title: Identification and occurrence of the LTR-Copia-like retrotransposon, PSCR and other Copia-like elements in the genome of Phytophthora sojae.
abstract: Sequence analysis of the genomic region of Phytophthora sojae close to the Avr4/6 locus specifying virulence on soybean identified a Ty1/Copia-like retrotransposon that we have named Phytophthora sojae Copia-like retrotransposon (PSCR). Twelve near-complete homologs of PSCR were found in the published P. sojae genome sequence, none of which encoded a full-length polyprotein characteristic of Copia-like retrotransposons, or appears to exhibit transcriptional activity or show evidence of recent movement, suggesting they are non-functional and unlikely to have caused pathogenic variability. However, reconstructed consensus PSCR sequence encoding a full-length polyprotein resembles a functional, ancestral retroelement within P. sojae. Homologs were also found in sequence databases of other Phytophthora species. Database searches found other families of Copia-like elements in genomes of P. sojae, P. ramorum and P. infestans that were different from members of the PSCR family and from Copia-like elements reported in other organisms. It is possible that the various families of Copia-like retroelements identified in this study represent introgressions into the genome of ancient ancestor(s) of current Phytophthora species, where they have evolved and diverged considerably during the speciation. Some Copia-like families are transcriptionally active with the potential to transpose and contribute to pathogenic variation in current populations of P. sojae.
authors.affiliation: School of Biological Sciences, The University of Queensland, Brisbane, QLD, 4072, Australia. s.basnayake@uq.edu.au
authors.forename: Shiromi
authors.initials: S
authors.lastname: Basnayake
authors.forename: Donald J
authors.initials: DJ
authors.lastname: Maclean
authors.forename: Stephen C
authors.initials: SC
authors.lastname: Whisson
authors.forename: Andre
authors.initials: A
authors.lastname: Drenth
mesh_terms: D000595:Amino Acid Sequence; D001483:Base Sequence; D017931:DNA Primers; D004274:DNA, Recombinant / Q000235:genetics; D020224:Expressed Sequence Tags; D005656:Fungal Proteins / Q000737:chemistry / Q000235:genetics; D016681:Genome, Fungal; D008969:Molecular Sequence Data; D010802:Phylogeny; D010838:Phytophthora / Q000235:genetics*; D018626:Retroelements; D017386:Sequence Homology, Amino Acid
chemical_list: D017931:DNA Primers; D004274:DNA, Recombinant; D005656:Fungal Proteins; D018626:Retroelements