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The hidden duplication past of the plant pathogen Phytophthora and its consequences for infection

Cindy Martens UGent and Yves Van de Peer UGent (2010) BMC GENOMICS. 11.
abstract
Background: Oomycetes of the genus Phytophthora are pathogens that infect a wide range of plant species. For dicot hosts such as tomato, potato and soybean, Phytophthora is even the most important pathogen. Previous analyses of Phytophthora genomes uncovered many genes, large gene families and large genome sizes that can partially be explained by significant repeat expansion patterns. Results: Analysis of the complete genomes of three different Phytophthora species, using a newly developed approach, unveiled a large number of small duplicated blocks, mainly consisting of two or three consecutive genes. Further analysis of these duplicated genes and comparison with the known gene and genome duplication history of ten other eukaryotes including parasites, algae, plants, fungi, vertebrates and invertebrates, suggests that the ancestor of P. infestans, P. sojae and P. ramorum most likely underwent a whole genome duplication (WGD). Genes that have survived in duplicate are mainly genes that are known to be preferentially retained following WGDs, but also genes important for pathogenicity and infection of the different hosts seem to have been retained in excess. As a result, the WGD might have contributed to the evolutionary and pathogenic success of Phytophthora. Conclusions: The fact that we find many small blocks of duplicated genes indicates that the genomes of Phytophthora species have been heavily rearranged following the WGD. Most likely, the high repeat content in these genomes have played an important role in this rearrangement process. As a consequence, the paucity of retained larger duplicated blocks has greatly complicated previous attempts to detect remnants of a large-scale duplication event in Phytophthora. However, as we show here, our newly developed strategy to identify very small duplicated blocks might be a useful approach to uncover ancient polyploidy events, in particular for heavily rearranged genomes.
Please use this url to cite or link to this publication:
author
organization
year
type
journalArticle (original)
publication status
published
subject
keyword
ANCIENT GENOME DUPLICATIONS, WHOLE-GENOME, CAENORHABDITIS-ELEGANS, SACCHAROMYCES-CEREVISIAE, SEGMENTAL DUPLICATION, PHYLOGENETIC ANALYSIS, GENE DUPLICATION, DNA-SEQUENCES, UNITED-STATES, YEAST GENOME
journal title
BMC GENOMICS
BMC Genomics
volume
11
article number
353
pages
16 pages
Web of Science type
Article
Web of Science id
000279868100004
JCR category
BIOTECHNOLOGY & APPLIED MICROBIOLOGY
JCR impact factor
4.206 (2010)
JCR rank
24/158 (2010)
JCR quartile
1 (2010)
ISSN
1471-2164
DOI
10.1186/1471-2164-11-353
language
English
UGent publication?
yes
classification
A1
copyright statement
I have retained and own the full copyright for this publication
id
1018418
handle
http://hdl.handle.net/1854/LU-1018418
date created
2010-08-05 15:10:46
date last changed
2016-12-21 15:42:38
@article{1018418,
  abstract     = {Background: Oomycetes of the genus Phytophthora are pathogens that infect a wide range of plant species. For dicot hosts such as tomato, potato and soybean, Phytophthora is even the most important pathogen. Previous analyses of Phytophthora genomes uncovered many genes, large gene families and large genome sizes that can partially be explained by significant repeat expansion patterns.
Results: Analysis of the complete genomes of three different Phytophthora species, using a newly developed approach, unveiled a large number of small duplicated blocks, mainly consisting of two or three consecutive genes. Further analysis of these duplicated genes and comparison with the known gene and genome duplication history of ten other eukaryotes including parasites, algae, plants, fungi, vertebrates and invertebrates, suggests that the ancestor of P. infestans, P. sojae and P. ramorum most likely underwent a whole genome duplication (WGD). Genes that have survived in duplicate are mainly genes that are known to be preferentially retained following WGDs, but also genes important for pathogenicity and infection of the different hosts seem to have been retained in excess. As a result, the WGD might have contributed to the evolutionary and pathogenic success of Phytophthora.
Conclusions: The fact that we find many small blocks of duplicated genes indicates that the genomes of Phytophthora species have been heavily rearranged following the WGD. Most likely, the high repeat content in these genomes have played an important role in this rearrangement process. As a consequence, the paucity of retained larger duplicated blocks has greatly complicated previous attempts to detect remnants of a large-scale duplication event in Phytophthora. However, as we show here, our newly developed strategy to identify very small duplicated blocks might be a useful approach to uncover ancient polyploidy events, in particular for heavily rearranged genomes.},
  articleno    = {353},
  author       = {Martens, Cindy and Van de Peer, Yves},
  issn         = {1471-2164},
  journal      = {BMC GENOMICS},
  keyword      = {ANCIENT GENOME DUPLICATIONS,WHOLE-GENOME,CAENORHABDITIS-ELEGANS,SACCHAROMYCES-CEREVISIAE,SEGMENTAL DUPLICATION,PHYLOGENETIC ANALYSIS,GENE DUPLICATION,DNA-SEQUENCES,UNITED-STATES,YEAST GENOME},
  language     = {eng},
  pages        = {16},
  title        = {The hidden duplication past of the plant pathogen Phytophthora and its consequences for infection},
  url          = {http://dx.doi.org/10.1186/1471-2164-11-353},
  volume       = {11},
  year         = {2010},
}

Chicago
Martens, Cindy, and Yves Van de Peer. 2010. “The Hidden Duplication Past of the Plant Pathogen Phytophthora and Its Consequences for Infection.” Bmc Genomics 11.
APA
Martens, Cindy, & Van de Peer, Y. (2010). The hidden duplication past of the plant pathogen Phytophthora and its consequences for infection. BMC GENOMICS, 11.
Vancouver
1.
Martens C, Van de Peer Y. The hidden duplication past of the plant pathogen Phytophthora and its consequences for infection. BMC GENOMICS. 2010;11.
MLA
Martens, Cindy, and Yves Van de Peer. “The Hidden Duplication Past of the Plant Pathogen Phytophthora and Its Consequences for Infection.” BMC GENOMICS 11 (2010): n. pag. Print.