I have a mental picture of the structure of a typical plant genome and typical animal genome, with their transposons (DNA and RNA), tandemly-repeated satellite sequences, minisatellites, microsatellites and other repeats. From this paper, I have a view of repeats in the second most important edible fungus (after yeast, Saccharomyces cerevisiae), the button mushroom Agaricus bisporus. Its genome, with n=13 chromosomes, is about 30Mb in size (cf yeast at 12.1Mb), consisting of about 8% gypsy- and copia-like retrotransposons, the vast majority of which are less than 500,000 years old. About two-thirds lie in clusters, which seem to occur anywhere along chromosomes (although the paper abstract claims they “were found clustered in the centromeric or telomeric regions”, to me this is not reflected in the heatmaps of Fig. 1). Notably, no signiﬁcant correlation between the number of TEs and the recombination rate (cM per 100 kbp) was detected. Small numbers of mini- and micro-satellites are present (0.18% and 0.43% of the sequence) and widely distributed in the genome, while satellites of >100bp represented less than 0.7% of the genome. The authors note that it will require considerable effort to find those that are useful as DNA markers.
The paper discussed here is one of 12 in a special issue of the Journal dedicated to the mushroom: Preface to Agaricus bisporus – Beyond the genome Special Issue Ronald de Vries, Ursula Kües, Patricia A. van Kuyk.
Foulongne-Oriol, M., Murat, C., Castanera, R., Ramírez, L., & Sonnenberg, A. S. M. (2013). Genome-wide survey of repetitive DNA elements in the button mushroom agaricus bisporus. Fungal Genetics and Biology. online first June 2013
Repetitive DNA elements are ubiquitous constituents of eukaryotic genomes. The biological roles of these repetitive elements, supposed to impact genome organization and evolution, are not completely elucidated yet. The availability of whole genome sequence offers the opportunity to draw a picture of the genome-wide distribution of these elements and provide insights into potential mechanisms of genome plasticity. The present study uses in silico approaches to describe tandem repeats and transposable elements distribution in the genome of the button mushroom, Agaricus bisporus. Transposable elements comprised 12.43% of the assembled genome, and 66% of them were found clustered in the centromeric or telomeric regions. Methylation of retrotransposon has been demonstrated. A total of 1996 mini-, 4062 micro-, and 37 satellites motifs were identified. The microsatellites appeared widely and evenly spread over the whole genome sequence, whereas the minisatellites were not randomly distributed. Indeed, minisatellites were found to be associated with transposable elements clusters. Telomeres exhibited a specific sequence with a TnAGnsignature. A comparison between the two available genome sequences of A. bisporus was also performed and sheds light on the genetic divergence between the two varieties. Beyond their role in genome structure, repeats provide a virtually endless source of molecular markers useful for genetic studies in this cultivated species.