BMC Genomics 2009, 10:58 http://www.biomedcentral.com/1471-2164/10/58 Conclusion: We have established an expression atlas for all known H. glycines parasitism genes. Furthermore, in an effort to identify additional H. glycines genes with putative functions in parasitism, we have reduced the currently known 6,860 H. glycines genes to a pool of 788 most promising candidate genes (including known parasitism genes) and documented their expression profiles. Using our approach to pre-select genes likely involved in parasitism now allows detailed functional analyses in a manner not feasible for larger numbers of genes. The generation of the candidate pool described here is an important enabling advance because it will significantly facilitate the unraveling of fascinating plant-animal interactions and deliver knowledge that can be transferred to other pathogen-host systems. Ultimately, the exploration of true parasitism genes verified from the gene pool delineated here will identify weaknesses in the nematode life cycle that can be exploited by novel anti-nematode efforts. Background Heterodera glycines, the soybean cyst nematode, is a devas- tating pathogen of soybean production. Upon hatching as second-stage juveniles (J2), these nematodes migrate through the soil as infective J2, invade roots of soybean plants to become parasitic J2, and move intracellulary through the root tissue until they reach the vicinity of the vascular system, where they become sedentary and induce the formation of a feeding site, the syncytium [1-3]. H. gly- cines completely depends on syncytia for nutrition. Fol- lowing the development through two more juvenile stages (J3, J4), the nematodes reach adulthood. While adult females remain sedentary, adult males regain motility and leave the root to fertilize females, whose posterior bodies have broken out of the root into the rhizosphere during the course of growth and development. Ultimately, the females die and their body walls harden to protect the eggs, which are mostly retained in utero, until the environ- ment is favorable again for a new generation of nema- todes to hatch [1,4]. Secreted proteins are key molecular interfaces between parasite and host and enable H. glycines to infect soybean plants, which results in an estimated annual damage of $800 million to soybean production in the USA alone [5]. More specifically, secretory proteins that are produced in three large esophageal gland cells (one dorsal and two subventral) and that are injected into host plant cells through the nematode's hollow mouth spear, the stylet, are thought to allow H. glycines to migrate through plant tissue by softening and degrading cell walls and to induce and maintain a feeding site, the syncytium, which consists of modified fused host plant root cells. Many genes are involved in adapting cyst nematodes to a parasitic life style. However, only genes whose products are expressed in the nematode secretory glands and are injected into the host cells through the stylet (i.e., parasitism proteins) are called parasitism genes, which in turn have been termed parasitome in their entirety [6-8]. Previous studies in cyst nematodes (Heterodera spp. and Globodera spp.) identified genes encoding cell wall-degrading and -softening enzymes like beta-1,4-endoglucanase [9,10], pectate lyase [11,12], a putative arabinogalactan endo-1,4-beta-galac- tosidase [13] and an expansin [14] as members of the par- asitome. Apart from genes related to cell wall modifications, other genes whose products likely alter the normal host cell physiology to establish and maintain a syncytium belong to the parasitome, e.g., chorismate mutases [15,16], ubiquitin extension proteins [16,17], as well as S phase kinetochore-associated protein 1 (SKP1) and RING-like proteins [16]. While a few more parasitism proteins have similarity to known proteins, like the venom allergen-like proteins [18] or a chitinase [19], for most H. glycines parasitism proteins no clear function can be ascribed [16], although it has been shown that some are imported into plant cell nuclei [20]. To date, more than sixty parasitism genes have been identified in H. gly- cines. Most likely, however, the H. glycines parasitome is even larger. Furthermore, there may be proteins produced in organs/tissues other than the esophageal glands or pro- teins released by means other than the signal peptide- dependent secretory pathway that play critical roles in mediating cyst nematode parasitism. While secretory parasitism proteins that are released into plant host tissue are key factors to understand host-parasite interactions, many secretory proteins exist that do not leave the body of the nematode. These secretory proteins are involved in a vast array of non-parasitic signaling events within the nematode and can be found for example in the extracellu- lar matrix, intestinal lumen, cuticle or neuronal synapse. Previous studies leading to the identification of parasitism genes in cyst nematodes were based on cloning approaches of single genes [10,11,14,15,17] or exploited smaller scale cDNA libraries constructed from microaspi- rated gland cell contents [16,21,22]. However, larger scale genomic approaches offer an additional avenue to iden- tify more genes with putative functions in parasitism. While studies to characterize the overall gene expression of parasitic nematodes based on expressed sequence tags (ESTs) have become relatively common in recent years [e.g., [23-32]], very few reports dealt specifically with ESTs Page 2 of 17 (page number not for citation purposes)