Ylt1, a highly repetitive retrotransposon in the genome of the dimorphic fungus Yarrowia lipolytica

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Abstract
A highly repetitive composite element, Ylt1, was detected in the genome of the dimorphic fungus Yarrowia lipolytica. Ylt1 resembles retrotransposons found in other eukaryotes. It is about 9.4 kb long and can transpose in the genome. The Ylt1 element is bounded by a long terminal repeat (LTR), the zeta element. Several copies of zeta were isolated and sequenced. The sequence of this element is well conserved. It is 714 bp long and is bounded by nucleotides 5'-TG...CA-3', which are part of a short inverted repeat, a feature conserved in the LTRs of retroviruses and retrotransposons. Sequence analysis revealed motifs commonly found in LTR elements, like signals for the start and termination of transcription. The zeta element exists as part of retrotransposon Ylt1, as well as a solo element in the genome. Ylt1 and solo zeta elements are flanked by a 4-bp directly repeated genomic sequence. The copy numbers of Ylt1 and solo zeta are dependent on the strain examined, but at least 35 copies of the composite Ylt1 element and more than 30 copies of the solo zeta element per haploid genome have been observed.