LTR-retrotransposons and MITEs: important players in the evolution of plant genomes

Wessler, Susan R.

doi:10.1016/0959-437x(95)80016-x

Cited by 461 publications

(345 citation statements)

References 63 publications

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“…Short interspersed elements (SINEs) 22 , short (80-600 bp) non-autonomous retrotransposons that are highly repeated in barley, showed no differential exclusion from the assemblies. However, miniature invertedrepeat transposable elements (MITEs), small non-autonomous DNA transposons 23 , were twofold enriched in the whole-genome shotgun assemblies compared with BES reads or random BACs, consistent with the gene richness of the assemblies and their association with genes 23 . Both MITEs and SINEs are 1.5 to 2-fold enriched in genebearing BACs which could indicate that SINEs are also preferentially integrated into gene-rich regions, or because they are older than LTR retroelements, may simply remain visible in and around genes where retro insertions have been selected against.…”

Section: Repetitive Nature Of the Barley Genomementioning

confidence: 86%

A physical, genetic and functional sequence assembly of the barley genome

2012

Nature

1,293

880

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Barley (Hordeum vulgare L.) is among the world's earliest domesticated and most important crop plants. It is diploid with a large haploid genome of 5.1 gigabases (Gb). Here we present an integrated and ordered physical, genetic and functional sequence resource that describes the barley gene-space in a structured whole-genome context. We developed a physical map of 4.98 Gb, with more than 3.90 Gb anchored to a high-resolution genetic map. Projecting a deep whole-genome shotgun assembly, complementary DNA and deep RNA sequence data onto this framework supports 79,379 transcript clusters, including 26,159 'high-confidence' genes with homology support from other plant genomes. Abundant alternative splicing, premature termination codons and novel transcriptionally active regions suggest that post-transcriptional processing forms an important regulatory layer. Survey sequences from diverse accessions reveal a landscape of extensive single-nucleotide variation. Our data provide a platform for both genome-assisted research and enabling contemporary crop improvement

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Section: Repetitive Nature Of the Barley Genomementioning

confidence: 86%

A physical, genetic and functional sequence assembly of the barley genome

2012

Nature

1,293

880

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“…4b). The IR secondary structure may be critical for recognition by trans-acting factors required for transposition (Wessler et al 1995), but lack of the IR suggests it may not be required for transposition of the PgMINE-1 or that the mutation has rendered the element immobile. Additionally, the termini of PgMINE-1 consisted of 5 0 C and a 3 0 TCAA sequences that are similar to those conserved among Helitron-like TEs (5 0 TC and a 3 0 CTRR; Kapitonov and Jurka 2001), which suggests that the PgMINE-1 from accession AY707868 could be classified as a non-autonomous Helitron.…”

Section: Mine-1 Superfamily Insertion At Lepidopteran (Gaaa) N Microsmentioning

confidence: 99%

“…Miniature inverted-repeat transposable elements (MITEs) are non-autonomous class II mobile DNA elements that are usually \500 bp, have a characteristically high A ? T nucleotide content, and secondary structures that include terminal inverted repeats (TIRs; Wessler et al 1995) or subterminal inverted repeats (SIRs; Tu 2000). MITEs lack an internal protein coding region, and mobility is mediated by trans-acting factors encoded by related autonomous TEs (Dufresne et al 2006).…”

Section: Introductionmentioning

confidence: 99%

A Helitron-Like Transposon Superfamily from Lepidoptera Disrupts (GAAA)n Microsatellites and is Responsible for Flanking Sequence Similarity within a Microsatellite Family

et al. 2010

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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. 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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“…Tourist and Stowaway, two large plant MITE families, also exhibited this remarkable length homogeneity Wessler 1992, 1994a). Since then, size homogeneity has been found to be one of the characteristics of MITEs that distinguish them from other nonautonomous elements (Wessler et al 1995). mimp subfamilies exhibit different degrees of variability.…”

Section: Discussionmentioning

confidence: 99%

“…With the progress of large-scale sequencing, it has become apparent that MITEs are important components of eukaryotic genomes. First identified in plants (Wessler et al 1995), they have been subsequently found, generally in large copy numbers, in a wide range of animal and fungal genomes (for a review, see Feschotte et al 2002). Similarity searches based on TIR sequences have allowed the identification of autonomous class II elements, potentially responsible for the mobilization of MITEs (Feschotte and Mouches 2000;Feschotte et al 2003;Jiang et al 2003;Kikuchi et al 2003;Macas et al 2005;Saito et al 2005;Quesneville et al 2006).…”

Section: Introductionmentioning

confidence: 99%

Genome-Wide Analysis of the Fusarium oxysporum mimp Family of MITEs and Mobilization of Both Native and De Novo Created mimps

et al. 2008

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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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LTR-retrotransposons and MITEs: important players in the evolution of plant genomes

Cited by 461 publications

References 63 publications

A physical, genetic and functional sequence assembly of the barley genome

A physical, genetic and functional sequence assembly of the barley genome

A Helitron-Like Transposon Superfamily from Lepidoptera Disrupts (GAAA)n Microsatellites and is Responsible for Flanking Sequence Similarity within a Microsatellite Family

Genome-Wide Analysis of the Fusarium oxysporum mimp Family of MITEs and Mobilization of Both Native and De Novo Created mimps

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