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Screening for rapidly evolving genes in the ectomycorrhizal fungus Paxillus involutus using cDNA microarrays

Le Quéré, Antoine LU ; Eriksen, Kasper LU ; Rajashekar, Balaji LU ; Schutzendubel, Andres LU ; Canbäck, Björn LU ; Johansson, Tomas LU and Tunlid, Anders LU (2006) In Molecular Ecology 15(2). p.535-550
Abstract
We have examined the variations in gene content and sequence divergence that could be associated with symbiotic adaptations in the ectomycorrhizal fungus Paxillus involutus and the closely related species Paxillus filamentosus. Strains with various abilities to form mycorrhizae were analysed by comparative genomic hybridizations using a cDNA microarray containing 1076 putative unique genes of P. involutus. To screen for genes diverging at an enhanced and presumably non-neutral rate, we implemented a simple rate test using information from both the variations in hybridizations signal and data on sequence divergence of the arrayed genes relative to the genome of Coprinus cinereus. C. cinereus is a free-living saprophyte and is the closest... (More)
We have examined the variations in gene content and sequence divergence that could be associated with symbiotic adaptations in the ectomycorrhizal fungus Paxillus involutus and the closely related species Paxillus filamentosus. Strains with various abilities to form mycorrhizae were analysed by comparative genomic hybridizations using a cDNA microarray containing 1076 putative unique genes of P. involutus. To screen for genes diverging at an enhanced and presumably non-neutral rate, we implemented a simple rate test using information from both the variations in hybridizations signal and data on sequence divergence of the arrayed genes relative to the genome of Coprinus cinereus. C. cinereus is a free-living saprophyte and is the closest evolutionary relative to P. involutus that has been fully sequenced. Approximately 17% of the genes investigated were detected as rapidly diverging within Paxillus. Furthermore, 6% of the genes varied in copy numbers between the analysed strains. Genome rearrangements associated with this variation including duplications and deletions may also play a role in adaptive evolution. The cohort of divergent and duplicated genes showed an over-representation of either orphans, genes whose products are located at membranes, or genes encoding for components of stress/defence reactions. Some of the identified genomic changes may be associated with the variation in host specificity of ectomycorrhizal fungi. The proposed procedure could be generally applicable to screen for rapidly evolving genes in closely related strains or species where at least one has been sequenced or characterized by expressed sequence tag analysis. (Less)
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author
organization
publishing date
type
Contribution to journal
publication status
published
subject
in
Molecular Ecology
volume
15
issue
2
pages
535 - 550
publisher
Wiley-Blackwell
external identifiers
  • wos:000235045500019
  • pmid:16448419
  • scopus:33645061798
ISSN
0962-1083
DOI
10.1111/j.1365-294X.2005.02796.x
language
English
LU publication?
yes
id
0040aefb-4f29-4eb4-b225-8ba289b63772 (old id 155469)
date added to LUP
2007-06-29 12:09:44
date last changed
2019-03-27 01:37:53
@article{0040aefb-4f29-4eb4-b225-8ba289b63772,
  abstract     = {We have examined the variations in gene content and sequence divergence that could be associated with symbiotic adaptations in the ectomycorrhizal fungus Paxillus involutus and the closely related species Paxillus filamentosus. Strains with various abilities to form mycorrhizae were analysed by comparative genomic hybridizations using a cDNA microarray containing 1076 putative unique genes of P. involutus. To screen for genes diverging at an enhanced and presumably non-neutral rate, we implemented a simple rate test using information from both the variations in hybridizations signal and data on sequence divergence of the arrayed genes relative to the genome of Coprinus cinereus. C. cinereus is a free-living saprophyte and is the closest evolutionary relative to P. involutus that has been fully sequenced. Approximately 17% of the genes investigated were detected as rapidly diverging within Paxillus. Furthermore, 6% of the genes varied in copy numbers between the analysed strains. Genome rearrangements associated with this variation including duplications and deletions may also play a role in adaptive evolution. The cohort of divergent and duplicated genes showed an over-representation of either orphans, genes whose products are located at membranes, or genes encoding for components of stress/defence reactions. Some of the identified genomic changes may be associated with the variation in host specificity of ectomycorrhizal fungi. The proposed procedure could be generally applicable to screen for rapidly evolving genes in closely related strains or species where at least one has been sequenced or characterized by expressed sequence tag analysis.},
  author       = {Le Quéré, Antoine and Eriksen, Kasper and Rajashekar, Balaji and Schutzendubel, Andres and Canbäck, Björn and Johansson, Tomas and Tunlid, Anders},
  issn         = {0962-1083},
  language     = {eng},
  number       = {2},
  pages        = {535--550},
  publisher    = {Wiley-Blackwell},
  series       = {Molecular Ecology},
  title        = {Screening for rapidly evolving genes in the ectomycorrhizal fungus Paxillus involutus using cDNA microarrays},
  url          = {http://dx.doi.org/10.1111/j.1365-294X.2005.02796.x},
  volume       = {15},
  year         = {2006},
}