Molecular relationships among some families of SSPs expressed during infection. (A) 31 related predicted SSPs common to four rust fungal species. Comparisons were seeded by Pt Contig5547 (arrow) which represents a gene expressed and, based on EST counts, possibly induced upon infection. Pt proteins predicted from the genome representing the unigenes were used in the comparison; several "unigenes" represented the same Pt protein indicating they did not collapse into one contig for various reasons (possibly representing allelic sequences). (B) Relationship of a small family of Puccinia-specific, small (~118 aa) SSPs; the two Pgt pairs are likely allelic proteins. Note that no proper gene calls exist (yet) for the Pt proteins and thus more members could exist. Relationships based on a ClustalW alignment (Additional file 10) were inferred using the Maximum Parsimony method (Close-Neighbor-Interchange algorithm, gaps and missing data were eliminated from the dataset). Bootstrap consensus tree (1000 replicates) with values at the nodes. SSPs indicated with an asterisk were used as outgroups. Phylogenetic analyses were conducted in MEGA4 .
Xu et al. BMC Genomics 2011 12:161 doi:10.1186/1471-2164-12-161