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Yıldız Akkamış H, Kaya EC, Tek AL. Discovery and genome-wide characterization of a novel miniature inverted repeat transposable element reveal genome-specific distribution in Glycine. Genes Genomics 2024; 46:1271-1280. [PMID: 38676850 DOI: 10.1007/s13258-024-01519-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2024] [Accepted: 04/22/2024] [Indexed: 04/29/2024]
Abstract
BACKGROUND Miniature inverted repeat transposable elements (MITEs) are a dynamic component responsible for genome evolution. Tourist MITEs are derived from and mobilized by elements from the harbinger superfamily. OBJECTIVE In this study, a novel family of Tourist-like MITE was characterized in wild soybean species Glycine falcata. The new GftoMITE1 was initially discovered as an insertional polymorphism of the centromere-specific histone H3 (CenH3) gene in G. falcata. METHODS Using polymerase chain reaction, cloning and sequencing approaches, we showed a high number of copies of the GftoMITE1 family. Extensive bioinformatic analyses revealed the genome-level distribution and locus-specific mapping of GftoMITE1 members in Glycine species. RESULTS Our results provide the first extensive characterization of the GftoMITE1 family and contribute to the understanding of the evolution of MITEs in the Glycine genus. Genome-specific GftoMITE1 was prominent in perennial wild soybean species, but not in annual cultivated soybean (Glycine max) or its progenitor (Glycine soja). CONCLUSIONS We discuss that the GftoMITE1 family reveals a single rapid amplification in G. falcata and could have potential implications for gene regulation and soybean breeding as an efficient genetic marker for germplasm utilization in the future.
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Affiliation(s)
- Hümeyra Yıldız Akkamış
- Department of Agricultural Genetic Engineering, Ayhan Şahenk Faculty of Agricultural Sciences and Technologies, Niğde Ömer Halisdemir University, 51240, Niğde, Turkey
| | - Emir Can Kaya
- Department of Agricultural Genetic Engineering, Ayhan Şahenk Faculty of Agricultural Sciences and Technologies, Niğde Ömer Halisdemir University, 51240, Niğde, Turkey
| | - Ahmet L Tek
- Department of Agricultural Genetic Engineering, Ayhan Şahenk Faculty of Agricultural Sciences and Technologies, Niğde Ömer Halisdemir University, 51240, Niğde, Turkey.
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Lin L, Sharma A, Yu Q. Recent amplification of microsatellite-associated miniature inverted-repeat transposable elements in the pineapple genome. BMC PLANT BIOLOGY 2021; 21:424. [PMID: 34537020 PMCID: PMC8449440 DOI: 10.1186/s12870-021-03194-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 08/09/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND Miniature inverted-repeat transposable elements (MITEs) are non-autonomous DNA transposable elements that play important roles in genome organization and evolution. Genome-wide identification and characterization of MITEs provide essential information for understanding genome structure and evolution. RESULTS We performed genome-wide identification and characterization of MITEs in the pineapple genome. The top two MITE families, accounting for 29.39% of the total MITEs and 3.86% of the pineapple genome, have insertion preference in (TA) n dinucleotide microsatellite regions. We therefore named these MITEs A. comosus microsatellite-associated MITEs (Ac-mMITEs). The two Ac-mMITE families, Ac-mMITE-1 and Ac-mMITE-2, shared sequence similarity in the terminal inverted repeat (TIR) regions, suggesting that these two Ac-mMITE families might be derived from a common or closely related autonomous elements. The Ac-mMITEs are frequently clustered via adjacent insertions. Among the 21,994 full-length Ac-mMITEs, 46.1% of them were present in clusters. By analyzing the Ac-mMITEs without (TA) n microsatellite flanking sequences, we found that Ac-mMITEs were likely derived from Mutator-like DNA transposon. Ac-MITEs showed highly polymorphic insertion sites between cultivated pineapples and their wild relatives. To better understand the evolutionary history of Ac-mMITEs, we filtered and performed comparative analysis on the two distinct groups of Ac-mMITEs, microsatellite-targeting MITEs (mt-MITEs) that are flanked by dinucleotide microsatellites on both sides and mutator-like MITEs (ml-MITEs) that contain 9/10 bp TSDs. Epigenetic analysis revealed a lower level of host-induced silencing on the mt-MITEs in comparison to the ml-MITEs, which partially explained the significantly higher abundance of mt-MITEs in pineapple genome. The mt-MITEs and ml-MITEs exhibited differential insertion preference to gene-related regions and RNA-seq analysis revealed their differential influences on expression regulation of nearby genes. CONCLUSIONS Ac-mMITEs are the most abundant MITEs in the pineapple genome and they were likely derived from Mutator-like DNA transposon. Preferential insertion in (TA) n microsatellite regions of Ac-mMITEs occurred recently and is likely the result of damage-limiting strategy adapted by Ac-mMITEs during co-evolution with their host. Insertion in (TA) n microsatellite regions might also have promoted the amplification of mt-MITEs. In addition, mt-MITEs showed no or negligible impact on nearby gene expression, which may help them escape genome control and lead to their amplification.
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Affiliation(s)
- Lianyu Lin
- Texas A&M AgriLife Research Center at Dallas, Texas A&M University System, Dallas, TX, 75252, USA
- College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Anupma Sharma
- Texas A&M AgriLife Research Center at Dallas, Texas A&M University System, Dallas, TX, 75252, USA
| | - Qingyi Yu
- Texas A&M AgriLife Research Center at Dallas, Texas A&M University System, Dallas, TX, 75252, USA.
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Taylor A, Armitage AD, Handy C, Jackson AC, Hulin MT, Harrison RJ, Clarkson JP. Basal Rot of Narcissus: Understanding Pathogenicity in Fusarium oxysporum f. sp. narcissi. Front Microbiol 2019; 10:2905. [PMID: 31921077 PMCID: PMC6930931 DOI: 10.3389/fmicb.2019.02905] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Accepted: 12/02/2019] [Indexed: 12/21/2022] Open
Abstract
Fusarium oxysporum is a globally distributed soilborne fungal pathogen causing root rots, bulb rots, crown rots and vascular wilts on a range of horticultural plants. Pathogenic F. oxysporum isolates are highly host specific and are classified as formae speciales. Narcissus is an important ornamental crop and both the quality and yield of flowers and bulbs can be severely affected by a basal rot caused by F. oxysporum f. sp. narcissi (FON); 154 Fusarium isolates were obtained from different locations and Narcissus cultivars in the United Kingdom, representing a valuable resource. A subset of 30 F. oxysporum isolates were all found to be pathogenic and were therefore identified as FON. Molecular characterisation of isolates through sequencing of three housekeeping genes, suggested a monophyletic origin with little divergence. PCR detection of 14 Secreted in Xylem (SIX) genes, previously shown to be associated with pathogenicity in other F. oxysporum f. spp., revealed different complements of SIX7, SIX9, SIX10, SIX12 and SIX13 within FON isolates which may suggest a race structure. SIX gene sequences were unique to FON and SIX10 was present in all isolates, allowing for molecular identification of FON for the first time. The genome of a highly pathogenic isolate was sequenced and lineage specific (LS) regions identified which harboured putative effectors including the SIX genes. Real-time RT-PCR, showed that SIX genes and selected putative effectors were expressed in planta with many significantly upregulated during infection. This is the first study to characterise molecular variation in FON and provide an analysis of the FON genome. Identification of expressed genes potentially associated with virulence provides the basis for future functional studies and new targets for molecular diagnostics.
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Affiliation(s)
- Andrew Taylor
- Warwick Crop Centre, School of Life Sciences, University of Warwick, Warwick, United Kingdom
| | | | - Claire Handy
- Warwick Crop Centre, School of Life Sciences, University of Warwick, Warwick, United Kingdom
| | - Alison C Jackson
- Warwick Crop Centre, School of Life Sciences, University of Warwick, Warwick, United Kingdom
| | | | | | - John P Clarkson
- Warwick Crop Centre, School of Life Sciences, University of Warwick, Warwick, United Kingdom
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Spanu F, Scherm B, Camboni I, Balmas V, Pani G, Oufensou S, Macciotta N, Pasquali M, Migheli Q. FcRav2, a gene with a ROGDI domain involved in Fusarium head blight and crown rot on durum wheat caused by Fusarium culmorum. MOLECULAR PLANT PATHOLOGY 2018; 19:677-688. [PMID: 28322011 PMCID: PMC6638036 DOI: 10.1111/mpp.12551] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2016] [Revised: 03/02/2017] [Accepted: 03/13/2017] [Indexed: 06/06/2023]
Abstract
Fusarium culmorum is a soil-borne fungal pathogen which causes foot and root rot and Fusarium head blight on small-grain cereals, in particular wheat and barley. It causes significant yield and quality losses and results in the contamination of kernels with type B trichothecene mycotoxins. Our knowledge of the pathogenicity factors of this fungus is still limited. A transposon tagging approach based on the mimp1/impala double-component system has allowed us to select a mutant altered in multiple metabolic and morphological processes, trichothecene production and virulence. The flanking regions of mimp1 were used to seek homologies in the F. culmorum genome, and revealed that mimp1 had reinserted within the last exon of a gene encoding a hypothetical protein of 318 amino acids which contains a ROGDI-like leucine zipper domain, supposedly playing a protein-protein interaction or regulatory role. By functional complementation and bioinformatic analysis, we characterized the gene as the yeast Rav2 homologue, confirming the high level of divergence in multicellular fungi. Deletion of FcRav2 or its orthologous gene in F. graminearum highlighted its ability to influence a number of functions, including virulence, trichothecene type B biosynthesis, resistance to azoles and resistance to osmotic and oxidative stress. Our results indicate that the FcRav2 protein (and possibly the RAVE complex as a whole) may become a suitable target for new antifungal drug development or the plant-mediated resistance response in filamentous fungi of agricultural interest.
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Affiliation(s)
- Francesca Spanu
- Dipartimento di AgrariaUniversità degli Studi di SassariSassariI‐07100Italy
| | - Barbara Scherm
- Dipartimento di AgrariaUniversità degli Studi di SassariSassariI‐07100Italy
| | - Irene Camboni
- Dipartimento di AgrariaUniversità degli Studi di SassariSassariI‐07100Italy
| | - Virgilio Balmas
- Dipartimento di AgrariaUniversità degli Studi di SassariSassariI‐07100Italy
| | - Giovanna Pani
- Dipartimento di AgrariaUniversità degli Studi di SassariSassariI‐07100Italy
| | - Safa Oufensou
- Dipartimento di AgrariaUniversità degli Studi di SassariSassariI‐07100Italy
- Faculté des Sciences de BizerteZarzouna TN‐7000Tunisia
| | - Nicolo’ Macciotta
- Dipartimento di AgrariaUniversità degli Studi di SassariSassariI‐07100Italy
| | - Matias Pasquali
- Dipartimento di Scienze per gli Alimenti la Nutrizione, l'AmbienteUniversità di MilanoMilanoI‐20133Italy
| | - Quirico Migheli
- Dipartimento di AgrariaUniversità degli Studi di SassariSassariI‐07100Italy
- Unità di Ricerca Istituto Nazionale di Biostrutture e BiosistemiSassariI‐07100Italy
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5
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van Dam P, Rep M. The Distribution of Miniature Impala Elements and SIX Genes in the Fusarium Genus is Suggestive of Horizontal Gene Transfer. J Mol Evol 2017; 85:14-25. [PMID: 28744785 PMCID: PMC5579170 DOI: 10.1007/s00239-017-9801-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 07/07/2017] [Indexed: 12/24/2022]
Abstract
The mimp family of miniature inverted-repeat transposable elements was previously found only in genomes of Fusarium oxysporum and is contextually associated with virulence genes in this species. Through extensive comparative analysis of 83 F. oxysporum and 52 other Fusarium genomes, we uncovered the distribution of different mimp families throughout the genus. We show that (i) mimps are not exclusive to F. oxysporum; (ii) pathogenic isolates generally possess more mimps than non-pathogenic strains and (iii) two isolates of F. hostae and one F. proliferatum isolate display evidence for horizontal transfer of genetic material to or from F. oxysporum. Multiple instances of mimp elements identical to F. oxysporum mimps were encountered in the genomes of these isolates. Moreover, homologs of effector genes (SIX1, 2, 6, 7, 11 and FomAVR2) were discovered here, several with very high (97-100%) pairwise nucleotide sequence identity scores. These three strains were isolated from infected flower bulbs (Hyacinthus and Lilium spp.). Their ancestors may thus have lived in close proximity to pathogenic strains of F. oxysporum f. sp. hyacinthi and f. sp. lilii. The Fo f. sp. lycopersici SIX2 effector gene was found to be widely distributed (15/18 isolates) throughout the F. fujikuroi species complex, exhibiting a predominantly vertical inheritance pattern. These findings shed light on the potential evolutionary mechanism underlying plant-pathogenicity in Fusarium and show that interspecies horizontal gene transfer may have occurred.
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Affiliation(s)
- Peter van Dam
- Molecular Plant Pathology, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Martijn Rep
- Molecular Plant Pathology, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands.
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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: 1.0] [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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Wang L, Peng Q, Zhao J, Ren F, Zhou H, Wang W, Liao L, Owiti A, Jiang Q, Han Y. Evolutionary origin of Rosaceae-specific active non-autonomous hAT elements and their contribution to gene regulation and genomic structural variation. PLANT MOLECULAR BIOLOGY 2016; 91:179-91. [PMID: 26941188 DOI: 10.1007/s11103-016-0454-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Accepted: 02/08/2016] [Indexed: 06/05/2023]
Abstract
Transposable elements account for approximately 30 % of the Prunus genome; however, their evolutionary origin and functionality remain largely unclear. In this study, we identified a hAT transposon family, termed Moshan, in Prunus. The Moshan elements consist of three types, aMoshan, tMoshan, and mMoshan. The aMoshan and tMoshan types contain intact or truncated transposase genes, respectively, while the mMoshan type is miniature inverted-repeat transposable element (MITE). The Moshan transposons are unique to Rosaceae, and the copy numbers of different Moshan types are significantly correlated. Sequence homology analysis reveals that the mMoshan MITEs are direct deletion derivatives of the tMoshan progenitors, and one kind of mMoshan containing a MuDR-derived fragment were amplified predominately in the peach genome. The mMoshan sequences contain cis-regulatory elements that can enhance gene expression up to 100-fold. The mMoshan MITEs can serve as potential sources of micro and long noncoding RNAs. Whole-genome re-sequencing analysis indicates that mMoshan elements are highly active, and an insertion into S-haplotype-specific F-box gene was reported to cause the breakdown of self-incompatibility in sour cherry. Taken together, all these results suggest that the mMoshan elements play important roles in regulating gene expression and driving genomic structural variation in Prunus.
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Affiliation(s)
- Lu Wang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden of the Chinese Academy of Sciences, Wuhan, 430074, People's Republic of China
| | - Qian Peng
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden of the Chinese Academy of Sciences, Wuhan, 430074, People's Republic of China
- Graduate University of Chinese Academy of Sciences, 19A Yuquanlu, Beijing, 100049, People's Republic of China
| | - Jianbo Zhao
- Institute of Forestry and Pomology, Beijing Academy of Agriculture and Forestry Sciences, A12, Ruiwangfen, Beijing, 100093, People's Republic of China
| | - Fei Ren
- Institute of Forestry and Pomology, Beijing Academy of Agriculture and Forestry Sciences, A12, Ruiwangfen, Beijing, 100093, People's Republic of China
| | - Hui Zhou
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden of the Chinese Academy of Sciences, Wuhan, 430074, People's Republic of China
- Graduate University of Chinese Academy of Sciences, 19A Yuquanlu, Beijing, 100049, People's Republic of China
| | - Wei Wang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden of the Chinese Academy of Sciences, Wuhan, 430074, People's Republic of China
| | - Liao Liao
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden of the Chinese Academy of Sciences, Wuhan, 430074, People's Republic of China
- Sino-African Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074, People's Republic of China
| | - Albert Owiti
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden of the Chinese Academy of Sciences, Wuhan, 430074, People's Republic of China
- Graduate University of Chinese Academy of Sciences, 19A Yuquanlu, Beijing, 100049, People's Republic of China
| | - Quan Jiang
- Institute of Forestry and Pomology, Beijing Academy of Agriculture and Forestry Sciences, A12, Ruiwangfen, Beijing, 100093, People's Republic of China.
| | - Yuepeng Han
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden of the Chinese Academy of Sciences, Wuhan, 430074, People's Republic of China.
- Sino-African Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074, People's Republic of China.
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Sun C, Feschotte C, Wu Z, Mueller RL. DNA transposons have colonized the genome of the giant virus Pandoravirus salinus. BMC Biol 2015; 13:38. [PMID: 26067596 PMCID: PMC4495683 DOI: 10.1186/s12915-015-0145-1] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Accepted: 06/03/2015] [Indexed: 01/06/2023] Open
Abstract
Background Transposable elements are mobile DNA sequences that are widely distributed in prokaryotic and eukaryotic genomes, where they represent a major force in genome evolution. However, transposable elements have rarely been documented in viruses, and their contribution to viral genome evolution remains largely unexplored. Pandoraviruses are recently described DNA viruses with genome sizes that exceed those of some prokaryotes, rivaling parasitic eukaryotes. These large genomes appear to include substantial noncoding intergenic spaces, which provide potential locations for transposable element insertions. However, no mobile genetic elements have yet been reported in pandoravirus genomes. Results Here, we report a family of miniature inverted-repeat transposable elements (MITEs) in the Pandoravirus salinus genome, representing the first description of a virus populated with a canonical transposable element family that proliferated by transposition within the viral genome. The MITE family, which we name Submariner, includes 30 copies with all the hallmarks of MITEs: short length, terminal inverted repeats, TA target site duplication, and no coding capacity. Submariner elements show signs of transposition and are undetectable in the genome of Pandoravirus dulcis, the closest known relative Pandoravirus salinus. We identified a DNA transposon related to Submariner in the genome of Acanthamoeba castellanii, a species thought to host pandoraviruses, which contains remnants of coding sequence for a Tc1/mariner transposase. These observations suggest that the Submariner MITEs of P. salinus belong to the widespread Tc1/mariner superfamily and may have been mobilized by an amoebozoan host. Ten of the 30 MITEs in the P. salinus genome are located within coding regions of predicted genes, while others are close to genes, suggesting that these transposons may have contributed to viral genetic novelty. Conclusions Our discovery highlights the remarkable ability of DNA transposons to colonize and shape genomes from all domains of life, as well as giant viruses. Our findings continue to blur the division between viral and cellular genomes, adhering to the emerging view that the content, dynamics, and evolution of the genomes of giant viruses do not substantially differ from those of cellular organisms. Electronic supplementary material The online version of this article (doi:10.1186/s12915-015-0145-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Cheng Sun
- Department of Biology, Colorado State University, Campus Delivery 1878, Fort Collins, CO, 80523-1878, USA.
| | - Cédric Feschotte
- Department of Human Genetics, The University of Utah, Salt Lake City, UT, 84112, USA.
| | - Zhiqiang Wu
- Department of Biology, Colorado State University, Campus Delivery 1878, Fort Collins, CO, 80523-1878, USA.
| | - Rachel Lockridge Mueller
- Department of Biology, Colorado State University, Campus Delivery 1878, Fort Collins, CO, 80523-1878, USA.
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Identification, Diversity and Evolution of MITEs in the Genomes of Microsporidian Nosema Parasites. PLoS One 2015; 10:e0123170. [PMID: 25898273 PMCID: PMC4405373 DOI: 10.1371/journal.pone.0123170] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2014] [Accepted: 01/27/2015] [Indexed: 11/29/2022] Open
Abstract
Miniature inverted-repeat transposable elements (MITEs) are short, non-autonomous DNA transposons, which are widespread in most eukaryotic genomes. However, genome-wide identification, origin and evolution of MITEs remain largely obscure in microsporidia. In this study, we investigated structural features for de novo identification of MITEs in genomes of silkworm microsporidia Nosema bombycis and Nosema antheraeae, as well as a honeybee microsporidia Nosema ceranae. A total of 1490, 149 and 83 MITE-related sequences from 89, 17 and five families, respectively, were found in the genomes of the above-mentioned species. Species-specific MITEs are predominant in each genome of microsporidian Nosema, with the exception of three MITE families that were shared by N. bombycis and N. antheraeae. One or multiple rounds of amplification occurred for MITEs in N. bombycis after divergence between N. bombycis and the other two species, suggesting that the more abundant families in N. bombycis could be attributed to the recent amplification of new MITEs. Significantly, some MITEs that inserted into the homologous protein-coding region of N. bombycis were recruited as introns, indicating that gene expansion occurred during the evolution of microsporidia. NbS31 and NbS24 had polymorphisms in different geographical strains of N. bombycis, indicating that they could still be active. In addition, several small RNAs in the MITEs in N. bombycis are mainly produced from both ends of the MITEs sequence.
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Abdel Wahab H. Characterization of Egyptian <i>Botrytis cinerea</i> Isolates from Different Host Plants. ACTA ACUST UNITED AC 2015. [DOI: 10.4236/aim.2015.53017] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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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: 1.6] [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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Santana MF, Silva JCF, Mizubuti ESG, Araújo EF, Queiroz MV. Analysis of Tc1-Mariner elements in Sclerotinia sclerotiorum suggests recent activity and flexible transposases. BMC Microbiol 2014; 14:256. [PMID: 25281292 PMCID: PMC4188875 DOI: 10.1186/s12866-014-0256-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2014] [Accepted: 09/25/2014] [Indexed: 12/12/2022] Open
Abstract
Background Sclerotinia sclerotiorum is a necrotrophic fungus that is pathogenic to many plants. Genomic analysis of its revealed transposable element expansion that has strongly influenced the evolutionary trajectory of several species. Transposons from the Tc1-Mariner superfamily are thought to be ubiquitous components of fungal genomes and are generally found in low copy numbers with large numbers of deleterious mutations in their transposase coding sequence. Results This study shows that the genome of S. sclerotiorum has a large number of copies of Tc1-Mariner transposons, and in silico analysis shows evidence that they were recently active. This finding was confirmed by expressed sequence tag (EST) analysis. Fourteen new Tc1-Mariner transposon families that were distributed throughout the genome were identified, and in some cases, due to the excision/retention of introns, different transcripts were observed for the same family, which might be the result of an efficient strategy to circumvent mutations that generate premature stop codons in the RNA sequence. In addition, the presence of these introns shows that the transposase protein has a flexible coding sequence and, consequently, conformation. No evidence for RIP-like gene silencing mechanisms, which are commonly found in fungi, was found in the identified Tc1-Mariner elements, and analysis of the genomic insertion sites of these elements showed that they were widely distributed throughout the genome with some copies located near the 3′ regions of genes. In particular, EST analysis demonstrated that one of these copies was co-expressed with a gene, which showed the potential for these elements to undergo exaptation. Conclusions Fourteen novel Tc1-Mariner families were characterized. Some families had evidence of introns, which might or might not be excised depending on the family or element in question, and this finding demonstrates a possible strategy for overcoming possible mutations that generate premature stop codons in a RNA sequence. Tc1-Mariner elements likely play an important role in the structure and evolution of the S. sclerotiorum genome.
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13
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Internal deletions of transposable elements: the case of Lemi elements. Genetica 2013; 141:369-79. [PMID: 24114377 DOI: 10.1007/s10709-013-9736-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2013] [Accepted: 09/05/2013] [Indexed: 12/21/2022]
Abstract
Mobile elements using a "cut and paste" mechanism of transposition (Class II) are frequently prone to internal deletions and the question of the origin of these copies remains elusive. In this study, we looked for copies belonging to the Lemi Family (Tc1-mariner-IS630 SuperFamily) in the plant genomes, and copies within internal deletions were analyzed in detail. Lemi elements are found exclusively in Eudicots, and more than half of the copies have been deleted. All deletions occur between microhomologies (direct repeats from 2 to 13 bp). Copies less than 500 bp long, similar to MITEs, are frequent. These copies seem to result from large deletions occurring between microhomologies present within a region of 300 bp at both extremities of the element. These regions are particularly A/T rich, compared to the internal part of the element, which increases the probability of observing short direct repeats. Most of the molecular mechanisms responsible for double strand break repair are able to induce deletions between microhomologies during the repair process. This could be a quick way to reduce the population of active copies within a genome and, more generally, to reduce the overall activity of the element after it has entered a naive genome.
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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: 1.0] [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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15
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Schmidt SM, Houterman PM, Schreiver I, Ma L, Amyotte S, Chellappan B, Boeren S, Takken FLW, Rep M. MITEs in the promoters of effector genes allow prediction of novel virulence genes in Fusarium oxysporum. BMC Genomics 2013; 14:119. [PMID: 23432788 PMCID: PMC3599309 DOI: 10.1186/1471-2164-14-119] [Citation(s) in RCA: 144] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2012] [Accepted: 02/11/2013] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND The plant-pathogenic fungus Fusarium oxysporum f.sp.lycopersici (Fol) has accessory, lineage-specific (LS) chromosomes that can be transferred horizontally between strains. A single LS chromosome in the Fol4287 reference strain harbors all known Fol effector genes. Transfer of this pathogenicity chromosome confers virulence to a previously non-pathogenic recipient strain. We hypothesize that expression and evolution of effector genes is influenced by their genomic context. RESULTS To gain a better understanding of the genomic context of the effector genes, we manually curated the annotated genes on the pathogenicity chromosome and identified and classified transposable elements. Both retro- and DNA transposons are present with no particular overrepresented class. Retrotransposons appear evenly distributed over the chromosome, while DNA transposons tend to concentrate in large chromosomal subregions. In general, genes on the pathogenicity chromosome are dispersed within the repeat landscape. Effector genes are present within subregions enriched for DNA transposons. A miniature Impala (mimp) is always present in their promoters. Although promoter deletion studies of two effector gene loci did not reveal a direct function of the mimp for gene expression, we were able to use proximity to a mimp as a criterion to identify new effector gene candidates. Through xylem sap proteomics we confirmed that several of these candidates encode proteins secreted during plant infection. CONCLUSIONS Effector genes in Fol reside in characteristic subregions on a pathogenicity chromosome. Their genomic context allowed us to develop a method for the successful identification of novel effector genes. Since our approach is not based on effector gene similarity, but on unique genomic features, it can easily be extended to identify effector genes in Fo strains with different host specificities.
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Affiliation(s)
- Sarah M Schmidt
- Plant Pathology, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, the Netherlands
| | - Petra M Houterman
- Plant Pathology, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, the Netherlands
| | - Ines Schreiver
- Plant Pathology, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, the Netherlands
- Current address: Fachgebiet Medizinische Biotechnologie, Institut für Biotechnologie, Technische Universität Berlin, Gustav-Meyer-Allee 25, Berlin, Germany
| | - Lisong Ma
- Plant Pathology, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, the Netherlands
| | - Stefan Amyotte
- Department of Plant Pathology, University of Kentucky, 201F Plant Science Building, 1405 Veterans Drive, 40546-0312, Lexington, KY, USA
| | - Biju Chellappan
- Plant Pathology, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, the Netherlands
| | - Sjef Boeren
- Laboratory for Biochemistry, Wageningen University, Dreijenlaan 3, 6703HA, Wageningen, the Netherlands
| | - Frank L W Takken
- Plant Pathology, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, the Netherlands
| | - Martijn Rep
- Plant Pathology, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, the Netherlands
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Pereira JF, Almeida APMM, Cota J, Pamphile JA, Ferreira da Silva G, de Araújo EF, Gramacho KP, Brommonschenkel SH, Pereira GAG, de Queiroz MV. Boto, a class II transposon in Moniliophthora perniciosa, is the first representative of the PIF/Harbinger superfamily in a phytopathogenic fungus. Microbiology (Reading) 2013; 159:112-125. [DOI: 10.1099/mic.0.062901-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Affiliation(s)
- Jorge Fernando Pereira
- Universidade Federal de Viçosa, Departamento de Microbiologia, CEP 36571-000, Viçosa, MG, Brazil
| | | | - Júnio Cota
- Universidade Federal de Viçosa, Departamento de Microbiologia, CEP 36571-000, Viçosa, MG, Brazil
| | - João Alencar Pamphile
- Universidade Estadual de Maringá, Departamento de Biologia Celular e Genética, CEP 87020-900, Maringá, PR, Brazil
| | - Gilvan Ferreira da Silva
- Universidade Federal de Viçosa, Departamento de Microbiologia, CEP 36571-000, Viçosa, MG, Brazil
| | - Elza Fernandes de Araújo
- Universidade Federal de Viçosa, Departamento de Microbiologia, CEP 36571-000, Viçosa, MG, Brazil
| | | | | | | | - Marisa Vieira de Queiroz
- Universidade Federal de Viçosa, Departamento de Microbiologia, CEP 36571-000, Viçosa, MG, Brazil
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Spanu F, Pasquali M, Scherm B, Balmas V, Marcello A, Ortu G, Dufresne M, Hoffmann L, Daboussi MJ, Migheli Q. Transposition of the miniature inverted-repeat transposable element mimp1 in the wheat pathogen Fusarium culmorum. MOLECULAR PLANT PATHOLOGY 2012; 13:1149-1155. [PMID: 22897438 PMCID: PMC6638673 DOI: 10.1111/j.1364-3703.2012.00823.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
High-throughput methods are needed for functional genomics analysis in Fusarium culmorum, the cause of crown and foot rot on wheat and a type B trichothecene producer. Our aim was to develop and test the efficacy of a double-component system based on the ability of the impala transposase to transactivate the miniature inverted-repeat transposable element mimp1 of Fusarium oxysporum. We report, for the first time, the application of a tagging system based on a heterologous transposon and of splinkerette-polymerase chain reaction to identify mimp1 flanking regions in the filamentous fungus F. culmorum. Similar to previous observations in Fusarium graminearum, mimp1 transposes in F. culmorum by a cut-and-paste mechanism into TA dinucleotides, which are duplicated on insertion. mimp1 was reinserted in open reading frames in 16.4% (i.e. 10 of 61) of the strains analysed, probably spanning throughout the entire genome of F. culmorum. The effectiveness of the mimp1/impala double-component system for gene tagging in F. culmorum was confirmed phenotypically for a putative aurofusarin gene. This system also allowed the identification of two genes putatively involved in oxidative stress-coping capabilities in F. culmorum, as well as a sequence specific to this fungus, thus suggesting the valuable exploratory role of this tool.
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Affiliation(s)
- Francesca Spanu
- Dipartimento di Agraria - Sezione di Patologia Vegetale ed Entomologia and Centro interdisciplinare per lo sviluppo della ricerca biotecnologica e per lo studio della biodiversità della Sardegna e dell'area Mediterranea, Università degli Studi di Sassari, Via E. De Nicola 9, I-07100 Sassari, Italy
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Zhao C, Waalwijk C, de Wit PJGM, van der Lee T, Tang D. EBR1, a novel Zn(2)Cys(6) transcription factor, affects virulence and apical dominance of the hyphal tip in Fusarium graminearum. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2011; 24:1407-1418. [PMID: 21830952 DOI: 10.1094/mpmi-06-11-0158] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Zn(2)Cys(6) transcription factors are unique to fungi and have been reported to be involved in different regulatory functions. Here, we characterized EBR1 (enhanced branching 1), a novel Zn(2)Cys(6) transcription factor of Fusarium graminearum. Knocking out EBR1 in F. graminearum PH-1 caused reduction of both radial growth and virulence. The conidia of knock-out strain PH-1?ebr1 germinated faster than those of wild-type PH-1, but the conidiation of the mutant was significantly reduced. Detailed analysis showed that the reduced radial growth might be due to reduced apical dominance of the hyphal tip, leading to increased hyphal branching. Inoculation assays on wheat heads with a green fluorescent protein (GFP)-labeled PH-1?ebr1 mutant showed that it was unable to penetrate the rachis of the spikelets. Protein fusion with GFP showed that EBR1 is localized in the nucleus of both conidia and hyphae. Knocking out the orthologous gene FOXG_05408 in F. oxysporum f. sp. lycopersici caused a much weaker phenotype than the PH-1?ebr1 mutant, which may be due to the presence of multiple orthologous genes in this fungus. Transformation of FOXG_05408 into PH-1?ebr1 restored the mutant phenotype. Similar to EBR1, FOXG_05408 is localized in the nucleus of F. oxysporum f. sp. lycopersici. Possible functions of EBR1 and its relation with other fungal transcription factors are discussed.
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19
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Fleetwood DJ, Khan AK, Johnson RD, Young CA, Mittal S, Wrenn RE, Hesse U, Foster SJ, Schardl CL, Scott B. Abundant degenerate miniature inverted-repeat transposable elements in genomes of epichloid fungal endophytes of grasses. Genome Biol Evol 2011; 3:1253-64. [PMID: 21948396 PMCID: PMC3227409 DOI: 10.1093/gbe/evr098] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/20/2011] [Indexed: 12/20/2022] Open
Abstract
Miniature inverted-repeat transposable elements (MITEs) are abundant repeat elements in plant and animal genomes; however, there are few analyses of these elements in fungal genomes. Analysis of the draft genome sequence of the fungal endophyte Epichloë festucae revealed 13 MITE families that make up almost 1% of the E. festucae genome, and relics of putative autonomous parent elements were identified for three families. Sequence and DNA hybridization analyses suggest that at least some of the MITEs identified in the study were active early in the evolution of Epichloë but are not found in closely related genera. Analysis of MITE integration sites showed that these elements have a moderate integration site preference for 5' genic regions of the E. festucae genome and are particularly enriched near genes for secondary metabolism. Copies of the EFT-3m/Toru element appear to have mediated recombination events that may have abolished synthesis of two fungal alkaloids in different epichloae. This work provides insight into the potential impact of MITEs on epichloae evolution and provides a foundation for analysis in other fungal genomes.
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Affiliation(s)
- Damien J Fleetwood
- Forage Biotechnology Section, AgResearch, Palmerston North, New Zealand.
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20
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Coates BS, Kroemer JA, Sumerford DV, Hellmich RL. A novel class of miniature inverted repeat transposable elements (MITEs) that contain hitchhiking (GTCY)(n) microsatellites. INSECT MOLECULAR BIOLOGY 2011; 20:15-27. [PMID: 20977507 DOI: 10.1111/j.1365-2583.2010.01046.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
The movement of miniature inverted repeat transposable elements (MITEs) modifies genome structure and function. We describe the microsatellite-associated interspersed nuclear element 2 (MINE-2), that integrates at consensus WTTTT target sites, creates dinucleotide TT target site duplications (TSDs), and forms predicted MITE-like secondary structures; a 5' subterminal inverted repeat (SIR; AGGGTTCCGTAG) that is partially complementary to a 5' inverted repeat (IR; ACGAAGCCCT) and 3'-SIRs (TTACGGAACCCT). A (GTCY)(n) microsatellite is hitchhiking downstream of conserved 5'MINE-2 secondary structures, causing flanking sequence similarity amongst mobile microsatellite loci. Transfection of insect cell lines indicates that MITE-like secondary structures are sufficient to mediate genome integration, and provides insight into the transposition mechanism used by MINE-2s.
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Affiliation(s)
- B S Coates
- USDA-ARS, Corn Insects & Crop Genetics Research Unit, Genetics Laboratory, Iowa State University, Ames, IA 50010, USA.
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21
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Wang S, Zhang L, Meyer E, Matz MV. Characterization of a group of MITEs with unusual features from two coral genomes. PLoS One 2010; 5:e10700. [PMID: 20502527 PMCID: PMC2872659 DOI: 10.1371/journal.pone.0010700] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2010] [Accepted: 04/27/2010] [Indexed: 01/24/2023] Open
Abstract
Background Miniature inverted-repeat transposable elements (MITEs), which are common in eukaryotic genomes, are small non-coding elements that transpose by utilizing transposases encoded by autonomous transposons. Recent genome-wide analyses and cross-mobilization assays have greatly improved our knowledge on MITE proliferation, however, specific mechanisms for the origin and evolution of MITEs are still unclear. Principal Findings A group of coral MITEs called CMITE were identified from two corals, Acropora millepora and Acropora palmata. CMITEs conform to many common characteristics of MITEs, but also present several unusual features. The most unusual feature of CMITEs is conservation of the internal region, which is more conserved between MITE families than the TIRs. The origin of this internal region remains unknown, although we found one CMITE family that seems to be derived from a piggyBac-like transposon in A. millepora. CMITEs can form tandem arrays, suggesting an unconventional way for MITEs to increase copy numbers. We also describe a case in which a novel transposable element was created by a CMITE insertion event. Conclusions To our knowledge, this is the first report of identification of MITEs from coral genomes. Proliferation of CMITEs seems to be related to the transposition machinery of piggyBac-like autonomous transposons. The highly conserved internal region of CMITEs suggests a potential role for this region in their successful transposition. However, the origin of these unusual features in CMITEs remains unclear, and thus represents an intriguing topic for future investigations.
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Affiliation(s)
- Shi Wang
- Section of Integrative Biology, University of Texas at Austin, Austin, Texas, United States of America.
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22
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Coates BS, Sumerford DV, Hellmich RL, Lewis LC. A helitron-like transposon superfamily from lepidoptera disrupts (GAAA)(n) microsatellites and is responsible for flanking sequence similarity within a microsatellite family. J Mol Evol 2010; 70:275-88. [PMID: 20217059 DOI: 10.1007/s00239-010-9330-6] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2008] [Accepted: 02/17/2010] [Indexed: 12/20/2022]
Abstract
Transposable elements (TEs) are mobile DNA regions that alter host genome structure and gene expression. A novel 588 bp non-autonomous high copy number TE in the Ostrinia nubilalis genome has features in common with miniature inverted-repeat transposable elements (MITEs): high A + T content (62.3%), lack of internal protein coding sequence, and secondary structure consisting of subterminal inverted repeats (SIRs). The O. nubilalis TE has inserted at (GAAA)(n) microsatellite loci, and was named the microsatellite-associated interspersed nuclear element (MINE-1). Non-autonomous MINE-1 superfamily members also were identified downstream of (GAAA)(n) microsatellites within Bombyx mori and Pectinophora gossypiella genomes. Of 316 (GAAA)(n) microsatellites from the B. mori whole genome sequence, 201 (63.6%) have associated autonomous or non-autonomous MINE-1 elements. Autonomous B. mori MINE-1s a encode a helicase and endonuclease domain RepHel-like protein (BMHELp1) indicating their classification as Helitron-like transposons and were renamed Helitron1_BM. Transposition of MINE-1 members in Lepidoptera has resulted in the disruption of (GAAA)(n) microsatellite loci, has impacted the application of microsatellite-based genetic markers, and suggests genome sequence that flanks TT/AA dinucleotides may be required for target site recognition by RepHel endonuclease domains.
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Marini MM, Zanforlin T, Santos PC, Barros RRM, Guerra ACP, Puccia R, Felipe MSS, Brigido M, Soares CMA, Ruiz JC, Silveira JF, Cisalpino PS. Identification and characterization of Tc1/mariner-like DNA transposons in genomes of the pathogenic fungi of the Paracoccidioides species complex. BMC Genomics 2010; 11:130. [PMID: 20178623 PMCID: PMC2836289 DOI: 10.1186/1471-2164-11-130] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2009] [Accepted: 02/23/2010] [Indexed: 12/18/2022] Open
Abstract
Background Paracoccidioides brasiliensis (Eukaryota, Fungi, Ascomycota) is a thermodimorphic fungus, the etiological agent of paracoccidioidomycosis, the most important systemic mycoses in Latin America. Three isolates corresponding to distinct phylogenetic lineages of the Paracoccidioides species complex had their genomes sequenced. In this study the identification and characterization of class II transposable elements in the genomes of these fungi was carried out. Results A genomic survey for DNA transposons in the sequence assemblies of Paracoccidioides, a genus recently proposed to encompass species P. brasiliensis (harboring phylogenetic lineages S1, PS2, PS3) and P. lutzii (Pb01-like isolates), has been completed. Eight new Tc1/mariner families, referred to as Trem (Transposable element mariner), labeled A through H were identified. Elements from each family have 65-80% sequence similarity with other Tc1/mariner elements. They are flanked by 2-bp TA target site duplications and different termini. Encoded DDD-transposases, some of which have complete ORFs, indicated that they could be functionally active. The distribution of Trem elements varied between the genomic sequences characterized as belonging to P. brasiliensis (S1 and PS2) and P. lutzii. TremC and H elements would have been present in a hypothetical ancestor common to P. brasiliensis and P. lutzii, while TremA, B and F elements were either acquired by P. brasiliensis or lost by P. lutzii after speciation. Although TremD and TremE share about 70% similarity, they are specific to P. brasiliensis and P. lutzii, respectively. This suggests that these elements could either have been present in a hypothetical common ancestor and have evolved divergently after the split between P. brasiliensis and P. Lutzii, or have been independently acquired by horizontal transfer. Conclusions New families of Tc1/mariner DNA transposons in the genomic assemblies of the Paracoccidioides species complex are described. Families were distinguished based on significant BLAST identities between transposases and/or TIRs. The expansion of Trem in a putative ancestor common to the species P. brasiliensis and P. lutzii would have given origin to TremC and TremH, while other elements could have been acquired or lost after speciation had occurred. The results may contribute to our understanding of the organization and architecture of genomes in the genus Paracoccidioides.
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Affiliation(s)
- Marjorie M Marini
- Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, 31270-901 Belo Horizonte, MG, Brazil
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Hikosaka A, Kawahara A. A systematic search and classification of T2 family miniature inverted-repeat transposable elements (MITEs) in Xenopus tropicalis suggests the existence of recently active MITE subfamilies. Mol Genet Genomics 2009; 283:49-62. [PMID: 19915867 DOI: 10.1007/s00438-009-0496-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2009] [Accepted: 10/23/2009] [Indexed: 01/06/2023]
Abstract
To reveal the genome-wide aspects of Xenopus T2 family miniature inverted-repeat transposable elements (MITEs), we performed a systematic search and classification of MITEs by a newly developed procedure. A terminal sequence motif (T2-motif: TTAAAGGRR) was retrieved from the Xenopus tropicalis genome database. We then selected 51- to 1,000-bp MITE candidates framed by an inverted pair of 2 T2-motifs. The 34,398 candidates were classified into possible clusters by a novel terminal sequence (TS)-clustering method on the basis of differences in their short terminal sequences. Finally, 19,242 MITEs were classified into 16 major MITE subfamilies (TS subfamilies), 10 of which showed apparent homologies to known T2 MITE subfamilies, and the rest were novel TS subfamilies. Intra- and inter-subfamily similarities or differences were investigated by analyses of diversity in GC content, total length, and sequence alignments. Furthermore, genome-wide conservation of the inverted pair structure of subfamily-specific TS stretches and their target site sequence (TTAA) were analyzed. The results suggested that some TS subfamilies might include active or at least recently active MITEs for transposition and/or amplification, but some others might have lost such activities a long time ago. The present methodology was efficient in identifying and classifying MITEs, thereby providing information on the evolutionary dynamics of MITEs.
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Affiliation(s)
- Akira Hikosaka
- Graduate School of Integrated Arts and Sciences, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8521, Japan.
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25
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Xu J, Wang M, Zhang X, Tang F, Pan G, Zhou Z. Identification of NbME MITE families: potential molecular markers in the microsporidia Nosema bombycis. J Invertebr Pathol 2009; 103:48-52. [PMID: 19861130 DOI: 10.1016/j.jip.2009.10.011] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2009] [Revised: 10/17/2009] [Accepted: 10/22/2009] [Indexed: 01/13/2023]
Abstract
Six novel families of miniature inverted-repeat transposable elements (MITEs) were characterized in the microsporidia Nosema bombycis and were named NbMEs. The structural characteristics and the distribution of NbME copies in the N. bombycis genome were investigated, and it was found that portions of NbMEs are associated with gene sections. Potential molecular markers for various N. bombycis strains were identified in this study through utilization of the MITE-AFLP technique. Three distinct pathogenic isolates collected from different areas were distinguished, and polymorphisms were detected using the NbME5 marker, thereby establishing this NbME as a potential marker for studying isolate variation in N. bombycis.
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Affiliation(s)
- Jinshan Xu
- Laboratory of Animal Biology, Chongqing Normal University, Chongqing, China
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Benjak A, Boué S, Forneck A, Casacuberta JM. Recent amplification and impact of MITEs on the genome of grapevine (Vitis vinifera L.). Genome Biol Evol 2009; 1:75-84. [PMID: 20333179 PMCID: PMC2817404 DOI: 10.1093/gbe/evp009] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/15/2009] [Indexed: 01/07/2023] Open
Abstract
Miniature inverted-repeat transposable elements (MITEs) are a particular type of defective class II transposons present in genomes as highly homogeneous populations of small elements. Their high copy number and close association to genes make their potential impact on gene evolution particularly relevant. Here, we present a detailed analysis of the MITE families directly related to grapevine "cut-and-paste" transposons. Our results show that grapevine MITEs have transduplicated and amplified genomic sequences, including gene sequences and fragments of other mobile elements. Our results also show that although some of the MITE families were already present in the ancestor of the European and American Vitis wild species, they have been amplified and have been actively transposing accompanying grapevine domestication and breeding. We show that MITEs are abundant in grapevine and some of them are frequently inserted within the untranslated regions of grapevine genes. MITE insertions are highly polymorphic among grapevine cultivars, which frequently generate transcript variability. The data presented here show that MITEs have greatly contributed to the grapevine genetic diversity which has been used for grapevine domestication and breeding.
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Affiliation(s)
- Andrej Benjak
- Department of Plant Molecular Genetics, Center for Research in Agricultural Genomics (Consejo Superior Investigaciones Científicas-Institut de Recerca I Tecnologia Agrícola-Universitat Autònoma de Barcelona), Barcelona, Spain
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27
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Coates BS, Sumerford DV, Hellmich RL, Lewis LC. Repetitive genome elements in a European corn borer, Ostrinia nubilalis, bacterial artificial chromosome library were indicated by bacterial artificial chromosome end sequencing and development of sequence tag site markers: implications for lepidopteran genomic research. Genome 2009; 52:57-67. [PMID: 19132072 DOI: 10.1139/g08-104] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The European corn borer, Ostrinia nubilalis, is a serious pest of food, fiber, and biofuel crops in Europe, North America, and Asia and a model system for insect olfaction and speciation. A bacterial artificial chromosome library constructed for O. nubilalis contains 36 864 clones with an estimated average insert size of >or=120 kb and genome coverage of 8.8-fold. Screening OnB1 clones comprising approximately 2.76 genome equivalents determined the physical position of 24 sequence tag site markers, including markers linked to ecologically important and Bacillus thuringiensis toxin resistance traits. OnB1 bacterial artificial chromosome end sequence reads (GenBank dbGSS accessions ET217010 to ET217273) showed homology to annotated genes or expressed sequence tags and identified repetitive genome elements, O. nubilalis miniature subterminal inverted repeat transposable elements (OnMITE01 and OnMITE02), and ezi-like long interspersed nuclear elements. Mobility of OnMITE01 was demonstrated by the presence or absence in O. nubilalis of introns at two different loci. A (GTCT)n tetranucleotide repeat at the 5' ends of OnMITE01 and OnMITE02 are evidence for transposon-mediated movement of lepidopteran microsatellite loci. The number of repetitive elements in lepidopteran genomes will affect genome assembly and marker development. Single-locus sequence tag site markers described here have downstream application for integration within linkage maps and comparative genomic studies.
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Affiliation(s)
- Brad S Coates
- USDA-ARS, Corn Insects and Crop Genetics Research Unit, Genetics Laboratory, Iowa State University, Ames, IA 50011, USA.
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28
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Bergemann M, Lespinet O, M'Barek SB, Daboussi MJ, Dufresne M. Genome-wide analysis of the Fusarium oxysporum mimp family of MITEs and mobilization of both native and de novo created mimps. J Mol Evol 2009; 67:631-42. [PMID: 18982380 DOI: 10.1007/s00239-008-9164-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2008] [Accepted: 08/28/2008] [Indexed: 01/15/2023]
Abstract
We have performed a genome-wide analysis of the mimp family of miniature inverted-repeat transposable elements, taking advantage of the recent release of the F. oxysporum genome sequence. Using different approaches, we detected 103 mimp elements, corresponding to 75 nonredundant copies, half of which are located on a single small chromosome. Phylogenetic analysis identified at least six subfamilies, all remarkably homogeneous in size and sequence. Based on high sequence identity in the terminal inverted repeats (TIRs), mimp elements were connected to different impala members. To gain insights into the mechanisms at the origin and amplification of mimps, we studied the potential of impala to cross-mobilize different mimps, native but also created de novo by inserting a short DNA segment between two TIRs. Our results show that TIR sequences are the main requirement for mobilization but that additional parameters in the internal region are likely to influence transposition efficiency. Finally, we show that integration site preference of native versus newly transposed mimps greatly varies in the host genomes used in this study.
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Affiliation(s)
- Mara Bergemann
- Institut de Génétique et Microbiologie, Université Paris-Sud 11, CNRS, UMR8621, 91405 Orsay, France
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29
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Chen Y, Zhou F, Li G, Xu Y. MUST: A system for identification of miniature inverted-repeat transposable elements and applications to Anabaena variabilis and Haloquadratum walsbyi. Gene 2009; 436:1-7. [DOI: 10.1016/j.gene.2009.01.019] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2008] [Revised: 01/23/2009] [Accepted: 01/24/2009] [Indexed: 01/30/2023]
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30
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López-Berges MS, DI Pietro A, Daboussi MJ, Wahab HA, Vasnier C, Roncero MIG, Dufresne M, Hera C. Identification of virulence genes in Fusarium oxysporum f. sp. lycopersici by large-scale transposon tagging. MOLECULAR PLANT PATHOLOGY 2009; 10:95-107. [PMID: 19161356 PMCID: PMC6640436 DOI: 10.1111/j.1364-3703.2008.00512.x] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Forward genetic screens are efficient tools for the dissection of complex biological processes, such as fungal pathogenicity. A transposon tagging system was developed in the vascular wilt fungus Fusarium oxysporum f. sp. lycopersici by inserting the novel modified impala element imp160::gfp upstream of the Aspergillus nidulans niaD gene, followed by transactivation with a constitutively expressed transposase. A collection of 2072 Nia(+) revertants was obtained from reporter strain T12 and screened for alterations in virulence, using a rapid assay for invasive growth on apple slices. Seven strains exhibited reduced virulence on both apple slices and intact tomato plants. Five of these were true revertants showing the re-insertion of imp160::gfp within or upstream of predicted coding regions, whereas the other two showed either excision without re-insertion or no excision. Linkage between imp160::gfp insertion and virulence phenotype was determined in four transposon-tagged loci using targeted deletion in the wild-type strain. Knockout mutants in one of the genes, FOXG_00016, displayed significantly reduced virulence, and complementation of the original revertant with the wild-type FOXG_00016 allele fully restored virulence. FOXG_00016 has homology to the velvet gene family of A. nidulans. The high rate of untagged virulence mutations in the T12 reporter strain appears to be associated with increased genetic instability, possibly as a result of the transactivation of endogenous transposable elements by the constitutively expressed transposase.
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Affiliation(s)
- Manuel Sánchez López-Berges
- Departamento de Genética, Universidad de Córdoba, Campus Universitario de Rabanales, Edif C5, 14071 Córdoba, Spain
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31
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Dufresne M, Lee TVD, M’Barek SB, Xu X, Zhang X, Liu T, Waalwijk C, Zhang W, Kema GH, Daboussi MJ. Transposon-tagging identifies novel pathogenicity genes in Fusarium graminearum. Fungal Genet Biol 2008; 45:1552-61. [DOI: 10.1016/j.fgb.2008.09.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2008] [Revised: 07/31/2008] [Accepted: 09/03/2008] [Indexed: 01/14/2023]
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Different strategies to persist: the pogo-like Lemi1 transposon produces miniature inverted-repeat transposable elements or typical defective elements in different plant genomes. Genetics 2008; 180:83-92. [PMID: 18757929 DOI: 10.1534/genetics.108.089615] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Miniature inverted-repeat transposable elements (MITEs) are a particular type of defective class II elements present in genomes as high-copy-number populations of small and highly homogeneous elements. While virtually all class II transposon families contain non-autonomous defective transposon copies, only a subset of them have a related MITE family. At present it is not known in which circumstances MITEs are generated instead of typical class II defective transposons. The ability to produce MITEs could be an exclusive characteristic of particular transposases, could be related to a particular structure of certain defective class II elements, or could be the consequence of particular constraints imposed by certain host genomes on transposon populations. We describe here a new family of pogo-like transposons from Medicago truncatula closely related to the Arabidopsis Lemi1 element that we have named MtLemi1. In contrast to the Arabidopsis Lemi1, present as a single-copy element and associated with hundreds of related Emigrant MITEs, MtLemi1 has attained >30 copies and has not generated MITEs. This shows that a particular transposon can adopt completely different strategies to colonize genomes. The comparison of AtLemi1 and MtLemi1 reveals transposase-specific domains and possible regulatory sequences that could be linked to the ability to produce MITEs.
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Miskey C, Papp B, Mátés L, Sinzelle L, Keller H, Izsvák Z, Ivics Z. The ancient mariner sails again: transposition of the human Hsmar1 element by a reconstructed transposase and activities of the SETMAR protein on transposon ends. Mol Cell Biol 2007; 27:4589-600. [PMID: 17403897 PMCID: PMC1900042 DOI: 10.1128/mcb.02027-06] [Citation(s) in RCA: 104] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Hsmar1, one of the two subfamilies of mariner transposons in humans, is an ancient element that entered the primate genome lineage approximately 50 million years ago. Although Hsmar1 elements are inactive due to mutational damage, one particular copy of the transposase gene has apparently been under selection. This transposase coding region is part of the SETMAR gene, in which a histone methylatransferase SET domain is fused to an Hsmar1 transposase domain. A phylogenetic approach was taken to reconstruct the ancestral Hsmar1 transposase gene, which we named Hsmar1-Ra. The Hsmar1-Ra transposase efficiently mobilizes Hsmar1 transposons by a cut-and-paste mechanism in human cells and zebra fish embryos. Hsmar1-Ra can also mobilize short inverted-repeat transposable elements (MITEs) related to Hsmar1 (MiHsmar1), thereby establishing a functional relationship between an Hsmar1 transposase source and these MITEs. MiHsmar1 excision is 2 orders of magnitude more efficient than that of long elements, thus providing an explanation for their high copy numbers. We show that the SETMAR protein binds and introduces single-strand nicks into Hsmar1 inverted-repeat sequences in vitro. Pathway choices for DNA break repair were found to be characteristically different in response to transposon cleavage mediated by Hsmar1-Ra and SETMAR in vivo. Whereas nonhomologous end joining plays a dominant role in repairing excision sites generated by the Hsmar1-Ra transposase, DNA repair following cleavage by SETMAR predominantly follows a homology-dependent pathway. The novel transposon system can be a useful tool for genome manipulations in vertebrates and for investigations into the transpositional dynamics and the contributions of these elements to primate genome evolution.
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Affiliation(s)
- Csaba Miskey
- Max Delbrück Center for Molecular Medicine, Robert Rössle Str 10, Berlin, Germany
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