Retrotransposon <i>BARE-1</i> and Its Role in Genome Evolution in the Genus <i>Hordeum</i>

Vicient, Carlos M.; Suoniemi, Annu; Anamthawat‐Jónsson, Kesara; Tanskanen, Jaakko; Beharav, Alex; Nevo, Eviatar; Schulman, Alan H.

doi:10.1105/tpc.11.9.1769

Cited by 324 publications

(187 citation statements)

References 76 publications

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“…The increased frequency of ESTs similar to retrotransposons in cDNA libraries from stressed plants also parallels similar results based on experimental evidence (Kumar and Bennetzen 1999;Vicient et al 1999) and suggests that the observed frequencies are the result of a particular transcription pattern rather than an artifact produced by genomic contamination of the cDNA libraries.…”

Section: Resultssupporting

confidence: 84%

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Frequencies of Ty1-copia and Ty3-gypsy retroelements within the Triticeae EST databases

et al. 2002

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The frequency of Ty1-copia-type and Ty3-gypsy-type retrotransposons in the International Triticeae EST Consortium (ITEC) database (61,942 sequences: 82% wheat, 10% barley, 8% rye) and the DuPont EST database (86,628 wheat sequences) was estimated using BLASTN searches. These ESTs were obtained from 94 cDNA libraries from different tissues (leaves, roots, spikes, flowers and seeds) and different growing conditions, excluding subtracted and normalized cDNA libraries. Triticeae EST databases were screened using four different Ty1-copia-type, 12 reverse transcriptase sequences, and three Ty3-gypsy-type Triticeae retrotransposon sequences. Using a selection threshold of BLASTN scores higher than 100 or E values smaller than e -20 , 0.145% of the ESTs were found to be significantly similar to at least one of the retrotransposons used in the search (0.064% Ty1-copia, 0.081% Ty3-gypsy). This percentage increased to 0.176% when the BLASTN threshold was changed to E

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Section: Resultssupporting

confidence: 84%

“…Ty1-copia-type and Ty3-gypsy-type retroelements are two abundant classes of retrotransposons in the Triticeae genomes (Suoniemi et al 1996a;Gribbon et al 1999;Vicient et al 1999), comprising approximately 35% of the rye genome (Pearce et al 1997) and a minimum of 20% of the wheat genome (Lagudah et al 2001).…”

Section: Introductionmentioning

confidence: 99%

Frequencies of Ty1-copia and Ty3-gypsy retroelements within the Triticeae EST databases

et al. 2002

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“…The most frequently occurring element from hybridization data was also Huck (Table 2), which identified most of the BAC clones that contained other dispersed repeats. The high frequency observed for Huck relative to the proportion estimated from sequence data may result from a higher frequency of solo LTRs than intact elements, as has been recently demonstrated for the BARE-1 element in barley (Vicient et al 1999;Shirasu et al 2000). In the case of Prem-1, the sequence abundance was definitely underestimated as it was derived only from homology to the LTRs, as the internal domain of the element has not been described.…”

Section: Hybridization To Bac Clones Determines Abundance and Distribmentioning

confidence: 80%

“…The copy number given here for Huck reflects the number of LTRs, so the number of entire elements should be exactly half. Excessive numbers of LTRs, however, may be a feature of complex plant genomes (Vicient et al 1999) and 85% of the LTRretrotransposons found in humans consist only of an isolated LTR (International Human Genome Sequencing Consortium 2001). Overall, the amplification of these retroelements in the Zea species may predate the most recent common ancestor because the same elements have successfully invaded all of these genomes to a similar extent.…”

Section: Maize Repetitive Elementsmentioning

confidence: 99%

Abundance, Distribution, and Transcriptional Activity of Repetitive Elements in the Maize Genome

Meyers

Tingey²,

Morgante³

2001

Genome Res.

373

313

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Long terminal repeat (LTR) retrotransposons have been shown to make up much of the maize genome. Although these elements are known to be prevalent in plant genomes of a middle-to-large size, little information is available on the relative proportions composed by specific families of elements in a single genome. We sequenced a library of randomly sheared genomic DNA from maize to characterize this genome. BLAST analysis of these sequences demonstrated that the maize genome is composed of diverse sequences that represent numerous families of retrotransposons. The largest families contain the previously described elements Huck, Ji, and Opie. Approximately 5% of the sequences are predicted to encode proteins. The genomic abundance of 16 families of elements was estimated by hybridization to an array of 10,752 maize bacterial artificial chromosome (BAC) clones. Comparisons of the number of elements present on individual BACs indicated that retrotransposons are in general randomly distributed across the maize genome. A second library was constructed that was selected to contain sequences hypomethylated in the maize genome. Sequence analysis of this library indicated that retroelements abundant in the genome are poorly represented in hypomethylated regions. Fifty-six retroelement sequences corresponding to the integrase and reverse transcriptase domains were isolated from ∼407,000 maize expressed sequence tags (ESTs). Phylogenetic analysis of these and the genomic retroelement sequences indicated that elements most abundant in the genome are less abundant at the transcript level than are more rare retrotransposons. Additional phylogenies also demonstrated that rice and maize retrotransposon families are frequently more closely related to each other than to families within the same species. An analysis of the GC content of the maize genomic library and that of maize ESTs did not support recently published data that the gene space in maize is found within a narrow GC range, but does indicate that genic sequences have a higher GC content than intergenic sequences (52% vs. 47% GC).

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“…Along with polyploidization, accumulation of repetitive DNA, particularly long terminal repeat retrotransposons (LTR-RTs), is the primary mechanism driving plant genome expansion . In large-genome species such as maize, barley, and wheat, LTR-RTs make up more than 60%-80% of their genomes, and the majority of these elements have amplified within the last few million years (SanMiguel et al 1996(SanMiguel et al , 1998Vicient et al 1999;Wicker et al 2001;Bruggmann et al 2006). A particularly striking study shows that Oryza australiensis, a wild species of rice, has accumulated more than 90,000 copies of LTR-RTs during the last three million years, leading to a twofold increase in genome size without polyploidization (Piegu et al 2006).…”

mentioning

confidence: 99%

Do genetic recombination and gene density shape the pattern of DNA elimination in rice long terminal repeat retrotransposons?

Tian

Rizzon²,

Du³

et al. 2009

Genome Res.

144

177

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In flowering plants, the accumulation of small deletions through unequal homologous recombination (UR) and illegitimate recombination (IR) is proposed to be the major process counteracting genome expansion, which is caused primarily by the periodic amplification of long terminal repeat retrotransposons (LTR-RTs). However, the full suite of evolutionary forces that govern the gain or loss of transposable elements (TEs) and their distribution within a genome remains unclear. Here, we investigated the distribution and structural variation of LTR-RTs in relation to the rates of local genetic recombination (GR) and gene densities in the rice (Oryza sativa) genome. Our data revealed a positive correlation between GR rates and gene densities and negative correlations between LTR-RT densities and both GR and gene densities. The data also indicate a tendency for LTR-RT elements and fragments to be shorter in regions with higher GR rates; the size reduction of LTR-RTs appears to be achieved primarily through solo LTR formation by UR. Comparison of indica and japonica rice revealed patterns and frequencies of LTR-RT gain and loss within different evolutionary timeframes. Different LTR-RT families exhibited variable distribution patterns and structural changes, but overall LTR-RT compositions and genes were organized according to the GR gradients of the genome. Further investigation of non-LTR-RTs and DNA transposons revealed a negative correlation between gene densities and the abundance of DNA transposons and a weak correlation between GR rates and the abundance of long interspersed nuclear elements (LINEs)/short interspersed nuclear elements (SINEs). Together, these observations suggest that GR and gene density play important roles in shaping the dynamic structure of the rice genome.

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Retrotransposon BARE-1 and Its Role in Genome Evolution in the Genus Hordeum

Cited by 324 publications

References 76 publications

Frequencies of Ty1-copia and Ty3-gypsy retroelements within the Triticeae EST databases

Frequencies of Ty1-copia and Ty3-gypsy retroelements within the Triticeae EST databases

Abundance, Distribution, and Transcriptional Activity of Repetitive Elements in the Maize Genome

Do genetic recombination and gene density shape the pattern of DNA elimination in rice long terminal repeat retrotransposons?

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