Repetitive DNA in the automictic fungus Microbotryum violaceum

Abstract

The small genomes of fungi are expected to have little repetitive content other than rDNA genes. Moreover, among asexual or highly selfing lineages, the diversity of repetitive elements is also expected to be very low. However, in the automictic fungus Microbotryum violaceum, a very large proportion of random DNA fragments from the autosomes and the fungal sex chromosomes are repetitive in nature, either as retrotransposon or helicase sequences. Among the retrotransposon sequences, examples were found from each major kind of elements, including copia, gypsy, and non-LTR sequences. The most numerous were copialike elements, which are believed to be rare in fungi, particularly among basidiomycetes. The many helicase sequences appear to belong to the recently discovered Helitron type of transposable elements. Also, sequences that could not be identified as a known type of gene were also very repetitive within the database of random fragments from M. violaceum. The differentiated pair of fungal sex chromosomes and suppression of recombination may be the major forces determining the highly repetitive content in the small genome of M. violaceum.

Repeat-Induced Point Mutation and the Population Structure of Transposable Elements in Microbotryum violaceum

“…We proalso present in the sequence variation of the other types of vide evidence of RIP activity in M. violaceum by identitransposable elements in M. violaceum, PCR primers were designed for a Helitron-type sequence (accession no. BZ782234) fying the target site for C-to-T mutations, the first such identified in a previous study (Hood 2005). Helitrons are rereported for a basidiomycete.…”

“…For example, despite the Repeat-induced point mutations in M. violaceum: This study has provided the first evidence of a RIP genome apparent activity of RIP, the high density of transposable element in M. violaceum is inconsistent with previously defense against transposable elements in a basidiomycete. The process has been sought in a small number of studied ascomycetes Hood 2005). Moreover, the mutational studies of Garber and Rudbasidiomycetes other than M. violaceum (Selker 2002), but not necessarily by similar methods, and its distribution dat (1994,1998,2000,2002) indicate that transposable elements continue to be active in M. violaceum.…”

“…This presents a strong contrast to our parasome-specific sample of DNA that was isolated from the karyotype gel. The resulting PCR products were then cloned using the digm of sequence evolution based on random mutation species contains a high density and diversity of transposAs a test to determine whether evidence of RIP activity is able elements Hood 2005). We proalso present in the sequence variation of the other types of vide evidence of RIP activity in M. violaceum by identitransposable elements in M. violaceum, PCR primers were designed for a Helitron-type sequence (accession no.…”

Helitrons , the Eukaryotic Rolling-circle Transposable Elements

“…They are also found in the two subgroups of Chromalveolates (Alveloates [e.g., Dinoflagellates and Perkinsus] and Stramenopiles [e.g., blightcausing microbes]) and in Unikonts (such as animals, fungi, and some amoebae). Although Helitron proteincoding genes but not the complete elements have been identified in the Unikont subgroup Ameobozoa (e.g., Entamoeba) and the Discicristate group of Excavates (e.g., Trichomonas) (Figure 9), among Ophistokonts, Helitrons are found in choanoflagellates, fungi, and multiple animals (56,94,115,116). Among animals, Helitrons are also found in many vertebrate (e.g., lampreys, reptiles, fish, mammals) (56,70,117,118) and invertebrate (e.g., insects, flatworms, nematodes, sea anemone, hydra, molluscs) (56,70) (1) Oxyhrris (0)…”

Helitron’s Periodicities Identification in C.Elegans based on the Smoothed Spectral Analysis and the Frequency Chaos Game Signal Coding

“…Helitrons are present in various organisms: like plants (such as corn, maize, rice, Arabidopsis Thaliana) [13], nematodes (such as the worm Caenorhabditis elegans) [14], fungus [15], [16] and animals [17] (such as lucifugus [8] and specifically in the vertebrates genomes like the fishes Danio rerio and Sphoeroides nephelus [16]). Approximately, the helitron DNA constitutes at most 2% of the A. thaliana, the C.elegans and the maize genomes [12], [14], [18] and 4.23% of the silkworm genome [19].…”