G. max InterPro domain Ubiquitin IPR000626 Extensin-like protein IPR003883 Glutamine amidotransferase IPR000583 ATP-sulfurylase IPR002650 Histone-fold IPR009072 Zinc finger, C2H2-type IPR007087 Major intrinsic protein IPR000425 EGF-like region IPR013032 DNA-binding WRKY IPR003657 Cytochrome c oxidase IPR000883 Cupredoxin IPR008972 Bet v I allergen IPR000916 Chlorophyll A-B binding protein IPR001344 Orn/DAP/Arg decarboxylase 2 IPR000183 No apical meristem (NAM) protein IPR003441 IQ calmodulin-binding region IPR000048 Zinc finger, RING-type IPR001841 BURP IPR004873 Ribosomal protein L7Ae/L30e/ IPR004038 S12e/Gadd45 UspA IPR006016 Ribosomal protein L32e IPR001515 Dehydrin Thioredoxin-like fold Thiamine pyrophosphate enzyme DNA photolyase *As defined in Methods **FDR 5% IPR000167 IPR012336 IPR011766 IPR005101 16 9 9 8 6 6 5 5 4 4 4 3 3 3 3 3 3 3 3 3 3 3 3 3 2 Sugar transporter superfamily IPR005829 EGF-like region IPR013032 Peptidase S8 and S53 IPR000209 HMG-I and HMG-Y, DNA-binding IPR000637 TonB box, N-terminal IPR010916 Penicillin-binding protein IPR012338 Rhodopsin-like GPCR superfamily IPR000276 DEAD/DEAH box helicase IPR001410 Prefoldin IPR009053 Helix-turn-helix, Fis-type IPR002197 Zinc finger, C2H2-type IPR007087 Ctr copper transporter IPR007274 Glycoside hydrolase IPR001764 Zinc finger, RING-type IPR001841 Protein prenyltransferase IPR002088 Whey acidic protein IPR008197 Histone-fold IPR009072 Ribosomal protein L10 IPR001790 Major facilitator superfamily IPR011701 MFS_1 Phosphotransferase KptA/Tpt1 IPR002745 Regulator of chromosome IPR000408 condensation Inositol 1, 3, 4-trisphosphate 56- IPR008656 kinase Serine carboxypeptidase IPR001563 Na+ solute symporter IPR001734 Fructose-bisphosphate aldolase IPR000741 3 3 2 2 2 2 2 2 2 2 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 BMC Genomics 2009, 10:58 http://www.biomedcentral.com/1471-2164/10/58 Table 2: The 25 most abundant InterPro domains for G. max and P. sojae probesets that cross-hybridized with H. glycines probes. P. sojae Number of probesets InterPro domain Number of probesets signals for cross-hybridizing soybean and P. sojae probesets must originate from homologous genes in H. glycines. Conclusion In summary, we have identified a novel pool of putative parasitism-associated genes, a significant proportion of which, we hypothesize, will turn out to have parasitic functions after functional assays have been performed. We also raise the possibility that H. glycines might have acquired many more genes through horizontal gene trans- fer and might mimic many more plant proteins, all of which could be involved in parasitism, than previously thought. Using powerful genomic tools, this study has reduced the total number of 6,860 currently known H. gly- cines genes to a pool of 788 candidate genes, from which additional true parasitism genes can be identified in future studies. The identification of these candidate genes is a very significant advance for the field, but also of broad interest for pathogen-host research in general because this new pool of genes will help unravel sophisticated plant- animal interactions leading to a successful parasitic rela- tionship and deliver knowledge that can be transferred to other pathogen-host systems. Ultimately, the verification of true parasitism genes from the pool of candidate genes isolated here and their subsequent functional characteri- zation will identify weaknesses in the nematode life cycle that can be targeted in novel anti-nematode efforts. Methods Nematode cultivation The microarray data analyzed here is based on our previ- ously published experiments [35]. Briefly, for that study, we planted forty pots of Kenwood 94 soybean seed under greenhouse conditions in three replications and all nema- todes used within a given replication were from the same experimental setup and the same batch of eggs. Two weeks after planting, each pot was inoculated with 15,000– 20,000 H. glycines strain OP-50 [51] infective J2. The inoc- ulum was collected from 4 day old hatch chambers, each containing about two million H. glycines OP-50 eggs. From the same batch of eggs used in the hatch chamber, 50,000 eggs were collected and flash frozen in liquid nitrogen, for use as the egg stage hybridization probe. After four days, an aliquot of 50,000 hatched infective J2 was flash frozen in liquid nitrogen, for use as the infective Page 12 of 17 (page number not for citation purposes)