Screening for rapidly evolving genes in the ectomycorrhizal fungus Paxillus involutus using cDNA microarrays.
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.
Le Quéré
Antoine
A
Department of Microbial Ecology, Lund University, Ecology Building, SE-223 62 Lund, Sweden.
Eriksen
Kasper Astrup
KA
Rajashekar
Balaji
B
Schützendübel
Andres
A
Canbäck
Björn
B
Johansson
Tomas
T
Tunlid
Anders
A
D000704:Analysis of Variance; D001487:Basidiomycota / Q000235:genetics; D019143:Evolution, Molecular; D020224:Expressed Sequence Tags; D005453:Fluorescence; D018628:Gene Dosage; D020440:Gene Duplication; D005800:Genes, Fungal; D014644:Genetic Variation; D017404:In Situ Hybridization, Fluorescence; D008957:Models, Genetic; D038821:Mycorrhizae / Q000235:genetics*; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*