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

Basnayake, S.W.V., Maclean, D.J., Whisson, S.C. and Drenth, A. (2009) Identification and occurrence of the LTR-Copia-like retrotransposon, PSCR and other Copia-like elements in the genome of Phytophthora sojae. Current Genetics, 55 5: 521-536. doi:10.1007/s00294-009-0263-9


Author Basnayake, S.W.V.
Maclean, D.J.
Whisson, S.C.
Drenth, A.
Title Identification and occurrence of the LTR-Copia-like retrotransposon, PSCR and other Copia-like elements in the genome of Phytophthora sojae
Formatted title
Identification and occurrence of the LTR-Copia-like retrotransposon, PSCR and other Copia-like elements in the genome of Phytophthora sojae
Journal name Current Genetics   Check publisher's open access policy
ISSN 0172-8083
Publication date 2009-10
Year available 2009
Sub-type Article (original research)
DOI 10.1007/s00294-009-0263-9
Volume 55
Issue 5
Start page 521
End page 536
Total pages 15
Editor Hohmann, S.
Place of publication Germany
Publisher Springer
Collection year 2010
Language eng
Subject C1
060409 Molecular Evolution
060704 Plant Pathology
820405 Soybeans
Formatted 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.
Keyword Linkage maps
O├Âmycetes
Transposable elements
Homologs
Phytophthora infestans
Phytophthora ramorum
Q-Index Code C1
Q-Index Status Confirmed Code

 
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Created: Thu, 17 Dec 2009, 12:37:06 EST by Hayley Ware on behalf of School of Biological Sciences