group. Further analysis of the fucata group and the virgifera group genome sequencing reads indicated that the genome size difference between the Diabrotica subgroups could be attributed to a higher content of transposable elements, mostly miniature inverted-transposable elements and gypsy-like long terminal repeat retroelements.
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Affiliation(s)
- Dimpal Lata
- Department of Biological Sciences, Illinois Institute of Technology, Chicago, IL 60616, USA
| | - Brad S Coates
- USDA-ARS, Corn Insects & Crop Genetics Research Unit, Ames, IA 50011, USA
| | - Kimberly K O Walden
- Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, IL 61820, USA
| | - Hugh M Robertson
- Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, IL 61820, USA
| | - Nicholas J Miller
- Department of Biological Sciences, Illinois Institute of Technology, Chicago, IL 60616, USA
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5
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Bertocchi NÁ, Oliveira TDD, Deprá M, Goñi B, Valente VLS. Interpopulation variation of transposable elements of the hAT superfamily in Drosophila willistoni (Diptera: Drosophilidae): in-situ approach. Genet Mol Biol 2022; 45:e20210287. [PMID: 35297941 PMCID: PMC8961557 DOI: 10.1590/1678-4685-gmb-2021-0287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 01/31/2022] [Indexed: 11/22/2022] Open
Abstract
Transposable elements are abundant and dynamic part of the genome, influencing
organisms in different ways through their presence or mobilization, or by acting
directly on pre- and post-transcriptional regulatory regions. We compared and
evaluated the presence, structure, and copy number of three hAT
superfamily transposons (hobo, BuT2, and mar)
in five strains of Drosophila willistoni
species. These D. willistoni strains are
of different geographical origins, sampled across the north-south occurrence of
this species. We used sequenced clones of the hAT elements in
fluorescence in-situ hybridizations in the polytene chromosomes
of three strains of D. willistoni. We also analyzed the
structural characteristics and number of copies of these hAT
elements in the 10 currently available sequenced genomes of the
willistoni group. We found that hobo,
BuT2, and mar were widely distributed in
D. willistoni polytene chromosomes and sequenced genomes of
the willistoni group, except for mar, which is
restricted to the subgroup willistoni. Furthermore, the
elements hobo, BuT2, and mar have different
evolutionary histories. The transposon differences among D.
willistoni strains, such as variation in the number, structure, and
chromosomal distribution of hAT transposons, could reflect the
genomic and chromosomal plasticity of D. willistoni species in
adapting to highly variable environments.
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Affiliation(s)
- Natasha Ávila Bertocchi
- Universidade Federal do Rio Grande do Sul, Programa de Pós-Graduação em Genética e Biologia Molecular, Porto Alegre, RS, Brazil
| | - Thays Duarte de Oliveira
- Universidade Federal do Rio Grande do Sul, Programa de Pós-Graduação em Biologia Animal, Porto Alegre, RS, Brazil
| | - Maríndia Deprá
- Universidade Federal do Rio Grande do Sul, Programa de Pós-Graduação em Genética e Biologia Molecular, Porto Alegre, RS, Brazil.,Universidade Federal do Rio Grande do Sul, Programa de Pós-Graduação em Biologia Animal, Porto Alegre, RS, Brazil
| | - Beatriz Goñi
- Universidad de la República, Facultad de Ciencias, Montevideo, Uruguay
| | - Vera Lúcia S Valente
- Universidade Federal do Rio Grande do Sul, Programa de Pós-Graduação em Genética e Biologia Molecular, Porto Alegre, RS, Brazil.,Universidade Federal do Rio Grande do Sul, Programa de Pós-Graduação em Biologia Animal, Porto Alegre, RS, Brazil
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6
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Bernardo LP, Mombach DM, Loreto ELS. Characterization of Herves-like transposable elements (hATs) in Drosophila species and their evolutionary scenario. INSECT MOLECULAR BIOLOGY 2019; 28:616-627. [PMID: 30793407 DOI: 10.1111/imb.12577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
A monophyletic group of Drosophila hAT transposable elements, referred to as Herves-like, was characterized and found to be present in 46% of 57 screened Drosophila species. A remarkable characteristic of these elements is the presence of a long array of minisatellite repeats (MnRs) in both subterminal extremities of the elements. The copy number of these minisatellites was highly variable between and within populations. Twenty-three strains of Drosophila willistoni, covering its geographic distribution, were screened for polymorphism in the copy number of 5' MnRs, showing a variation from 7 to 20 repeat copies. These MnRs are well conserved among Drosophila species and probably function as transposase binding sequences, as provided by short subterminal repeats in other hAT elements. Miniature inverted repeat transposable elements were found in 27% of species carrying Herves-like elements. Phylogenetic analysis showed incongruences between transposable elements and species phylogenies, suggesting that at least four horizontal transfer events have occurred.
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Affiliation(s)
- L P Bernardo
- PPG Biodiverdade Animal, Universidade Federal de Santa Maria (UFSM), Santa Maria, Brazil
| | - D M Mombach
- Department of Biochemistry and Molecular Biology, CCNE, Univeridade Federal de Santa Maria, Santa Maria, Brazil
| | - E L S Loreto
- Department of Biochemistry and Molecular Biology, CCNE, Univeridade Federal de Santa Maria, Santa Maria, Brazil
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7
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Xin Y, Ma B, Xiang Z, He N. Amplification of miniature inverted-repeat transposable elements and the associated impact on gene regulation and alternative splicing in mulberry ( Morus notabilis). Mob DNA 2019; 10:27. [PMID: 31289464 PMCID: PMC6593561 DOI: 10.1186/s13100-019-0169-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 06/17/2019] [Indexed: 12/13/2022] Open
Abstract
Background Miniature inverted-repeat transposable elements (MITEs) are common in eukaryotic genomes, and are important for genomic evolution. Results In the present study, the identification of MITEs in the mulberry genome revealed 286,122 MITE-related sequences, including 90,789 full-length elements. The amplification of mulberry MITEs and the influence of MITEs on the evolution of the mulberry genome were analyzed. The timing of MITE amplifications varied considerably among the various MITE families. Fifty-one MITE families have undergone a single round of amplification, while the other families developed from multiple amplifications. Most mulberry MITEs were inserted near genes and some could regulate gene expression through small RNAs. An analysis of transgenic plants indicated that MITE insertions can upregulate the expression of a target gene. Moreover, MITEs are frequently associated with alternative splicing events (exonizations). Conclusion The data presented herein provide insights into the generation of MITEs as well as their impact on gene regulation and evolution in mulberry. Electronic supplementary material The online version of this article (10.1186/s13100-019-0169-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Youchao Xin
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Beibei, Chongqing, 400715 China
| | - Bi Ma
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Beibei, Chongqing, 400715 China
| | - Zhonghuai Xiang
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Beibei, Chongqing, 400715 China
| | - Ningjia He
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Beibei, Chongqing, 400715 China
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8
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Chen J, Wu C, Zhang B, Cai Z, Wei L, Li Z, Li G, Guo T, Li Y, Guo W, Wang X. PiggyBac Transposon-Mediated Transgenesis in the Pacific Oyster ( Crassostrea gigas) - First Time in Mollusks. Front Physiol 2018; 9:811. [PMID: 30061837 PMCID: PMC6054966 DOI: 10.3389/fphys.2018.00811] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Accepted: 06/08/2018] [Indexed: 11/25/2022] Open
Abstract
As an effective method of transgenesis, the plasmid of PiggyBac transposon containing GFP (PiggyBac) transposon system has been widely used in various organisms but not yet in mollusks. In this work, piggyBac containing green fluorescent protein (GFP) was transferred into the Pacific oyster (Crassostrea gigas) by sperm-mediated gene transfer with or without electroporation. Fluorescent larvae were then observed and isolated under an inverted fluorescence microscope, and insertion of piggyBac was tested by polymerase chain reaction (PCR) using genomic DNA as template. Oyster larvae with green fluorescence were observed after transgenesis with or without electroporation, but electroporation increased the efficiency of sperm-mediated transgenesis. Subsequently, the recombinant piggyBac plasmid containing gGH (piggyBac-gGH) containing GFP and a growth hormone gene from orange-spotted grouper (gGH) was transferred into oysters using sperm mediation with electroporation, and fluorescent larvae were observed and isolated. The insertion of piggyBac-gGH was tested by PCR and genome walking analysis. PCR analysis indicated that piggyBac-gGH was transferred into oyster larvae; genome walking analysis further showed the detailed location where piggyBac-gGH was inserted in the oyster genome. This is the first time that piggyBac transposon-mediated transgenesis has been applied in mollusks.
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Affiliation(s)
- Jun Chen
- School of Agriculture, Ludong University, Yantai, China
| | - Changlu Wu
- School of Agriculture, Ludong University, Yantai, China
| | - Baolu Zhang
- Consultation Center, State Oceanic Administration, Beijing, China
| | - Zhongqiang Cai
- Changdao Enhancement and Experiment Station, Chinese Academy of Fishery Sciences, Yantai, China
| | - Lei Wei
- School of Agriculture, Ludong University, Yantai, China
| | - Zhuang Li
- School of Agriculture, Ludong University, Yantai, China
| | - Guangbin Li
- School of Agriculture, Ludong University, Yantai, China
| | - Ting Guo
- School of Agriculture, Ludong University, Yantai, China
| | - Yongchuan Li
- School of Agriculture, Ludong University, Yantai, China
| | - Wen Guo
- Center for Mollusc Study and Development, Marine Biology Institute of Shandong Province, Qingdao, China
| | - Xiaotong Wang
- School of Agriculture, Ludong University, Yantai, China
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9
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Amorim IC, Costa RGC, Xavier C, de Moura RDC. Characterization and chromosomal mapping of the DgmarMITE transposon in populations of Dichotomius (Luederwaldtinia) sericeus species complex (Coleoptera: Scarabaeidae). Genet Mol Biol 2018; 41:419-425. [PMID: 29870572 PMCID: PMC6082228 DOI: 10.1590/1678-4685-gmb-2017-0230] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Accepted: 11/23/2017] [Indexed: 01/01/2023] Open
Abstract
Transposable elements are dispersed repetitive DNA sequences that can move within the genome and are related to genome and chromosome evolution, adaptation, and speciation. The aim of this study was to characterize and determine the chromosomal location and accumulation of a Mariner-like element in populations of four phylogenetically related species of the Dichotomius (Luederwaldtinia) sericeus complex. Mapping of the isolated element was performed by fluorescent in situ hybridization in different populations of analyzed species. Characterization of the isolated element revealed a degenerated transposon, named DgmarMITE. This transposon is 496-bp-long, AT rich (57%), and contains 24 bp terminal inverted repeats. In situ mapping revealed presence of this element only in two out of four species analyzed. DgmarMITE sites were located in heterochromatic and euchromatic regions and varied in location and number on the karyotypes of Dichotomius (L.) gilletti and D. (L.) guaribensis across different populations. These results demonstrate differential accumulation of the DgmarMITE in genomes of these species, which is probably due to the occurrence of ectopic recombination and cross-mobilization of the element mediated by the transposase of closely related or unrelated transposable elements.
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Affiliation(s)
- Igor Costa Amorim
- Universidade de PernambucoUniversidade de PernambucoInstituto de Ciências
BiológicasLaboratório de Biodiversidade e Genética de
InsetosRecifePEBrazilLaboratório de Biodiversidade e Genética de
Insetos, Instituto de Ciências Biológicas, Universidade de Pernambuco,
Recife, PE, Brazil
- Universidade Federal de
PernambucoUniversidade Federal de
PernambucoCentro de BiociênciasDepartamento de GenéticaRecifePEBrazilDepartamento de Genética, Centro de
Biociências, Universidade Federal de Pernambuco, Recife, PE,
Brazil
| | - Rafaelle Grazielle Coelho Costa
- Universidade de PernambucoUniversidade de PernambucoInstituto de Ciências
BiológicasLaboratório de Biodiversidade e Genética de
InsetosRecifePEBrazilLaboratório de Biodiversidade e Genética de
Insetos, Instituto de Ciências Biológicas, Universidade de Pernambuco,
Recife, PE, Brazil
| | - Crislaine Xavier
- Universidade de PernambucoUniversidade de PernambucoInstituto de Ciências
BiológicasLaboratório de Biodiversidade e Genética de
InsetosRecifePEBrazilLaboratório de Biodiversidade e Genética de
Insetos, Instituto de Ciências Biológicas, Universidade de Pernambuco,
Recife, PE, Brazil
- Universidade Federal de
PernambucoUniversidade Federal de
PernambucoCentro de BiociênciasDepartamento de GenéticaRecifePEBrazilDepartamento de Genética, Centro de
Biociências, Universidade Federal de Pernambuco, Recife, PE,
Brazil
| | - Rita de Cássia de Moura
- Universidade de PernambucoUniversidade de PernambucoInstituto de Ciências
BiológicasLaboratório de Biodiversidade e Genética de
InsetosRecifePEBrazilLaboratório de Biodiversidade e Genética de
Insetos, Instituto de Ciências Biológicas, Universidade de Pernambuco,
Recife, PE, Brazil
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10
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Loreto ELS, Deprá M, Diesel JF, Panzera Y, Valente-Gaiesky VLS. Drosophila relics hobo and hobo-MITEs transposons as raw material for new regulatory networks. Genet Mol Biol 2018; 41:198-205. [PMID: 29668013 PMCID: PMC5913719 DOI: 10.1590/1678-4685-gmb-2017-0068] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Accepted: 08/01/2017] [Indexed: 12/22/2022] Open
Abstract
Hypermutable strains of Drosophila simulans have been studied
for 20 years. Several mutants were isolated and characterized, some of which had
phenotypes associated with alteration in development; for example, showing
ectopic legs with eyes being expressed in place of antennae. The causal agent of
this hypermutability is a non-autonomous hobo-related sequence
(hoboVA). Around 100 mobilizable copies of this element are
present in the D. simulans genome, and these are likely
mobilized by the autonomous and canonical hobo element. We have
shown that hoboVA has transcription factor binding sites for
the developmental genes, hunchback and
even-skipped, and that this transposon is expressed in
embryos, following the patterns of these genes. We suggest that
hobo and hobo-related elements can be
material for the emergence of new regulatory networks.
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Affiliation(s)
- Elgion L S Loreto
- Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil.,Departamento de Bioquímica e Biologia Molecular (CCNE), Universidade Federal de Santa Maria (UFSM), Santa Maria, RS, Brazil
| | - Maríndia Deprá
- Departamento de Genética, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - José F Diesel
- Departamento de Bioquímica e Biologia Molecular (CCNE), Universidade Federal de Santa Maria (UFSM), Santa Maria, RS, Brazil
| | - Yanina Panzera
- Departamento de Genetica, Universidad de la República de Uruguay (UDELAR), Montevideo, Uruguay
| | - Vera Lucia S Valente-Gaiesky
- Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil.,Departamento de Genética, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
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11
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Bertocchi NA, Torres FP, Garnero ADV, Gunski RJ, Wallau GL. Evolutionary history of the mariner element galluhop in avian genomes. Mob DNA 2017; 8:11. [PMID: 28814978 PMCID: PMC5556988 DOI: 10.1186/s13100-017-0094-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Accepted: 07/21/2017] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND Transposable elements (TEs) are highly abundant genomic parasites in eukaryote genomes. Although several genomes have been screened for TEs, so far very limited information is available regarding avian TEs and their evolutionary histories. Taking advantage of the rich genomic data available for birds, we characterized the evolutionary history of the galluhop element, originally described in Gallus gallus, through the use of several bioinformatic analyses. RESULTS galluhop homologous sequences were found in 6 of 72 genomes analyzed: 5 species of Galliformes (Gallus gallus, Meleagris gallopavo, Coturnix japonica, Colinus virginianus, Lyrurus tetrix) and one Buceritiformes (Buceros rhinoceros). The copy number ranged from 5 to 10,158, in the genomes of C. japonica and G. gallus respectively. All 6 species possessed short elements, suggesting the presence of Miniature Inverted repeats Transposable Elements (MITEs), which underwent an ancient massive amplification in the G. gallus and M. gallopavo genomes. Only 4 species showed potential MITE full-length partners, although no potential coding copies were detected. Phylogenetic analysis of reconstructed coding sequences showed that galluhop homolog sequences form a new mariner subfamily, which we termed Gallus. Inter-species and intragenomic galluhop distance analyses indicated a high identity between the consensus of B. rhinoceros and the other 5 related species, and different emergence ages of the element between the Galliformes species and B. rhinocerus, suggesting that horizontal transfer took place from Galliformes to a Buceritiformes ancestor, probably through an intermediate species. CONCLUSIONS Overall, our results showed that mariner elements have amplified to high copy numbers in some avian species, and that this transposition burst probably occurred in the common ancestor of G. gallus and M. gallopavo. In addition, although no coding sequences could be found currently, they probably existed, allowing an ancient massive MITE amplification in these 2 species. The other 4 species also have MITEs, suggesting that this new mariner family is prone to give rise to such non-autonomous derivatives. Last, our results suggest that a horizontal transfer event of a galluhop element occurred between Galliformes and Buceritiformes.
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Affiliation(s)
- Natasha Avila Bertocchi
- Programa de Pós-graduação em Ciências Biológicas, Universidade Federal do Pampa (Unipampa), São Gabriel, Rio Grande do sul 97300-000 Brazil
- Laboratório de Diversidade Genética Animal, Universidade Federal do Pampa (Unipampa), São Gabriel, Rio Grande do sul 97300-000 Brazil
| | - Fabiano Pimentel Torres
- Programa de Pós-graduação em Ciências Biológicas, Universidade Federal do Pampa (Unipampa), São Gabriel, Rio Grande do sul 97300-000 Brazil
- Laboratório de Diversidade Genética Animal, Universidade Federal do Pampa (Unipampa), São Gabriel, Rio Grande do sul 97300-000 Brazil
| | - Analía del Valle Garnero
- Programa de Pós-graduação em Ciências Biológicas, Universidade Federal do Pampa (Unipampa), São Gabriel, Rio Grande do sul 97300-000 Brazil
- Laboratório de Diversidade Genética Animal, Universidade Federal do Pampa (Unipampa), São Gabriel, Rio Grande do sul 97300-000 Brazil
| | - Ricardo José Gunski
- Programa de Pós-graduação em Ciências Biológicas, Universidade Federal do Pampa (Unipampa), São Gabriel, Rio Grande do sul 97300-000 Brazil
- Laboratório de Diversidade Genética Animal, Universidade Federal do Pampa (Unipampa), São Gabriel, Rio Grande do sul 97300-000 Brazil
| | - Gabriel Luz Wallau
- Departamento de Entomologia, Instituto Aggeu Magalhães – FIOCRUZ-CPqAM, Recife, Pernambuco Brazil
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12
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Patel S. Drivers of bacterial genomes plasticity and roles they play in pathogen virulence, persistence and drug resistance. INFECTION GENETICS AND EVOLUTION 2016; 45:151-164. [DOI: 10.1016/j.meegid.2016.08.030] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2016] [Revised: 08/26/2016] [Accepted: 08/27/2016] [Indexed: 12/11/2022]
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Zhou M, Tao G, Pi P, Zhu Y, Bai Y, Meng X. Genome-wide characterization and evolution analysis of miniature inverted-repeat transposable elements (MITEs) in moso bamboo (Phyllostachys heterocycla). PLANTA 2016; 244:775-787. [PMID: 27160169 DOI: 10.1007/s00425-016-2544-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Accepted: 05/01/2016] [Indexed: 06/05/2023]
Abstract
Moso bamboo MITEs were genome-wide identified first time, and data shows that MITEs contribute to the genomic diversity and differentiation of bamboo. Miniature inverted-repeat transposable elements (MITEs) are widespread in animals and plants. There are a large number of transposable elements in moso bamboo (Phyllostachys heterocycla var. pubescens) genome, but the genome-wide information of moso bamboo MITEs is not known yet. Here we identified 362 MITE families with a total of 489,592 MITE-related sequences, accounting for 4.74 % of the moso bamboo genome. The 362 MITE families are clustered into six known and one unknown super-families. Our analysis indicated that moso bamboo MITEs preferred to reside in or near the genes that might be involved in regulation of host gene expression. Of the seven super-families, three might undergo major expansion event twice, respectively, during 8-11 million years ago (mya) ago and 22-28 mya ago; two might experience a long expansion period from 6 to 13 mya. Almost 1/3 small RNAs might be derived from the MITE sequences. Some MITE families generate small RNAs mainly from the terminals, while others predominantly from the central region. Given the high copy number of MITEs, many siRNAs and miRNAs derived from MITE sequences and the preferential insertion of MITE into gene regions, MITEs may contribute to the genomic diversity and differentiation of bamboo.
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Affiliation(s)
- Mingbing Zhou
- The Nurturing Station for the State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, LinAn, 311300, Zhejiang Province, People's Republic of China.
| | - Guiyun Tao
- The Nurturing Station for the State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, LinAn, 311300, Zhejiang Province, People's Republic of China
| | - Peiyao Pi
- The Nurturing Station for the State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, LinAn, 311300, Zhejiang Province, People's Republic of China
| | - Yihang Zhu
- The Nurturing Station for the State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, LinAn, 311300, Zhejiang Province, People's Republic of China
| | - Youhuang Bai
- The Nurturing Station for the State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, LinAn, 311300, Zhejiang Province, People's Republic of China
| | - Xianwen Meng
- The Nurturing Station for the State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, LinAn, 311300, Zhejiang Province, People's Republic of China
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Dai S, Hou J, Long Y, Wang J, Li C, Xiao Q, Jiang X, Zou X, Zou J, Meng J. Widespread and evolutionary analysis of a MITE family Monkey King in Brassicaceae. BMC PLANT BIOLOGY 2015; 15:149. [PMID: 26084405 PMCID: PMC4471910 DOI: 10.1186/s12870-015-0490-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Accepted: 04/07/2015] [Indexed: 05/24/2023]
Abstract
BACKGROUND Miniature inverted repeat transposable elements (MITEs) are important components of eukaryotic genomes, with hundreds of families and many copies, which may play important roles in gene regulation and genome evolution. However, few studies have investigated the molecular mechanisms involved. In our previous study, a Tourist-like MITE, Monkey King, was identified from the promoter region of a flowering time gene, BnFLC.A10, in Brassica napus. Based on this MITE, the characteristics and potential roles on gene regulation of the MITE family were analyzed in Brassicaceae. RESULTS The characteristics of the Tourist-like MITE family Monkey King in Brassicaceae, including its distribution, copies and insertion sites in the genomes of major Brassicaceae species were analyzed in this study. Monkey King was actively amplified in Brassica after divergence from Arabidopsis, which was indicated by the prompt increase in copy number and by phylogenetic analysis. The genomic variations caused by Monkey King insertions, both intra- and inter-species in Brassica, were traced by PCR amplification. Genomic sequence analysis showed that most complete Monkey King elements are located in gene-rich regions, less than 3kb from genes, in both the B. rapa and A. thaliana genomes. Sixty-seven Brassica expressed sequence tags carrying Monkey King fragments were also identified from the NCBI database. Bisulfite sequencing identified specific DNA methylation of cytosine residues in the Monkey King sequence. A fragment containing putative TATA-box motifs in the MITE sequence could bind with nuclear protein(s) extracted from leaves of B. napus plants. A Monkey King-related microRNA, bna-miR6031, was identified in the microRNA database. In transgenic A. thaliana, when the Monkey King element was inserted upstream of 35S promoter, the promoter activity was weakened. CONCLUSION Monkey King, a Brassicaceae Tourist-like MITE family, has amplified relatively recently and has induced intra- and inter-species genomic variations in Brassica. Monkey King elements are most abundant in the vicinity of genes and may have a substantial effect on genome-wide gene regulation in Brassicaceae. Monkey King insertions potentially regulate gene expression and genome evolution through epigenetic modification and new regulatory motif production.
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Affiliation(s)
- Shutao Dai
- National Key Lab of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, China.
| | - Jinna Hou
- National Key Lab of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, China.
- Crop Designing Centre, Henan Academy of Agricultural Sciences, Zhenzhou, Henan, 450002, China.
| | - Yan Long
- National Key Lab of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, China.
| | - Jing Wang
- National Key Lab of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, China.
| | - Cong Li
- National Key Lab of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, China.
| | - Qinqin Xiao
- National Key Lab of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, China.
| | - Xiaoxue Jiang
- National Key Lab of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, China.
| | - Xiaoxiao Zou
- National Key Lab of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, China.
| | - Jun Zou
- National Key Lab of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, China.
| | - Jinling Meng
- National Key Lab of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, China.
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Sarilar V, Bleykasten-Grosshans C, Neuvéglise C. Evolutionary dynamics of hAT DNA transposon families in Saccharomycetaceae. Genome Biol Evol 2014; 7:172-90. [PMID: 25532815 PMCID: PMC4316626 DOI: 10.1093/gbe/evu273] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Transposable elements (TEs) are widespread in eukaryotes but uncommon in yeasts of the Saccharomycotina subphylum, in terms of both host species and genome fraction. The class II elements are especially scarce, but the hAT element Rover is a noteworthy exception that deserves further investigation. Here, we conducted a genome-wide analysis of hAT elements in 40 ascomycota. A novel family, Roamer, was found in three species, whereas Rover was detected in 15 preduplicated species from Kluyveromyces, Eremothecium, and Lachancea genera, with up to 41 copies per genome. Rover acquisition seems to have occurred by horizontal transfer in a common ancestor of these genera. The detection of remote Rover copies in Naumovozyma dairenensis and in the sole Saccharomyces cerevisiae strain AWRI1631, without synteny, suggests that two additional independent horizontal transfers took place toward these genomes. Such patchy distribution of elements prevents any anticipation of TE presence in incoming sequenced genomes, even closely related ones. The presence of both putative autonomous and defective Rover copies, as well as their diversification into five families, indicate particular dynamics of Rover elements in the Lachancea genus. Especially, we discovered the first miniature inverted-repeat transposable elements (MITEs) to be described in yeasts, together with their parental autonomous copies. Evidence of MITE insertion polymorphism among Lachancea waltii strains suggests their recent activity. Moreover, 40% of Rover copies appeared to be involved in chromosome rearrangements, showing the large structural impact of TEs on yeast genome and opening the door to further investigations to understand their functional and evolutionary consequences.
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Affiliation(s)
- Véronique Sarilar
- INRA, UMR 1319 Micalis, Jouy-en-Josas, France AgroParisTech, UMR Micalis, Jouy-en-Josas, France
| | - Claudine Bleykasten-Grosshans
- CNRS, UMR 7156, Laboratoire de Génétique Moléculaire, Génomique et Microbiologie, Université de Strasbourg, Strasbourg, France
| | - Cécile Neuvéglise
- INRA, UMR 1319 Micalis, Jouy-en-Josas, France AgroParisTech, UMR Micalis, Jouy-en-Josas, France
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16
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Xavier C, Cabral-de-Mello DC, de Moura RC. Heterochromatin and molecular characterization of DsmarMITE transposable element in the beetle Dichotomius schiffleri (Coleoptera: Scarabaeidae). Genetica 2014; 142:575-81. [DOI: 10.1007/s10709-014-9805-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Accepted: 11/26/2014] [Indexed: 11/28/2022]
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17
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Gonçalves JW, Valiati VH, Delprat A, Valente VLS, Ruiz A. Structural and sequence diversity of the transposon Galileo in the Drosophila willistoni genome. BMC Genomics 2014; 15:792. [PMID: 25218200 PMCID: PMC4168063 DOI: 10.1186/1471-2164-15-792] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2014] [Accepted: 09/09/2014] [Indexed: 01/07/2023] Open
Abstract
Background Galileo is one of three members of the P superfamily of DNA transposons. It was originally discovered in Drosophila buzzatii, in which three segregating chromosomal inversions were shown to have been generated by ectopic recombination between Galileo copies. Subsequently, Galileo was identified in six of 12 sequenced Drosophila genomes, indicating its widespread distribution within this genus. Galileo is strikingly abundant in Drosophila willistoni, a neotropical species that is highly polymorphic for chromosomal inversions, suggesting a role for this transposon in the evolution of its genome. Results We carried out a detailed characterization of all Galileo copies present in the D. willistoni genome. A total of 191 copies, including 133 with two terminal inverted repeats (TIRs), were classified according to structure in six groups. The TIRs exhibited remarkable variation in their length and structure compared to the most complete copy. Three copies showed extended TIRs due to internal tandem repeats, the insertion of other transposable elements (TEs), or the incorporation of non-TIR sequences into the TIRs. Phylogenetic analyses of the transposase (TPase)-encoding and TIR segments yielded two divergent clades, which we termed Galileo subfamilies V and W. Target-site duplications (TSDs) in D. willistoni Galileo copies were 7- or 8-bp in length, with the consensus sequence GTATTAC. Analysis of the region around the TSDs revealed a target site motif (TSM) with a 15-bp palindrome that may give rise to a stem-loop secondary structure. Conclusions There is a remarkable abundance and diversity of Galileo copies in the D. willistoni genome, although no functional copies were found. The TIRs in particular have a dynamic structure and extend in different ways, but their ends (required for transposition) are more conserved than the rest of the element. The D. willistoni genome harbors two Galileo subfamilies (V and W) that diverged ~9 million years ago and may have descended from an ancestral element in the genome. Galileo shows a significant insertion preference for a 15-bp palindromic TSM. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-792) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | - Vera L S Valente
- Programa de Pós-Graduação em Genética e Biologia Molecular, Departamento de Genética, Universidade Federal do Rio Grande do Sul (UFRGS), CP 15053, Porto Alegre, Rio Grande do Sul 91501-970, Brazil.
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18
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Wallau GL, Capy P, Loreto E, Hua-Van A. Genomic landscape and evolutionary dynamics of mariner transposable elements within the Drosophila genus. BMC Genomics 2014; 15:727. [PMID: 25163909 PMCID: PMC4161770 DOI: 10.1186/1471-2164-15-727] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2014] [Accepted: 08/01/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The mariner family of transposable elements is one of the most widespread in the Metazoa. It is subdivided into several subfamilies that do not mirror the phylogeny of these species, suggesting an ancient diversification. Previous hybridization and PCR studies allowed a partial survey of mariner diversity in the Metazoa. In this work, we used a comparative genomics approach to access the genus-wide diversity and evolution of mariner transposable elements in twenty Drosophila sequenced genomes. RESULTS We identified 36 different mariner lineages belonging to six distinct subfamilies, including a subfamily not described previously. Wide variation in lineage abundance and copy number were observed among species and among mariner lineages, suggesting continuous turn-over. Most mariner lineages are inactive and contain a high proportion of damaged copies. We showed that, in addition to substitutions that rapidly inactivate copies, internal deletion is a major mechanism contributing to element decay and the generation of non-autonomous sublineages. Hence, 23% of copies correspond to several Miniature Inverted-repeat Transposable Elements (MITE) sublineages, the first ever described in Drosophila for mariner. In the most successful MITEs, internal deletion is often associated with internal rearrangement, which sheds light on the process of MITE origin. The estimation of the transposition rates over time revealed that all lineages followed a similar progression consisting of a rapid amplification burst followed by a rapid decrease in transposition. We detected some instances of multiple or ongoing transposition bursts. Different amplification times were observed for mariner lineages shared by different species, a finding best explained by either horizontal transmission or a reactivation process. Different lineages within one species have also amplified at different times, corresponding to successive invasions. Finally, we detected a preference for insertion into short TA-rich regions, which appears to be specific to some subfamilies. CONCLUSIONS This analysis is the first comprehensive survey of this family of transposable elements at a genus scale. It provides precise measures of the different evolutionary processes that were hypothesized previously for this family based on PCR data analysis. mariner lineages were observed at almost all "life cycle" stages: recent amplification, subsequent decay and potential (re)-invasion or invasion of genomes.
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Affiliation(s)
- Gabriel Luz Wallau
- Pós-Graduaíão em Biodiversidade Animal, Universidade Federal de Santa Maria, Santa Maria, Brasil.
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19
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Rossato DO, Ludwig A, Deprá M, Loreto ELS, Ruiz A, Valente VLS. BuT2 is a member of the third major group of hAT transposons and is involved in horizontal transfer events in the genus Drosophila. Genome Biol Evol 2014; 6:352-65. [PMID: 24459285 PMCID: PMC3942097 DOI: 10.1093/gbe/evu017] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/15/2014] [Indexed: 12/24/2022] Open
Abstract
The hAT superfamily comprises a large and diverse array of DNA transposons found in all supergroups of eukaryotes. Here we characterized the Drosophila buzzatii BuT2 element and found that it harbors a five-exon gene encoding a 643-aa putatively functional transposase. A phylogeny built with 85 hAT transposases yielded, in addition to the two major groups already described, Ac and Buster, a third one comprising 20 sequences that includes BuT2, Tip100, hAT-4_BM, and RP-hAT1. This third group is here named Tip. In addition, we studied the phylogenetic distribution and evolution of BuT2 by in silico searches and molecular approaches. Our data revealed BuT2 was, most often, vertically transmitted during the evolution of genus Drosophila being lost independently in several species. Nevertheless, we propose the occurrence of three horizontal transfer events to explain its distribution and conservation among species. Another aspect of BuT2 evolution and life cycle is the presence of short related sequences, which contain similar 5' and 3' regions, including the terminal inverted repeats. These sequences that can be considered as miniature inverted repeat transposable elements probably originated by internal deletion of complete copies and show evidences of recent mobilization.
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Affiliation(s)
- Dirleane Ottonelli Rossato
- Programa de Pós-Graduação em
Ecologia, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do
Sul, Brazil
| | - Adriana Ludwig
- Laboratório de Genômica Funcional, Instituto
Carlos Chagas (ICC), Fiocruz-PR, Curitiba, Paraná, Brazil
| | - Maríndia Deprá
- Programa de Pós-Graduação em Biologia
Animal, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do
Sul, Brazil
- Departamento de Genética, Universidade Federal do
Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul, Brazil
| | - Elgion L. S. Loreto
- Programa de Pós-Graduação em
Genética e Biologia Molecular Universidade Federal do Rio Grande do Sul (UFRGS),
Porto Alegre, Rio Grande do Sul, Brazil
- Departamento de Biologia, Universidade Federal de Santa
Maria (UFSM), Santa Maria, Rio Grande do Sul, Brazil
| | - Alfredo Ruiz
- Departament de Genètica i Microbiologia, Facultat
de Biociènces, Universitat Autònoma de Barcelona, Spain
| | - Vera L. S. Valente
- Programa de Pós-Graduação em Biologia
Animal, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do
Sul, Brazil
- Departamento de Genética, Universidade Federal do
Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul, Brazil
- Programa de Pós-Graduação em
Genética e Biologia Molecular Universidade Federal do Rio Grande do Sul (UFRGS),
Porto Alegre, Rio Grande do Sul, Brazil
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20
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Rius N, Delprat A, Ruiz A. A divergent P element and its associated MITE, BuT5, generate chromosomal inversions and are widespread within the Drosophila repleta species group. Genome Biol Evol 2013; 5:1127-41. [PMID: 23682154 PMCID: PMC3698922 DOI: 10.1093/gbe/evt076] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The transposon BuT5 caused two chromosomal inversions fixed in two Drosophila species of the repleta group, D. mojavensis and D. uniseta. BuT5 copies are approximately 1-kb long, lack any coding capacity, and do not resemble any other transposable element (TE). Because of its elusive features, BuT5 has remained unclassified to date. To fully characterize BuT5, we carried out bioinformatic similarity searches in available sequenced genomes, including 21 Drosophila species. Significant hits were only recovered for D. mojavensis genome, where 48 copies were retrieved, 22 of them approximately 1-kb long. Polymerase chain reaction (PCR) and dot blot analyses on 54 Drosophila species showed that BuT5 is homogeneous in size and has a widespread distribution within the repleta group. Thus, BuT5 can be considered as a miniature inverted-repeat TE. A detailed analysis of the BuT5 hits in D. mojavensis revealed three partial copies of a transposon with ends very similar to BuT5 and a P-element-like transposase-encoding region in between. A putatively autonomous copy of this P element was isolated by PCR from D. buzzatii. This copy is 3,386-bp long and possesses a seven-exon gene coding for an 822-aa transposase. Exon–intron boundaries were confirmed by reverse transcriptase-PCR experiments. A phylogenetic tree built with insect P superfamily transposases showed that the D. buzzatii P element belongs to an early diverging lineage within the P-element family. This divergent P element is likely the master transposon mobilizing BuT5. The BuT5/P element partnership probably dates back approximately 16 Ma and is the ultimate responsible for the generation of the two chromosomal inversions in the Drosophila repleta species group.
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Affiliation(s)
- Nuria Rius
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain
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21
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Zhang HH, Shen YH, Xu HE, Liang HY, Han MJ, Zhang Z. A novel hAT element in Bombyx mori and Rhodnius prolixus: its relationship with miniature inverted repeat transposable elements (MITEs) and horizontal transfer. INSECT MOLECULAR BIOLOGY 2013; 22:584-596. [PMID: 23889491 DOI: 10.1111/imb.12047] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Comparative analysis of transposable elements (TEs) from different species can make it possible to reconstruct their history over evolutionary time. In this study, we identified a novel hAT element in Bombyx mori and Rhodnius prolixus with characteristic GGGCGGCA repeats in its subterminal region. Meanwhile, phylogenetic analysis demonstrated that the elements in these two species might represent a separate cluster of the hAT superfamily. Strikingly, a previously identified miniature inverted repeat transposable element (MITE) shared high identity with this autonomous element across the entire length, supporting the hypothesis that MITEs are derived from the internal deletion of DNA transposons. Interestingly, identity of the consensus sequences of this novel hAT element between B. mori and R. prolixus, which diverged about 370 million years ago, was as high as 96.5% over their full length (about 3.6 kb) at the nucleotide level. The patchy distribution amongst species, coupled with overall lack of intense purifying selection acting on this element, suggest that this novel hAT element might have experienced horizontal transfer between the ancestors of B. mori and R. prolixus. Our results highlight that this novel hAT element could be used as a potential tool for germline transformation of R. prolixus to control the transmission of Trypanosoma cruzi, which causes Chagas disease.
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Affiliation(s)
- H-H Zhang
- School of Life Sciences, Chongqing University, Chongqing, China
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22
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Elliott TA, Stage DE, Crease TJ, Eickbush TH. In and out of the rRNA genes: characterization of Pokey elements in the sequenced Daphnia genome. Mob DNA 2013; 4:20. [PMID: 24059783 PMCID: PMC3849761 DOI: 10.1186/1759-8753-4-20] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2013] [Accepted: 08/29/2013] [Indexed: 11/16/2022] Open
Abstract
Background Only a few transposable elements are known to exhibit site-specific insertion patterns, including the well-studied R-element retrotransposons that insert into specific sites within the multigene rDNA. The only known rDNA-specific DNA transposon, Pokey (superfamily: piggyBac) is found in the freshwater microcrustacean, Daphnia pulex. Here, we present a genome-wide analysis of Pokey based on the recently completed whole genome sequencing project for D. pulex. Results Phylogenetic analysis of Pokey elements recovered from the genome sequence revealed the presence of four lineages corresponding to two divergent autonomous families and two related lineages of non-autonomous miniature inverted repeat transposable elements (MITEs). The MITEs are also found at the same 28S rRNA gene insertion site as the Pokey elements, and appear to have arisen as deletion derivatives of autonomous elements. Several copies of the full-length Pokey elements may be capable of producing an active transposase. Surprisingly, both families of Pokey possess a series of 200 bp repeats upstream of the transposase that is derived from the rDNA intergenic spacer (IGS). The IGS sequences within the Pokey elements appear to be evolving in concert with the rDNA units. Finally, analysis of the insertion sites of Pokey elements outside of rDNA showed a target preference for sites similar to the specific sequence that is targeted within rDNA. Conclusions Based on the target site preference of Pokey elements and the concerted evolution of a segment of the element with the rDNA unit, we propose an evolutionary path by which the ancestors of Pokey elements have invaded the rDNA niche. We discuss how specificity for the rDNA unit may have evolved and how this specificity has played a role in the long-term survival of these elements in the subgenus Daphnia.
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Affiliation(s)
- Tyler A Elliott
- Department of Integrative Biology, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Deborah E Stage
- Department of Biology, University of Rochester, Rochester, NY 14627, USA.,Department of Biology, Butler County Community College, Butler, PA 16002, USA
| | - Teresa J Crease
- Department of Integrative Biology, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Thomas H Eickbush
- Department of Biology, University of Rochester, Rochester, NY 14627, USA
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23
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Fattash I, Rooke R, Wong A, Hui C, Luu T, Bhardwaj P, Yang G. Miniature inverted-repeat transposable elements: discovery, distribution, and activity. Genome 2013; 56:475-86. [PMID: 24168668 DOI: 10.1139/gen-2012-0174] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Eukaryotic organisms have dynamic genomes, with transposable elements (TEs) as a major contributing factor. Although the large autonomous TEs can significantly shape genomic structures during evolution, genomes often harbor more miniature nonautonomous TEs that can infest genomic niches where large TEs are rare. In spite of their cut-and-paste transposition mechanisms that do not inherently favor copy number increase, miniature inverted-repeat transposable elements (MITEs) are abundant in eukaryotic genomes and exist in high copy numbers. Based on the large number of MITE families revealed in previous studies, accurate annotation of MITEs, particularly in newly sequenced genomes, will identify more genomes highly rich in these elements. Novel families identified from these analyses, together with the currently known families, will further deepen our understanding of the origins, transposase sources, and dramatic amplification of these elements.
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Affiliation(s)
- Isam Fattash
- a Department of Biology, University of Toronto at Mississauga, 3359 Mississauga Road, Mississauga, ON L5L 1C6, Canada
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