On the Coevolution of Transposable Elements and Plant Genomes

Civáň, Peter; Švec, Miroslav; Hauptvogel, Pavol

doi:10.1155/2011/893546

Cited by 27 publications

(35 citation statements)

References 84 publications

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“…The highly redundant genomes in plant species were mainly derived from the extreme copies of LTR-retrotransposons (Kumar and Bennetzen 1999;Devos 2010;Civáň et al 2011). However, reports on the LTR-retrotransposons are limited in the genus Lilium (Smyth et al 1989;Lee et al 2013).…”

Section: Discussionmentioning

confidence: 99%

LTR-retrotransposons and inter-retrotransposon amplified polymorphism (IRAP) analysis in Lilium species

et al. 2015

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LTR-retrotransposons are ubiquitous and highly abundant in plant genomes. Moreover, LTR-retrotransposons can often cause genome obesity in plants. Although Lilium species have been known carrying large genomes among flowering plants, reports on the LTR-retrotransposons in Lilium species are rather limited. We isolated a novel Ty3/gypsy-like retrotransposon, LIRE-del, and two Ty1/copia-like retrotransposons, a LIRE-del and an unclassified, from a fosmid clone of Lilium longiflorum. Decayed internal ORF sequences indicated that they were non-autonomous elements. IRAP protocol was developed based on the LTR sequences of the isolated LTR-retrotransposons. Fourteen primer combinations showed clear distinctive PCR amplification bands that were highly informative in the analysis of species relationship among Lilium species. The phylogenetic relationship based on the IRAP profile revealed some discordant with phylogenetic studies based on the ITS sequences of 45S ribosomal gene and matK gene variations in a few species. Thus, the phylogenetic relationship among Lilium species may need to be re-evaluated with other tools such as cross compatibility and selectively neutral genetic markers.

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Section: Discussionmentioning

confidence: 99%

LTR-retrotransposons and inter-retrotransposon amplified polymorphism (IRAP) analysis in Lilium species

et al. 2015

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“…Accordingly, animal and plant genomes typically contain far more copies of retrotransposons than of DNA transposons. For example, retrotransposons constitute about 40% and 75% of the human and Zea mays genomes, respectively, while DNA transposons contribute 3% and 8.6% [3], [4]. In striking contrast, retrotransposons constitute only 0.6% of the C. elegans genome, while DNA transposons make up about 12% 5–7.…”

Section: Introductionmentioning

confidence: 99%

C. elegans Germ Cells Show Temperature and Age-Dependent Expression of Cer1, a Gypsy/Ty3-Related Retrotransposon

et al. 2012

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Virus-like particles (VLPs) have not been observed in Caenorhabditis germ cells, although nematode genomes contain low numbers of retrotransposon and retroviral sequences. We used electron microscopy to search for VLPs in various wild strains of Caenorhabditis, and observed very rare candidate VLPs in some strains, including the standard laboratory strain of C. elegans, N2. We identified the N2 VLPs as capsids produced by Cer1, a retrotransposon in the Gypsy/Ty3 family of retroviruses/retrotransposons. Cer1 expression is age and temperature dependent, with abundant expression at 15°C and no detectable expression at 25°C, explaining how VLPs escaped detection in previous studies. Similar age and temperature-dependent expression of Cer1 retrotransposons was observed for several other wild strains, indicating that these properties are common, if not integral, features of this retroelement. Retrotransposons, in contrast to DNA transposons, have a cytoplasmic stage in replication, and those that infect non-dividing cells must pass their genomic material through nuclear pores. In most C. elegans germ cells, nuclear pores are largely covered by germline-specific organelles called P granules. Our results suggest that Cer1 capsids target meiotic germ cells exiting pachytene, when free nuclear pores are added to the nuclear envelope and existing P granules begin to be removed. In pachytene germ cells, Cer1 capsids concentrate away from nuclei on a subset of microtubules that are exceptionally resistant to microtubule inhibitors; the capsids can aggregate these stable microtubules in older adults, which exhibit a temperature-dependent decrease in egg viability. When germ cells exit pachytene, the stable microtubules disappear and capsids redistribute close to nuclei that have P granule-free nuclear pores. This redistribution is microtubule dependent, suggesting that capsids that are released from stable microtubules transfer onto new, dynamic microtubules to track toward nuclei. These studies introduce C. elegans as a model to study the interplay between retroelements and germ cell biology.

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“…They are also useful as genetic markers in basic and applied science [7,8]. TEs occupy a substantial fraction of sequenced plant genomes [9], ranging from over 14% in Arabidopsis [10] to more than 80% in maize [11]. Because of their nature and characteristic patterns of insertion [12], TEs may influence large portions of the genome.…”

Section: Introductionmentioning

confidence: 99%

“…The assembly contained 23.06% TEs as defined by sequence coverage. While the calculated proportion of the genome covered by TEs in flax is slightly lower than other plant species with small genomes, much variation exists in TE content in plants [9]. Only a small proportion of the TEs described in the flax genome could be identified through alignment to previously characterized elements from other species [40].…”

Section: Introductionmentioning

confidence: 99%

Identification, characterization and distribution of transposable elements in the flax (Linum usitatissimum L.) genome

Galindo‐González

Deyholos

2012

BMC Genomics

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BackgroundFlax (Linum usitatissimum L.) is an important crop for the production of bioproducts derived from its seed and stem fiber. Transposable elements (TEs) are widespread in plant genomes and are a key component of their evolution. The availability of a genome assembly of flax (Linum usitatissimum) affords new opportunities to explore the diversity of TEs and their relationship to genes and gene expression.ResultsFour de novo repeat identification algorithms (PILER, RepeatScout, LTR_finder and LTR_STRUC) were applied to the flax genome assembly. The resulting library of flax repeats was combined with the RepBase Viridiplantae division and used with RepeatMasker to identify TEs coverage in the genome. LTR retrotransposons were the most abundant TEs (17.2% genome coverage), followed by Long Interspersed Nuclear Element (LINE) retrotransposons (2.10%) and Mutator DNA transposons (1.99%). Comparison of putative flax TEs to flax transcript databases indicated that TEs are not highly expressed in flax. However, the presence of recent insertions, defined by 100% intra-element LTR similarity, provided evidence for recent TE activity. Spatial analysis showed TE-rich regions, gene-rich regions as well as regions with similar genes and TE density. Monte Carlo simulations for the 71 largest scaffolds (≥ 1 Mb each) did not show any regional differences in the frequency of TE overlap with gene coding sequences. However, differences between TE superfamilies were found in their proximity to genes. Genes within TE-rich regions also appeared to have lower transcript expression, based on EST abundance. When LTR elements were compared, Copia showed more diversity, recent insertions and conserved domains than the Gypsy, demonstrating their importance in genome evolution.ConclusionsThe calculated 23.06% TE coverage of the flax WGS assembly is at the low end of the range of TE coverages reported in other eudicots, although this estimate does not include TEs likely found in unassembled repetitive regions of the genome. Since enrichment for TEs in genomic regions was associated with reduced expression of neighbouring genes, and many members of the Copia LTR superfamily are inserted close to coding regions, we suggest Copia elements have a greater influence on recent flax genome evolution while Gypsy elements have become residual and highly mutated.

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On the Coevolution of Transposable Elements and Plant Genomes

Cited by 27 publications

References 84 publications

LTR-retrotransposons and inter-retrotransposon amplified polymorphism (IRAP) analysis in Lilium species

LTR-retrotransposons and inter-retrotransposon amplified polymorphism (IRAP) analysis in Lilium species

C. elegans Germ Cells Show Temperature and Age-Dependent Expression of Cer1, a Gypsy/Ty3-Related Retrotransposon

Identification, characterization and distribution of transposable elements in the flax (Linum usitatissimum L.) genome

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