Research article
Sequence mining and transcript profiling to explore cyst nematode parasitism
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* Corresponding author: Thomas J Baum tbaum@iastate.edu
1 Interdepartmental Genetics Program, Iowa State University, Ames, IA 50011, USA
2 Department of Plant Pathology, Iowa State University, Ames, IA 50011, USA
3 Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520, USA
4 Genome Sequencing Center, Department of Genetics, Washington University School of Medicine, St. Louis, MO 63108, USA
5 Center for Biomedical Informatics, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
6 Department of Statistics, Iowa State University, Ames, IA 50011, USA
7 Eli Lilly and Company, Lilly Research Laboratories, Greenfield, IN 46140, USA
8 Department of Plant Pathology, North Carolina State University, Raleigh, NC 27695, USA
9 Department of Plant Pathology, University of Georgia, Athens, GA 30602, USA
10 Divergence Inc., St. Louis, MO 63141, USA
BMC Genomics 2009, 10:58 doi:10.1186/1471-2164-10-58
Published: 30 January 2009Additional files
Additional 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