Recent transposition activity of Xenopus T2 family miniature inverted-repeat transposable elements

Hikosaka, Akira; Nishimura, Kazuki; Hikosaka-Katayama, Tomoe; Kawahara, Akira

doi:10.1007/s00438-010-0599-3

Cited by 7 publications

(8 citation statements)

References 22 publications

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“…Accordingly, the groupings of sequences in the network, represented by large circles, indicate that the sequences are identical ; therefore, these sequences are very recent and have not had sufficient time to diverge. Similar events have been reported for other transposable elements (Yang et Konovalov et al, 2010 ;Lerat, 2010) and MITE-like sequences in different organisms (Jiang et al, 2003 ;Chen et al, 2008;Zhou et al, 2008 ;Han et al, 2010 ;Hikosaka et al, 2011). This recent origin is also supported by the average time of origin of the insertions of each subfamily, 155 000 years (msechBari1) and 127 000 years (msechBari2).…”

Section: Resultssupporting

confidence: 82%

“…Descriptions in other organisms, such as bacteria (Chen et al, 2008), cyanobacteria , fungi (Xu et al, 2010), silkworms (Han et al, 2010), fish (de Boer et al, 2007) and amphibians (Hikosaka et al, 2011) are also found in the literature, but few occurrences have been reported in the Drosophila genus (Tudor et al, 1992 ;Miller et al, 2000 ;Ortiz et al, 2010). Although numerous MITEs have been identified, the association with autonomous elements is often absent.…”

Section: Introductionmentioning

confidence: 98%

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msechBari, a new MITE-like element inDrosophila sechelliarelated to theBaritransposon

Dias

Carareto

2011

Genet. Res.

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SummaryA few occurrences of miniature inverted-repeat transposable elements (MITEs) have been reported in species of the genus Drosophila. Here, we describe msechBari, a MITE-like element in Drosophila sechellia. The element is short, approximately 90 bp in length, AT-rich and occurs in association with, or close to, genes, characteristics that are typical for MITEs. The identification was performed in silico using the sequenced genome of D. sechellia and confirmed in a laboratory strain. This short element is related to the Bari_DM transposon of Drosophila melanogaster, having terminal inverted repeats (TIRs) of a similar length and a high identity with the full-length Bari_DM element. The estimated recent origin of the element and the homogeneity observed between copies found in the genome suggests that msechBari could be active in D. sechellia.

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Section: Resultssupporting

confidence: 82%

Section: Introductionmentioning

confidence: 98%

msechBari, a new MITE-like element inDrosophila sechelliarelated to theBaritransposon

Dias

Carareto

2011

Genet. Res.

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“…Both subfamilies include highly homogeneous ('young') members and show a high conservation rate of the target site duplication sequence despite such an old origin. We have also provided evidence for intraspecific T2-A1 and T2-C insertion polymorphisms [Hikosaka et al, 2011]. These data suggest that these subfamilies have been actively transposing for more than 50 million years.…”

supporting

confidence: 54%

“…Xenopus is an interesting organism because its genome carries an exceptionally high number of DNA transposons [Hellsten et al, 2010], and some are extremely long-lived and recently active [Hikosaka et al, , 2011Hikosaka and Kawahara, 2010]. T2-MITE includes at least 2 such active subfamilies: T2-A1 and T2-C.…”

Section: Discussionmentioning

confidence: 99%

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Distribution of the T2-MITE Family Transposons in the <b><i>Xenopus (Silurana) tropicalis </i></b>Genome

Hikosaka

Uno²,

Matsuda³

2015

Cytogenet Genome Res

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The T2 family of miniature inverted-repeat transposable elements (T2-MITE) is a prevalent MITE family found in both Xenopus(Silurana) tropicalis and X. laevis. Some subfamilies, particularly T2-A1 and T2-C, may have originated prior to the diversification of the 2 Xenopus lineages and currently include active members in X. tropicalis, whereas another subfamily, T2-E, may have lost its transposition activity even earlier. The distribution of each T2-MITE subfamily in X. tropicalis was investigated and compared to evaluate the evolutionary dynamics of the T2-MITE subfamilies. The subfamilies showed differences in chromosomal distribution, uniformity of insertion density on scaffolds, ratios of upstream to downstream insertions with respect to genes, and their distance from genes. Among these, the T2-C subfamily was interesting because it was frequently inserted upstream and close to genes and because genes with close insertions of this subfamily showed high correlations in spatial expression patterns. This unique distribution and long-lived transposition activity may reflect a mutual relationship evolved between this subfamily and the host.

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Evolutionary genomics of miniature inverted-repeat transposable elements (MITEs) in Brassica

2015

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Miniature inverted-repeat transposable elements (MITEs) are truncated derivatives of autonomous DNA transposons, and are dispersed abundantly in most eukaryotic genomes. We aimed to characterize various MITEs families in Brassica in terms of their presence, sequence characteristics and evolutionary activity. Dot plot analyses involving comparison of homoeologous bacterial artificial chromosome (BAC) sequences allowed identification of 15 novel families of mobile MITEs. Of which, 5 were Stowaway-like with TA Target Site Duplications (TSDs), 4 Tourist-like with TAA/TTA TSDs, 5 Mutator-like with 9-10 bp TSDs and 1 novel MITE (BoXMITE1) flanked by 3 bp TSDs. Our data suggested that there are about 30,000 MITE-related sequences in Brassica rapa and B. oleracea genomes. In situ hybridization showed one abundant family was dispersed in the A-genome, while another was located near 45S rDNA sites. PCR analysis using primers flanking sequences of MITE elements detected MITE insertion polymorphisms between and within the three Brassica (AA, BB, CC) genomes, with many insertions being specific to single genomes and others showing evidence of more recent evolutionary insertions. Our BAC sequence comparison strategy enables identification of evolutionarily active MITEs with no prior knowledge of MITE sequences. The details of MITE families reported in Brassica enable their identification, characterization and annotation. Insertion polymorphisms of MITEs and their transposition activity indicated important mechanism of genome evolution and diversification. MITE families derived from known Mariner, Harbinger and Mutator DNA transposons were discovered, as well as some novel structures. The identification of Brassica MITEs will have broad applications in Brassica genomics, breeding, hybridization and phylogeny through their use as DNA markers.

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Recent transposition activity of Xenopus T2 family miniature inverted-repeat transposable elements

Cited by 7 publications

References 22 publications

msechBari, a new MITE-like element inDrosophila sechelliarelated to theBaritransposon

msechBari, a new MITE-like element inDrosophila sechelliarelated to theBaritransposon

Distribution of the T2-MITE Family Transposons in the <b><i>Xenopus (Silurana) tropicalis </i></b>Genome

Evolutionary genomics of miniature inverted-repeat transposable elements (MITEs) in Brassica

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