Ty3/Gypsy Retrotransposons: Description of New Arabidopsis thaliana Elements and Evolutionary Perspectives Derived from Comparative Genomic Data

Marı́n, Ignacio; Lloréns, Carlos

doi:10.1093/oxfordjournals.molbev.a026385

Cited by 96 publications

(107 citation statements)

References 32 publications

Supporting

Mentioning

101

Contrasting

Order By: Relevance

“…Sequences isolated from sunflower did not exhibit exclusive monophyly but rather were found distributed throughout the evolutionary tree ( Figure 5). Given the taxonomic breadth of the host species used in this analysis (11 genera from 5 families and including both monocots and dicots), it is clear that several ancient and diverse lineages of Ty1/copia-like elements exist in the sunflower genome, a situation considered normal for plant species (Flavell et al, 1992b;Marin and Llorens, 2000;Zhang and Wessler, 2004).…”

Section: Discussionmentioning

confidence: 99%

Different scales of Ty1/copia-like retrotransposon proliferation in the genomes of three diploid hybrid sunflower species

et al. 2010

View full text Add to dashboard Cite

Activation of transposable elements in species' genomes represents an important mechanism of new mutation and of potential rapid change in genome size. Thus, it is increasingly recognized that transposable elements likely have played a significant role in shaping species' evolution. In an earlier report, we showed that the genomes of three sunflower species of ancient hybrid origin have experienced large-scale proliferation events of sequences within the Ty3/ gypsy-like superfamily of long terminal repeat (LTR) retrotransposons. In this report, we investigate whether another superfamily of LTR retrotransposon (Ty1/copia-like elements) have experienced similar derepression and proliferation events in the genomes of these sunflower hybrid taxa. We show that Ty1/copia-like elements also have undergone copy number increases following or associated with the origins of these species, although the scale of proliferation is less than that for Ty3/gypsy-like elements. Surveys of sequence heterogeneity of Ty1/copia-like elements in the genomes of the three hybrid and two parental species' genomes reveal that a single sub-lineage of these elements exhibits characteristics of recent amplification, and likely served as the proliferative source lineage. These findings indicate that the genomic and/or environmental conditions associated with the origins of these sunflower hybrid taxa were conducive to derepression of at least two major groups of transposable elements.

show abstract

Section: Discussionmentioning

confidence: 99%

Different scales of Ty1/copia-like retrotransposon proliferation in the genomes of three diploid hybrid sunflower species

et al. 2010

View full text Add to dashboard Cite

show abstract

“…The difference is largely the result of similarities in the INT domains of these elements and those of the chromoviruses. Marin and Llorens (2000) have previously noted this discrepancy for Ty3 and skipper. They proposed that it may result from differing rates of evolution or reflect a recombinant origin for these elements.…”

Section: T J D Goodwin and R T M Poultermentioning

confidence: 90%

“…A group of plant retrotransposons, represented here by dea1 from pineapple and an element from tomato, form a sister group to the Tf1/sushi elements. These two groups, together, have been termed the 'chromoviruses' by Marin and Llorens (2000), because most contain a chromodomain-like module at the Cterminal end of their integrase . Loosely associated with this chromovirus group are Ty3 from S. cerevisiae, skipper from Dictyostelium discoideum and Tcn2, 3, 4 and 5.…”

Section: T J D Goodwin and R T M Poultermentioning

confidence: 99%

The diversity of retrotransposons in the yeast Cryptococcus neoformans

Goodwin

Poulter

2001

Yeast

View full text Add to dashboard Cite

We have undertaken an analysis of the retrotransposons in the medically important basidiomycetous fungus Cryptococcus neoformans. Using the data generated by a C. neoformans genome sequencing project at the Stanford Genome Technology Center, 15 distinct families of LTR retrotransposons and several families of non-LTR retrotransposons were identified. Members of at least seven families have transposed recently and are probably still active. For several families, only partial elements could be identified and these are quite diverse in sequence, suggesting that they are ancient components of the C. neoformans genome. Most C. neoformans elements are not closely related to previously identified fungal retrotransposons, suggesting that the diversity of fungal retrotransposons has been only sparsely sampled to date. C. neoformans has fewer distinct retrotransposon families than Candida albicans (37 or more), in particular fewer families represented solely by ancient and inactive elements, but it has considerably more families than either Saccharomyces cerevisiae (five) or Schizosaccharomyces pombe (two). The findings suggest that elimination of retrotransposons is faster in C. neoformans than in C. albicans, but perhaps not as rapid as in S. cerevisiae or Sz. pombe. The identification of the retrotransposons of C. neoformans should assist in the molecular characterization of this important pathogen, and also further our understanding of the role played by retroelements in genome evolution.

show abstract

“…Approximately 60 gypsy-like elements in A. thaliana were previously described and grouped into eight lineages (35). TBLASTN searches using, as query, the most conserved coding sequence (a 156-aa segment of the RT domain) identified 286 and 714 sequences with the entire query region from A. thaliana and B. oleracea, respectively.…”

Section: Gypsy-like Ltr-retrotransposonsmentioning

confidence: 99%

Genome-wide comparative analysis of the transposable elements in the related species Arabidopsis thaliana and Brassica oleracea

Zhang

Wessler

2004

Proc. Natl. Acad. Sci. U.S.A.

141

111

View full text Add to dashboard Cite

Transposable elements (TEs) are the major component of plant genomes where they contribute significantly to the >1,000-fold genome size variation. To understand the dynamics of TE-mediated genome expansion, we have undertaken a comparative analysis of the TEs in two related organisms: the weed Arabidopsis thaliana (125 megabases) and Brassica oleracea (Ϸ600 megabases), a species with many crop plants. Comparison of the whole genome sequence of A. thaliana with a partial draft of B. oleracea has permitted an estimation of the patterns of TE amplification, diversification, and loss that has occurred in related species since their divergence from a common ancestor. Although we find that nearly all TE lineages are shared, the number of elements in each lineage is almost always greater in B. oleracea. Class 1 (retro) elements are the most abundant TE class in both species with LTR and non-LTR elements comprising the largest fraction of each genome. However, several families of class 2 (DNA) elements have amplified to very high copy number in B. oleracea where they have contributed significantly to genome expansion. Taken together, the results of this analysis indicate that amplification of both class 1 and class 2 TEs is responsible, in part, for B. oleracea genome expansion since divergence from a common ancestor with A. thaliana. In addition, the observation that B. oleracea and A. thaliana share virtually all TE lineages makes it unlikely that wholesale removal of TEs is responsible for the compact genome of A. thaliana.

show abstract

Ty3/Gypsy Retrotransposons: Description of New Arabidopsis thaliana Elements and Evolutionary Perspectives Derived from Comparative Genomic Data

Cited by 96 publications

References 32 publications

Different scales of Ty1/copia-like retrotransposon proliferation in the genomes of three diploid hybrid sunflower species

Different scales of Ty1/copia-like retrotransposon proliferation in the genomes of three diploid hybrid sunflower species

The diversity of retrotransposons in the yeast Cryptococcus neoformans

Genome-wide comparative analysis of the transposable elements in the related species Arabidopsis thaliana and Brassica oleracea

Contact Info

Product

Resources

About