Identification and occurrence of the LTR-Copia-like retrotransposon, PSCR and other Copia-like elements in the genome of Phytophthora sojae

Curr Genet. 2009 Oct;55(5):521-36. doi: 10.1007/s00294-009-0263-9. Epub 2009 Jul 30.

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.

Publication types

  • Research Support, Non-U.S. Gov't
  • Review

MeSH terms

  • Amino Acid Sequence
  • Base Sequence
  • DNA Primers
  • DNA, Recombinant / genetics
  • Expressed Sequence Tags
  • Fungal Proteins / chemistry
  • Fungal Proteins / genetics
  • Genome, Fungal*
  • Molecular Sequence Data
  • Phylogeny
  • Phytophthora / genetics*
  • Retroelements*
  • Sequence Homology, Amino Acid

Substances

  • DNA Primers
  • DNA, Recombinant
  • Fungal Proteins
  • Retroelements