Miniature inverted-repeat transposable elements: discovery, distribution, and activity

Fattash, Isam; Rooke, Rebecca; Wong, Amy P.; Hui, Caleb; Luu, Tina; Bhardwaj, Priyanka; Yang, Guojun

doi:10.1139/gen-2012-0174

Cited by 84 publications

(79 citation statements)

References 167 publications

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“…These shorter elements showed all the characteristics of MITEs [19] and amplified successfully in G. gallus and M. gallopavo, composing the large majority of galluhop copies found in these genomes (97.7% in G. gallus and 98.4% in M. gallopavo genomes). C. virginianus and L. tetrix also showed amplification of MITEs on a smaller scale, and C. japonica and B. rhinocerus possessed only MITEs elements and no trace of their possible autonomous counterparts (Fig.…”

Section: Results and Discussion Galluhop Homologs In Bird Genomesmentioning

confidence: 98%

“…Internally deleted non-autonomous elements originating from Class II transposons are known as Miniature Inverted-repeat Transposable Elements (MITEs) [2]. These elements possess deletions or a degenerated coding region, but preserved Terminal Inverted Repeats (TIRs) which can be recognized by functional transposases [18,19]. MITEs have been associated with several Class II superfamilies such as hAT, P and Tc1/mariner [20][21][22].…”

Section: Introductionmentioning

confidence: 99%

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Evolutionary history of the mariner element galluhop in avian genomes

et al. 2017

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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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Section: Results and Discussion Galluhop Homologs In Bird Genomesmentioning

confidence: 98%

Section: Introductionmentioning

confidence: 99%

Evolutionary history of the mariner element galluhop in avian genomes

et al. 2017

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“…The internal sequences of MITEs have sequence diversity, due to the influence of unrelated autonomous TEs during transposition (Sampath et al 2013;Yaakov and Kashkush 2012). Unlike TRIMs and SINEs, transposition of MITEs occurs by cut-and-paste mechanisms; and MITEs can be amplified in the genome by abortive gap repair, bursts of amplification, or as yet unknown mechanisms under stress (Casacuberta 2013;Fattash et al 2013).…”

Section: Characteristics and Distribution Of Mitesmentioning

confidence: 99%

“…MITEs were first identified in the maize genome, and later in various other plant and animal genomes Wessler 1992, 1994;Feschotte et al 2002). So far, seven MITE superfamilies have been identified in plants, although 15 superfamilies of DNA transposons have been reported (Fattash et al 2013). MITEs comprise two major families, namely Stowaway-like (with TA as the TSD), and Touristlike (with TAA as the TSD), as well as several other minor families, including hAT-like (with 5, 6, or 8 bp TSDs), MULE (with 9-10 bp TSDs), and En/Spm (3-bp TSDs) MITEs (Oki et al 2008).…”

Section: Characteristics and Distribution Of Mitesmentioning

confidence: 99%

Miniature Inverted-repeat Transposable Elements (MITEs) as Valuable Genomic Resources for the Evolution and Breeding of Brassica Crops

Sampath¹,

Yang²

2014

Plant Breed. Biotech.

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This is an Open-Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. ABSTRACT Transposable elements (TEs) play important roles in structural and functional diversification, genome enlargement, and speciation in plant genome. Their derivatives or small non-autonomous TEs play important roles in the alteration of homologous genes by epigenetic control or structural modification. The miniature inverted-repeat transposable element (MITE) is one of the representative non-autonomous class II TEs. MITEs include high copy members that are widely distributed and in close association with genic regions, which make MITEs useful targets and resources for in-depth understanding of genome evolution, as well as practical applications in molecular breeding. Here, we discuss the important features of MITEs, such as the identification tools of a novel MITE family, structural characterization, distribution pattern analysis, and impact on evolution in highly duplicated Brassica genome. We show the characteristics, copy numbers, and distribution patterns of 20 novel MITE families, and represent their putative roles in the evolution of the triplicated Brassica genome. We also introduce our MITE database, and discuss the utility of MITEs for developing MITE-derived markers that are useful for molecular breeding of Brassica crops.

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“…DNA polymorphisms are used to identify molecular markers for important agronomic traits controlled by single gene or quantitative trait loci (Monden et al 2009;Kalendar et al 2011;Fattash et al 2013). TD is a modified AFLP method which target the transposon to detect TE insertion polymorphisms (Casa et al 2000).…”

Section: Introductionmentioning

confidence: 99%

Next-Generation Sequencing Based Transposon Display to Detect High-Throughput Insertion Polymorphism Markers in Brassica

Perumal¹,

Waminal²,

Lee³

et al. 2016

Plant Breed. Biotech.

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This is an Open-Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. Crop Biotechnology Institute/GreenBio Science and Technology, Seoul National University, Pyeongchang 25354, Korea ABSTRACT Miniature transposable elements (mTEs) such as miniature inverted-repeat transposable element (MITE), terminal repeat retrotransposon in miniature, and short interspersed element are exquisite sources for marker development. mTEs are short, non-autonomous and stably inherited. The high-copy members are widely distributed into the gene rich euchromatic regions. Here, we conducted a modified transposon display (TD) for a high-copy MITE family, BraSto-2 (Bs2). The Bs2-specific primers derived from conserved sequences of Bs2 members as well as MseI adapter primers were used for polymerase chain reaction (PCR) in two Brassica rapa accessions, 'Chiifu' and 'Kenshin'. The pooled PCR products were sequenced by Illumina sequencing platform instead of high-resolution gel electrophoresis. Subsequent in silico-based insertion polymorphism (IP) analysis (next-generation sequencing [NGS]-based Bs2 transposon display) was conducted, which generated more than 99 putative polymorphic insertion sites between 'Chiifu' and 'Kenshin'. Among 90 successful PCR amplification, 34 showed Bs2 IP (IP-Bs2) between 'Chiifu' and 'Kenshin' accessions, 27 and seven 'Chiifu'-and 'Kenshin'-unique insertions, respectively. When the 90 IP-Bs2 primer sets were applied to 10 Brassica accessions, including four additional B. rapa and B. oleracea accessions, 69 (76%) showed insertion olymorphism among accessions. The IP-Bs2 were evenly distributed through all the chromosomes and provide rich polymorphism among various B. rapa and B. oleracea accessions demonstrating the usefulness of these markers for various genetic diversity and molecular breeding studies in Brassica. In addition, NGS-based TD will be applicable to various high copy transposable elements family for high throughput and rapid polymorphic marker development which will be helpful for efficient plant genomics and breeding purposes.

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Miniature inverted-repeat transposable elements: discovery, distribution, and activity

Cited by 84 publications

References 167 publications

Evolutionary history of the mariner element galluhop in avian genomes

Evolutionary history of the mariner element galluhop in avian genomes

Miniature Inverted-repeat Transposable Elements (MITEs) as Valuable Genomic Resources for the Evolution and Breeding of Brassica Crops

Next-Generation Sequencing Based Transposon Display to Detect High-Throughput Insertion Polymorphism Markers in Brassica

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