Volcano plot depicting differentially expressed homeologous gene copies obtained using P. fastigiatum full-lengths ESTs as a reference for tag mapping. With gene loci for which gene expression of individual homeologous copies could be studied we identified 245 genes up-regulated in P. enysii and 136 genes up-regulated in P. fastigiatum. 392 such loci were not differentially expressed between species (black cross). Among the up-regulated genes, six different patterns were detected. In 111 cases all copies of one locus were up-regulated in P. enysii ( dark blue stars); in 38 cases both copies were up-regulated in P. fastigiatum (light blue stars); for 101 and 65 sequences, one copy was up-regulated in P. enysii (yellow circles) and P. fastigiatum (orange circles), respectively, whereas the other copy was not differentially expressed and in 66 cases one copy was up-regulated in one species while the other was up-regulated in the other (red triangles). Log fold ratios >30 and < −30 indicate genes with zero tags in either of both species whereas log fold ratios between −10 and 10 indicate genes with tags present in both species but differing in abundance.