Large-Scale Gene Discovery in the OomycetePhytophthora infestansReveals Likely Components of Phytopathogenicity Shared with True Fungi

Abstract

To overview the gene content of the important pathogen Phytophthora infestans, large-scale cDNA and genomic sequencing was performed. A set of 75,757 high-quality expressed sequence tags (ESTs) from P. infestans was obtained from 20 cDNA libraries representing a broad range of growth conditions, stress responses, and developmental stages. These included libraries from P. infestans-potato and -tomato interactions, from which 963 pathogen ESTs were identified. To complement the ESTs, onefold coverage of the P. infestans genome was obtained and regions of coding potential identified. A unigene set of 18,256 sequences was derived from the EST and genomic data and characterized for potential functions, stage-specific patterns of expression, and codon bias. Cluster analysis of ESTs revealed major differences between the expressed gene content of mycelial and spore-related stages, and affinities between some growth conditions. Comparisons with databases of fungal pathogenicity genes revealed conserved elements of pathogenicity, such as class III pectate lyases, despite the considerable evolutionary distance between oomycetes and fungi. Thirty-seven genes encoding components of flagella also were identified. Several genes not anticipated to occur in oomycetes were detected, including chitin synthases, phosphagen kinases, and a bacterial-type FtsZ cell-division protein. The sequence data described are available in a searchable public database.

Nonneutral GC3 and Retroelement Codon Mimicry in Phytophthora

“…Except for the stop codon, all the other redundant amino acid codons have a preference for the degenerate third position ending with C or G. A slightly lower GC% was found in P. ramorum codons. The preference of high GC3 codons in P. sojae and P. ramorum agrees with the results from P. infestans (Hraber and Weller 2001;Jiang et al 2005;Randall et al 2005). Therefore it can be concluded that the high GC3 of Phytophthora genes is due to biased usage of codons ending with C or G.…”

“…High GC content was found in the ORFs as previously reported (Jiang et al 2005;Randall et al 2005). The average GC percentage is 60.0% for P. sojae and 58.6% for P. ramorum.…”

“…The P. infestans EST databases are accessible at http:// www.pfgd.org and http://staff.vbi.vt.edu/estap and most Phytophthora EST sequences are available through GenBank (Kamoun et al 1999;Qutob et al 2000;Randall et al 2005) and http:// phytophthora.vbi.vt.edu/EST. Blumeria graminis and P. sojae EST databases were downloaded from Phytopathogenic Fungi and Oomycete EST Database Version 1.4 (Soanes et al 2002); http:// cogeme.ex.ac.uk.…”

“…The notorious plant pathogen Phytophthora infestans is one of the organisms that clearly shows codon bias (Randall et al 2005;Jiang et al 2005). Phytophthora is a genus comprised of over 65 phytopathogenic species which cause severe damage in agriculture, forestry, and natural habitats.…”

“…P. sojae and P. infestans, the two species for which extensive EST data sets are available (Randall et al 2005;Gajendran et al 2006;Qutob et al 2000), have an estimated GC content of about 50% overall in the genome and about 60% in coding regions (Jiang et al 2005). In P. infestans, high GC3 has been reported to correlate with a high GC content and was found to be related to codon bias (Jiang et al 2005;Randall et al 2005). An elevated GC content is not found in the marine diatom Thalassiosira pseudonana, the only other heterokont that has been sequenced to date.…”