Multiple LTR-Retrotransposon Families in the Asexual Yeast Candida albicans

Abstract

We have begun a characterization of the long terminal repeat (LTR) retrotransposons in the asexual yeast Candida albicans. A database of assembled C. albicans genomic sequence at Stanford University, which represents 14.9 Mb of the 16-Mb haploid genome, was screened and >350 distinct retrotransposon insertions were identified. The majority of these insertions represent previously unrecognized retrotransposons. The various elements were classified into 34 distinct families, each family being similar, in terms of the range of sequences that it represents, to a typical Ty element family of the related yeast Saccharomyces cerevisiae. These C. albicans retrotransposon families are generally of low copy number and vary widely in coding capacity. For only three families, was a full-length and apparently intact retrotransposon identified. For many families, only solo LTRs and LTR fragments remain. Several families of highly degenerate elements appear to be still capable of transposition, presumably via trans-activation. The overall structure of the retrotransposon population in C. albicans differs considerably from that of S. cerevisiae. In that species, retrotransposon insertions can be assigned to just five families. Most of these families still retain functional examples, and they generally appear at higher copy numbers than the C. albicans families. The possibility that these differences between the two species are attributable to the nonstandard genetic code of C. albicans or the asexual nature of its genome is discussed. A region rich in retrotransposon fragments, that lies adjacent to many of the CARE-2/Rel-2 sub-telomeric repeats, and which appears to have arisen through multiple rounds of duplication and recombination, is also described.

Genome sequence of the lignocellulose degrading fungus Phanerochaete chrysosporium strain RP78

“…Most of these elements appear truncated and/or rearranged, and the long terminal repeats (LTRs), typical of retroelements, often lie apart as "solo LTRs" 16,17 . Several non-LTR retrotransposons, similar to other fungal long interdispersed nuclear elements (LINEs)-like retroelements, were also identified.…”

Evolutionary History of Cer Elements and Their Impact on the C. elegans Genome

“…In general, the C. elegans genome appears to have a relatively low tolerance for LTR retrotransposons (<1%). Whereas we have identified 124 full-length, fragmented, or solo LTR Cer elements in the sequenced (N2) C. elegans genome, >350 LTR retrotransposon elements have been described in the yeast Candida albicans (Goodwin and Poulter 2000) and >300 in Saccharomyces cerevisiae (Kim et al 1998), both species with genomes nearly an order of magnitude smaller than C. elegans (C. elegans Sequencing Consortium 1998).…”

Cryptons: a group of tyrosine-recombinase-encoding DNA transposons from pathogenic fungi

“…Sequencing was performed using an ABI377 DNA sequencer at the University of Otago. Southern blots were performed as described previously (Goodwin & Poulter, 2000). Autoradiographs were scanned using a Bio-Rad GS-800 Calibrated Densitometer and Quantity One software.…”