BMC Genomics 2009, 10:58 http://www.biomedcentral.com/1471-2164/10/58 'present' by Affymetrix' GCOS software (Affymetrix, Santa Clara, CA) in all three replications. BLAST searches All 6,860 unique Affymetrix H. glycines gene sequences (contigs) were aligned against the non-redundant Gen- Bank database (downloaded November 2005) using the following parameters in BLASTX with a post-processing cutoff value of 1e-05: filter = seg, lcfilter, W = 4, T = 20, E = 100, B = 25, V = 25, topcomboN = 1, golmax = 10. For Additional data file 1, all H. glycines parasitism gene nucleotide sequences (as found in GenBank) were aligned against the non-redundant GenBank database using standard NCBI BLASTX parameters with a post-processing cutoff value of 1e-15 (dated March 2008). To analyze cross-hybridizing G. max and P. sojae probesets, the respective Affymetrix probeset nucleotide sequences were aligned against the non-redundant GenBank database (downloaded December 2005) using the following parameters in BLASTX with a post-processing cutoff value of 1e-10: filter = seg, lcfilter, W = 4, T = 20, E = 100, B = 10, V = 10, topcomboN = 1, golmax = 10. Additionally, the same G. max and P. sojae probeset sequences were aligned against the non-redundant GenBank database (down- loaded February 2006) using the following parameters in BLASTN with a post-processing cutoff value of 1e-05: M = 1, N = -1, Q = 3, R = 3, lcmask, golmax = 10, topcomboN = 1, filter = seg, B = 100, V = 100, as well as against the 'est_other' database of dbEST (all ESTs other than human and mouse, dated May 12, 2006) using the following parameters in BLASTN with a post-processing cutoff value of 1e-05: M = 1, N = -1, Q = 3, R = 3, lcmask, golmax = 10, topcomboN = 1, filter = seg, and against an in-house cyst nematode nucleotide database (dated March 2006) [35] using the following parameters in BLASTN with a post- processing cutoff value of 1e-05: M = 1, N = -1, Q = 3, R = 3, lcmask, golmax = 10, topcomboN = 1, filter = seg, B = 20, V = 20. Identification of plant- or microbe-like H. glycines sequences BLASTX search results (cutoff value 1e-05) of 6,860 Affymetrix contigs against the non-redundant GenBank database were manually sorted into best matches to sequences from plants, phytopathogens/phytosymbionts, soil-living microbes and 'other' microbes. As a counter selection, all matches were removed from further analyses for which a Caenorhabditis spp. hit was within 15% of the BLAST score of the best plant or microbe alignment. InterProScan analyses InterProScan was run using InterPro data files dated November 2005 (iprscan_PTHR_DATA_12.0.tar). Inter- ProScan translated all 576 cross-hybridizing soybean and all 134 cross-hybridizing P. sojae probesets in six frames and then ran its suite of domain finding tools. We required a minimum translation length of 20 amino acids to be considered by InterProScan, and we used the EGC.0 translation table. Due to the six frames translation, each probeset typically had several alignments amongst the sig- nificant open reading frames (ORFs) found in the transla- tion. We kept, as representative of each probeset, the single longest aligning ORF that contained an InterPro domain, even though InterProScan may have found sev- eral ORFs for each probeset with alignments to some domain or motif. Results were parsed into files represent- ing expression clusters. Sequence alignment and phylogenetic tree for HDA2 sequences CLUSTAL W [43] was used to align selected HDA2 sequences and to construct a phylogenetic tree. For the phylogenetic tree, the 'neighbor joining' output format from CLUSTAL W was chosen and the 'correct distances' and 'ignore gaps' options were turned off. Data All Affymetrix Soybean Genome Array GeneChip raw and normalized data files analyzed here were deposited previ- ously in the MIAME-compliant ArrayExpress database [57] by these authors [35] and are freely available under accession number E-MEXP-1110. Abbreviations EST: expressed sequence tag; FDR: false discovery rate; HDA2: histone deacetylase-2; HDA19: histone deacety- lase-19; infJ2: infective second-stage juvenile; parJ2: para- sitic second-stage juvenile; J3: third-stage juvenile; J4: fourth-stage juvenile; ORF: open reading frame; qRT-PCR: quantitative real-time polymerase chain reaction Authors' contributions AAE planned and coordinated the study, analyzed the data and wrote the manuscript. MM and JPM oversaw sequencing and sequence analyses and edited the manu- script. XG and JM assisted in sequence analyses. JR assisted in statistical analyses. ELD provided material. RSH edited the manuscript. DN performed and directed statistical analyses and edited the manuscript. TJB planned the study and edited the manuscript. All authors read and approved the final manuscript. Additional material Additional file 1 H. glycines parasitome. Excel file showing H. glycines parasitome mem- bers, their contigs, probesets, expression cluster membership, mean expres- sion data and q values. Click here for file [http://www.biomedcentral.com/content/supplementary/1471- 2164-10-58-S1.xls] Page 14 of 17 (page number not for citation purposes)