  Research articleSequence mining and transcript profiling to explore cyst nematode parasitismAxel A Elling1,2,3 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 10Divergence Inc., St. Louis, MO 63141, USA
BMC Genomics 2009, 10:58doi:10.1186/1471-2164-10-58
Additional filesAdditional file 1: H. glycines parasitome. Excel file showing H. glycines parasitome members, their contigs, probesets, expression cluster membership, mean expression data and q values. Format: XLS Size: 40KB Download file This file can be viewed with: Microsoft Excel Viewer Additional file 2: H. glycines secretome. Excel file showing H. glycines secretome members identified here, their contigs, probesets, expression cluster membership, mean expression data and q values. Format: XLS Size: 519KB Download file This file can be viewed with: Microsoft Excel Viewer Additional file 3: Plant-like H. glycines genes. Excel file showing H. glycines plant-like contigs, probesets, expression cluster membership, mean expression data and q values. Format: XLS Size: 40KB Download file This file can be viewed with: Microsoft Excel Viewer Additional file 4: Phytomicrobe-like H. glycines genes. Excel file showing H. glycines phytopathogen- and phytosymbiont-like contigs, probesets, expression cluster membership, mean expression data and q values. Format: XLS Size: 60KB Download file This file can be viewed with: Microsoft Excel Viewer Additional file 5: Soilmicrobe-like H. glycines genes. Excel file showing H. glycines soilmicrobe-like contigs, probesets, expression cluster membership, mean expression data and q values. Format: XLS Size: 47KB Download file This file can be viewed with: Microsoft Excel Viewer Additional file 6: 'Other' microbe-like H. glycines genes. Excel file showing H. glycines 'other' microbe-like contigs, probesets, expression cluster membership, mean expression data and q values. Format: XLS Size: 65KB Download file This file can be viewed with: Microsoft Excel Viewer Additional file 7: H. glycines parasitism-associated candidate genes. Excel file showing the combined H. glycines genes identified (pooled from additional files 1, 2, 3, 4, 5, 6). Format: XLS Size: 150KB Download file This file can be viewed with: Microsoft Excel Viewer Additional file 8: Expression patterns of plant-like H. glycines genes. TIFF file showing temporal expression patterns of H. glycines probesets with highest similarity to plant sequences. All H. glycines probesets encoding plant-like proteins were grouped into five expression clusters. The average expression pattern of each cluster is represented by a bold line. Format: TIFF Size: 478KB Download file Additional file 9: Expression patterns of phytomicrobe-like H. glycines genes. TIFF file showing temporal expression patterns of H. glycines probesets with highest similarity to phytopathogen and phytosymbiont sequences. All H. glycines probesets encoding phytopathogen- and phytosymbiont-like proteins were grouped into six expression clusters. The average expression pattern of each cluster is represented by a bold line. Format: TIFF Size: 483KB Download file Additional file 10: Expression patterns of soilmicrobe-like H. glycines genes. TIFF file showing temporal expression patterns of H. glycines probesets with highest similarity to soilmicrobe sequences. All H. glycines probesets encoding soilmicrobe-like proteins were grouped into six expression clusters. The average expression pattern of each cluster is represented by a bold line. Format: TIFF Size: 550KB Download file Additional file 11: Expression patterns of 'other' microbe-like H. glycines genes. TIFF file showing temporal expression patterns of H. glycines probesets with highest similarity to sequences from 'other' microbe sequences. All H. glycines probesets encoding 'other' microbe-like proteins were grouped into six expression clusters. The average expression pattern of each cluster is represented by a bold line. Format: TIFF Size: 635KB Download file Additional file 12: HDA2 multiple alignment. PDF file showing CLUSTAL W multiple alignment 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; Arabidopsis thaliana (At) AAM34784.1; Medicago truncatula (Mt) EV261025; Lotus japonicus (Lj) BW625394. The putative signal peptide-encoding sequence for the H. glycines HDA2 is underlined. Format: PDF Size: 317KB Download file This file can be viewed with: Adobe Acrobat Reader Additional file 13: Cross-hybridizing Glycine max probesets. Excel file showing cross-hybridizing G. max probesets, expression cluster membership, mean expression data and q values. Format: XLS Size: 391KB Download file This file can be viewed with: Microsoft Excel Viewer Additional file 14: Cross-hybridizing Phytophthora sojae probesets. Excel file showing cross-hybridizing P. sojae probesets, expression cluster membership, mean expression data and q values. Format: XLS Size: 57KB Download file This file can be viewed with: Microsoft Excel Viewer |
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