BMC Genomics 2009, 10:58 http://www.biomedcentral.com/1471-2164/10/58 sFCeiLqgUuueSrnTecA4eLs W phylogenetic tree for HDA2 homolog CLUSTAL W phylogenetic tree for HDA2 homolog sequences. Including H. glycines (Hg) Affymetrix consensus sequence for probeset HgAffx.19783.1.S1_AT; C. elegans (Ce) Wormbase entry CE01472; Trichinella spiralis (Ts) ES567375; Globodera rostochiensis (Gr) AW506399; Arabidop- sis thaliana (At) AAM34784.1; Medicago truncatula (Mt) EV261025; Lotus japonicus (Lj) BW625394. proteins. If so, these genes would be interesting candi- dates for further studies as they might be involved in para- sitism. Particularly intriguing examples were genes encoding proteins for which secretion would not be expected in plants or microbes, but for which homolo- gous sequences in H. glycines possessed a signal peptide- encoding region. For example, we found two H. glycines genes (HgAffx.19783.1, HgAffx.19046.1) with similarity to Arabidopsis histone deacetylase 2 (AAM34784.1) and Arabidopsis RNA polymerase II transcription factor (NP_175948.1), none of which are secreted in Arabidop- sis, but both contained a signal peptide in H. glycines (Additional file 12). Given the fact that these proteins had higher similarity with plant proteins than with homologs in the fully sequenced C. elegans or C. briggsae genomes, secretion of these proteins into host plants and a role in parasitism seems very likely and warrants further experi- ments. It has been demonstrated that histone modifica- tions are involved in gene regulation [42] so that a secreted Arabidopsis-like histone deacetylase would be an exciting example of how cyst nematodes could modify gene expression of their host plants and mimic plant pro- teins to interfere with the physiology of the host. It has been shown that in Arabidopsis, histone acetylation is involved in vernalization [45], is responsive to light [46], and that histone deacetylase 19 (HDA19) can be induced by wounding, pathogen attack and plant hormones [47]. Furthermore, overexpression of HDA19 resulted in increased pathogen resistance [47]. What role a secreted H. glycines histone deacetylase might have during the infection process remains elusive at this point. As stated earlier, the sequences upon which the Affymetrix GeneChip is based are mostly ESTs, which frequently are incomplete at their 5'-ends, which is the location of the signal peptide-encoding sequence. Consequently, we expect that more of the plant and microbe-like H. glycines genes encode secretory proteins than we were able to identify. On the other hand, not all of the H. glycines pro- teins that matched plant or microbe sequences and that did have a signal peptide are necessarily secreted into the environment (i.e., the host plant) but are rather involved in processes within the nematode. Further experimental studies are needed to localize the putative secretory pro- teins identified here in the nematode either by in situ hybridizations or immune localizations. Also, it needs to be noted that certain proteins can be secreted even with- out a canonical N-terminal signal peptide [48], which adds an additional layer of complexity to the study of cyst nematode parasitism. Our findings of H. glycines genes with similarity to plant or microbe sequences identified here do not imply that all these genes have been acquired by horizontal gene trans- fer or have evolved to mimic host proteins. The set of genes identified here is rather meant as a first step to iden- tify a pool of candidates from which true parasitism- related genes can be isolated from highly conserved, but not parasitism-related ones, in the future. Interestingly, recent studies have demonstrated that cellulase genes must have been present in an ancient ancestor of bilate- rian animals [49,50] and, therefore, may not have been acquired by nematodes through horizontal gene transfer. A direct demonstration of H. glycines genes that are con- served in microbes and plants could be seen in the P. sojae and soybean probesets of the Affymetrix Soybean Genome Array GeneChip to which H. glycines probes cross-hybridized in our experiments. While many of the Page 9 of 17 (page number not for citation purposes)