Population dynamics of miniature inverted-repeat transposable elements (MITEs) in Medicago truncatula

Grzebelus, Dariusz; Gładysz, Mirosława; Macko-Podgórni, Alicja; Gambin, Tomasz; Golis, Barbara; Rakoczy, Roksana; Gambin, Anna

doi:10.1016/j.gene.2009.06.004

Cited by 20 publications

(19 citation statements)

References 26 publications

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“…The closest association has been found between Stowaway elements and genes (Oki et al 2008), in agreement with our current data on the Brassica Stowaway family BraSto. Nevertheless, our results strongly support an exclusion of BraSto from gene coding regions, as no copies have been found in the 1.20 Mb-CDS analyzed, in accordance with previous studies performed on various plant genomes (Benjak et al 2009;Grzebelus et al 2009). It may suggest purifying selection resulting in rapid removal of MITEs from coding sequences, in which insertions of mobile elements are expected to be highly disadvantageous by disrupting functional sequences.…”

Section: Discussionsupporting

confidence: 93%

“…Recent reports on MITE transposition demonstrated that they can be effectively mobilized by class II transposases (Yang et al 2007a). Frequent association of MITEs with plant genes was first depicted in the maize genome (Bureau and Wessler 1992) and then observed in the genome of other monocotyledonous and dicotyledonous plants (Bureau and Wessler 1994a, b;Grzebelus et al 2009). In subsequent studies, MITEs were found in the regulatory regions of genes (e.g.…”

Section: Introductionmentioning

confidence: 99%

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BraSto, a Stowaway MITE from Brassica: recently active copies preferentially accumulate in the gene space

et al. 2011

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We characterized a Brassica miniature inverted repeat transposable element (MITE) from the Stowaway superfamily, designated BraSto (Bra ssica Sto waway). BraSto copy number was assessed using real-time quantitative PCR in the two diploid species B. rapa (genome A) and B. oleracea (genome C) and the corresponding allotetraploid species B. napus (genome AC). Phylogenetic relationships among a set of 131 BraSto copies were then analyzed. BraSto appears to have been only moderately amplified in the Brassica genome and was still active recently with marks of proliferation in both diploid Brassica species, which diverged 3.75 million years ago, but also in the allotetraploid species after reuniting of the two differentiated genomes. We characterized insertion sites for low-divergence BraSto copies among the gene space of the B. rapa genome using bioinformatics approaches. For BraSto copies localized nearby or within genes, we observed frequent associations of BraSto with putative promoters and regulatory regions of genes, but exclusion from coding regions. In addition, BraSto was significantly similar to several Brassica expressed sequence tags (ESTs), including stress-induced ESTs. We also demonstrated the enrichment of BraSto sequences in binding sites for transcription factors and other regulatory elements. Our results lead to the question of a role for BraSto in the regulation of gene expression: this putative role, if further confirmed experimentally, would help to obtain a new insight into the significance of MITEs in the functional plant genome.

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Section: Discussionsupporting

confidence: 93%

Section: Introductionmentioning

confidence: 99%

BraSto, a Stowaway MITE from Brassica: recently active copies preferentially accumulate in the gene space

et al. 2011

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“…In both plants and animals, different patterns of MITE insertion in germplasms or individuals have also been used as DNA markers (Bonin et al 2008; Monden et al 2009; Grzebelus et al 2009). Therefore, it is worth considering the use of AhMITE1 s as DNA markers.…”

Section: Discussionmentioning

confidence: 99%

Characterization of active miniature inverted-repeat transposable elements in the peanut genome

et al. 2012

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Miniature inverted-repeat transposable elements (MITEs), some of which are known as active non-autonomous DNA transposons, are found in the genomes of plants and animals. In peanut (Arachis hypogaea), AhMITE1 has been identified in a gene for fatty-acid desaturase, and possessed excision activity. However, the AhMITE1 distribution and frequency of excision have not been determined for the peanut genome. In order to characterize AhMITE1s, their genomic diversity and transposition ability was investigated. Southern blot analysis indicated high AhMITE1 copy number in the genomes of A. hypogaea, A. magna and A. monticola, but not in A. duranensis. A total of 504 AhMITE1s were identified from the MITE-enriched genomic libraries of A. hypogaea. The representative AhMITE1s exhibited a mean length of 205.5 bp and a GC content of 30.1%, with AT-rich, 9 bp target site duplications and 25 bp terminal inverted repeats. PCR analyses were performed using primer pairs designed against both flanking sequences of each AhMITE1. These analyses detected polymorphisms at 169 out of 411 insertional loci in the four peanut lines. In subsequent analyses of 60 gamma-irradiated mutant lines, four AhMITE1 excisions showed footprint mutations at the 109 loci tested. This study characterizes AhMITE1s in peanut and discusses their use as DNA markers and mutagens for the genetics, genomics and breeding of peanut and its relatives.Electronic supplementary materialThe online version of this article (doi:10.1007/s00122-012-1798-6) contains supplementary material, which is available to authorized users.

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“…MITEs also exist in high copy numbers in other plant genomes, e.g., rice mPing (70 copies in 'Nipponbare'; Jiang et al 2003), maize Tourist ([5,000 copies; Wessler 1992, 1994a), maize Heartbreaker (4,000 copies; Zhang et al 2000) and alfalfa Bigfoot (1,000 to 10,000 copies; Charrier et al 1999). However, there are also lower copy MITE families, e.g., Emigrant in Arabidopsis (Santiago et al 2002), and MetMIT and MITRAV in Medicago truncatula (Grzebelus et al 2009). Southern blot analysis using a GtMITE1 probe showed the presence of a relatively low copy number in the Japanese gentian genome (Fig.…”

Section: Discussionmentioning

confidence: 99%

A single-base substitution suppresses flower color mutation caused by a novel miniature inverted-repeat transposable element in gentian

Nishihara

Hikage²,

Yamada

et al. 2011

Mol Genet Genomics

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We investigated the genetic basis for the derivation of pink coloration in petals from blue flowers in cultivated gentians. Using a revertant blue-flower phenotype that arose spontaneously from a pink-flowered cultivar, we sought to elucidate the molecular mechanism of flower color restoration caused by a suppressor mutation. Detailed sequencing analysis identified three novel deficient flavonoid 3',5'-hydroxylase (F3'5'H) alleles in pink-flowered gentians in addition to two mutations identified previously (Nakatsuka et al. in Mol Genet Genomics 275:231-241, 2006). Among the deficient alleles, one allele that contained a novel miniature inverted-repeat transposable element (GtMITE1) insertion in an intron of F3'5'H was shown to cause missplicing, resulting in abnormal F3'5'H transcripts and the pink-flower phenotype. The other two mutations were identified as a single-nucleotide insertion and gypsy-Ty3 retrotransposon (Tgt1) insertion within exon 1 and exon 2 of the F3'5'H gene, respectively. The blue-flowered revertant mutant contained a single-nucleotide spontaneous mutation immediately 3' of the TAA target site duplication and the GtMITE1 insertion, which caused restoration of normal splicing of F3'5'H and the normal blue-flower phenotype. Transient expression assays in gentian flowers in vivo demonstrated that normal F3'5'H splicing pattern was recovered from missplicing induced by the GtMITE1 insertion by the single-nucleotide substitution. These findings extend our knowledge of genomic evolution by transposable elements and spontaneous mutations in Gentiana species of economic and medical importance.

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Population dynamics of miniature inverted-repeat transposable elements (MITEs) in Medicago truncatula

Cited by 20 publications

References 26 publications

BraSto, a Stowaway MITE from Brassica: recently active copies preferentially accumulate in the gene space

BraSto, a Stowaway MITE from Brassica: recently active copies preferentially accumulate in the gene space

Characterization of active miniature inverted-repeat transposable elements in the peanut genome

A single-base substitution suppresses flower color mutation caused by a novel miniature inverted-repeat transposable element in gentian

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