BMC Genomics Research article BioMed Central Open Access Sequence mining and transcript profiling to explore cyst nematode parasitism Axel A Elling1,2,3, Makedonka Mitreva4, Xiaowu Gai5, John Martin4, Justin Recknor6,7, Eric L Davis8, Richard S Hussey9, Dan Nettleton6, James P McCarter4,10 and Thomas J Baum*1,2 Address: 1Interdepartmental Genetics Program, Iowa State University, Ames, IA 50011, USA, 2Department of Plant Pathology, Iowa State University, Ames, IA 50011, USA, 3Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520, USA, 4Genome Sequencing Center, Department of Genetics, Washington University School of Medicine, St. Louis, MO 63108, USA, 5Center for Biomedical Informatics, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA, 6Department of Statistics, Iowa State University, Ames, IA 50011, USA, 7Eli Lilly and Company, Lilly Research Laboratories, Greenfield, IN 46140, USA, 8Department of Plant Pathology, North Carolina State University, Raleigh, NC 27695, USA, 9Department of Plant Pathology, University of Georgia, Athens, GA 30602, USA and 10Divergence Inc., St. Louis, MO 63141, USA Email: Axel A Elling - axel.elling@yale.edu; Makedonka Mitreva - mmitreva@watson.wustl.edu; Xiaowu Gai - xgai@genome.chop.edu; John Martin - jmartin@watson.wustl.edu; Justin Recknor - justin.recknor@gmail.com; Eric L Davis - eric_davis@ncsu.edu; Richard S Hussey - hussey@uga.edu; Dan Nettleton - dnett@iastate.edu; James P McCarter - jmccarte@watson.wustl.edu; Thomas J Baum* - tbaum@iastate.edu * Corresponding author Published: 30 January 2009 BMC Genomics 2009, 10:58 doi:10.1186/1471-2164-10-58 This article is available from: http://www.biomedcentral.com/1471-2164/10/58 Received: 2 August 2008 Accepted: 30 January 2009 © 2009 Elling et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Abstract Background: Cyst nematodes are devastating plant parasites that become sedentary within plant roots and induce the transformation of normal plant cells into elaborate feeding cells with the help of secreted effectors, the parasitism proteins. These proteins are the translation products of parasitism genes and are secreted molecular tools that allow cyst nematodes to infect plants. Results: We present here the expression patterns of all previously described parasitism genes of the soybean cyst nematode, Heterodera glycines, in all major life stages except the adult male. These insights were gained by analyzing our gene expression dataset from experiments using the Affymetrix Soybean Genome Array GeneChip, which contains probeset sequences for 6,860 genes derived from preparasitic and parasitic H. glycines life stages. Targeting the identification of additional H. glycines parasitism-associated genes, we isolated 633 genes encoding secretory proteins using algorithms to predict secretory signal peptides. Furthermore, because some of the known H. glycines parasitism proteins have strongest similarity to proteins of plants and microbes, we searched for predicted protein sequences that showed their highest similarities to plant or microbial proteins and identified 156 H. glycines genes, some of which also contained a signal peptide. Analyses of the expression profiles of these genes allowed the formulation of hypotheses about potential roles in parasitism. This is the first study combining sequence analyses of a substantial EST dataset with microarray expression data of all major life stages (except adult males) for the identification and characterization of putative parasitism-associated proteins in any parasitic nematode. Page 1 of 17 (page number not for citation purposes)