Dataset Information

Massive Expansion of Gypsy-Like Retrotransposons in Microbotryum Fungi.

ABSTRACT: Transposable elements (TEs) are selfish, autonomously replicating DNA sequences that constitute a major component of eukaryotic genomes and contribute to genome evolution through their movement and amplification. Many fungal genomes, including the anther-smut fungi in the basidiomycete genus Microbotryum, have genome defense mechanisms, such as repeat-induced point mutation (RIP), which hypermutate repetitive DNA and limit TE activity. Little is known about how hypermutation affects the tempo of TE activity and their sequence evolution. Here we report the identification of a massive burst-like expansion of Gypsy-like retrotransposons in a strain of Microbotryum. This TE expansion evidently occurred in the face of RIP-like hypermutation activity. By examining the fitness of individual TE insertion variants, we found that RIP-like mutations impair TE fitness and limit proliferation. Our results provide evidence for a punctuated pattern of TE expansion in a fungal genome, similar to that observed in animals and plants. While targeted hypermutation is often thought of as an effective protection against mobile element activity, our findings suggest that active TEs can persist and undergo selection while they proliferate in genomes that have RIP-like defenses.

SUBMITTER: Horns F

PROVIDER: S-EPMC5381629 | biostudies-literature | 2017 Feb

REPOSITORIES: biostudies-literature

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Massive Expansion of Gypsy-Like Retrotransposons in Microbotryum Fungi.

Horns Felix F Petit Elsa E Hood Michael E ME

Genome biology and evolution 20170201 2

Transposable elements (TEs) are selfish, autonomously replicating DNA sequences that constitute a major component of eukaryotic genomes and contribute to genome evolution through their movement and amplification. Many fungal genomes, including the anther-smut fungi in the basidiomycete genus Microbotryum, have genome defense mechanisms, such as repeat-induced point mutation (RIP), which hypermutate repetitive DNA and limit TE activity. Little is known about how hypermutation affects the tempo of ...[more]

PMID: 28164239

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Project description:BACKGROUND:Chromodomain-containing Gypsy LTR retrotransposons or chromoviruses are widely distributed among eukaryotes and have been found in plants, fungi and vertebrates. The previous comprehensive survey of chromoviruses from mosses (Bryophyta) suggested that genomes of non-seed plants contain the clade which is closely related to the retrotransposons from fungi. The origin, distribution and evolutionary history of this clade remained unclear mainly due to the absence of information concerning the diversity and distribution of LTR retrotransposons in other groups of non-seed plants as well as in fungal genomes. RESULTS:In present study we preformed in silico analysis of chromodomain-containing LTR retrotransposons in 25 diverse fungi and a number of plant species including spikemoss Selaginella moellendorffii (Lycopodiophyta) coupled with an experimental survey of chromodomain-containing Gypsy LTR retrotransposons from diverse non-seed vascular plants (lycophytes, ferns, and horsetails). Our mining of Gypsy LTR retrotransposons in genomic sequences allowed identification of numerous families which have not been described previously in fungi. Two new well-supported clades, Galahad and Mordred, as well as several other previously unknown lineages of chromodomain-containing Gypsy LTR retrotransposons were described based on the results of PCR-mediated survey of LTR retrotransposon fragments from ferns, horsetails and lycophytes. It appeared that one of the clades, namely Tcn1 clade, was present in basidiomycetes and non-seed plants including mosses (Bryophyta) and lycophytes (genus Selaginella). CONCLUSIONS:The interkingdom distribution is not typical for chromodomain-containing LTR retrotransposons clades which are usually very specific for a particular taxonomic group. Tcn1-like LTR retrotransposons from fungi and non-seed plants demonstrated high similarity to each other which can be explained by strong selective constraints and the 'retained' genes theory or by horizontal transmission.

Dataset Information

Massive Expansion of Gypsy-Like Retrotransposons in Microbotryum Fungi.

Publications

Massive Expansion of Gypsy-Like Retrotransposons in Microbotryum Fungi.

Similar Datasets

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