ABSTRACT Molecular Biology and Evolution 19, 1313-1322.

A family of sequences resembling Gypsy retroelements was identified and shown to be widely distributed throughout the genus Phytophthora, a member of the algal-like oomycete fungi. Polymerase chain reaction (PCR) using specific and degenerate primers detected the family in 29 of 37 species tested. DNA hybridization also failed to detect the sequences in the eight species that were negative in PCR. Within species containing the element, its abundance varied drastically from about 10 to more than 10,000 copies per genome. Family members diverged from each other by single base changes, insertions, and deletions, with a mean nucleotide divergence of 16.7%. By constructing phylogenies of the elements, lineages were identified that predated speciation events within Phytophthora, and subfamilies that had diverged more recently. The element was studied in detail in P. infestans, in which about 30 copies are dispersed throughout the genome. Phylogenetic comparisons of the reverse transcriptases placed the family within the Ty3/Gypsy group of LTR retrotransposons, with the closest affinities to elements from plants. However, each of twelve family members sequenced contained defects that would render their protein products inactive, including frameshift mutations within reverse transcriptase domains and truncations that appeared to eliminate gag, protease, and terminal repeat sequences.