Transcriptomic analysis of the entomopathogenic nematode Heterorhabditis bacteriophora TTO1

doi:10.1186/1471-2164-10-205

BMC Genomics
Volume 10

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Bai X
Adams BJ
Ciche TA
Clifton S
Gaugler R
Hogenhout SA
Spieth J
Sternberg PW
Wilson RK
Grewal PS

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Adams BJ
Ciche TA
Clifton S
Gaugler R
Hogenhout SA
Spieth J
Sternberg PW
Wilson RK
Grewal PS
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Research article

Transcriptomic analysis of the entomopathogenic nematode Heterorhabditis bacteriophora TTO1

Xiaodong Bai¹ , Byron J Adams² , Todd A Ciche³ , Sandra Clifton⁴^,5 , Randy Gaugler⁶ , Saskia A Hogenhout⁷ , John Spieth⁴^,5 , Paul W Sternberg⁸ , Richard K Wilson⁴^,5 and Parwinder S Grewal¹

¹Department of Entomology, The Ohio State University – OARDC, Wooster, Ohio, USA

²Department of Biology and Evolutionary Ecology Laboratories, Brigham Young University, Provo, UT, USA

³Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA

⁴Department of Genetics, Washington University School of Medicine, St Louis, MO, USA

⁵Genome Center, Washington University School of Medicine, St Louis, MO, USA

⁶Department of Entomology, Rutgers University, New Brunswick, NJ, USA

⁷Department of Disease and Stress Biology, The John Innes Centre, Norwich, UK

⁸Howard Hughes Medical Institute and Division of Biology, California Institute of Technology, Pasadena, CA, USA

author email corresponding author email

BMC Genomics 2009, 10:205doi:10.1186/1471-2164-10-205


Published:	30 April 2009

Additional files

Additional file 1:

ContigComponents. Components of H. bacteriophora assembled contigs. The table includes the components of H. bacteriophora assembled contigs, including contig names and their comma-delimited components in GenBank accession numbers.

Format: XLS Size: 444KB Download file

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Additional file 2:

defense_stress_response_genes. H. bacteriophora distinct ESTs similar to C. elegans genes involved in defense and stress responses. This table contains H. bacteriophora distinct ESTs matching to C. elegans genes that are involved in defense and stress responses. Information of each H. bacteriophora distinct EST includes matching C. elegans gene, its description, E value of the BLASTx search, alignment, and percentage similarity.

Format: XLS Size: 34KB Download file

This file can be viewed with: Microsoft Excel Viewer

Additional file 3:

NematodeTaxa. Nematode species that ESTs used in the analysis came from. The table includes the nematode species in the categories of AHPNs, FLNs, and PPNs, the clade they belong to, and their corresponding number of ESTs in GenBank when the analysis was done.

Format: XLS Size: 24KB Download file

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Additional file 4:

panESTs. Summary of BLASTx identification of parasitic nematode-specific H. bacteriophora ESTs. The table describes the best BLASTx matches to GenBank's nr database of the 554 parasitic nematode-specific H. bacteriophora ESTs, including distinct EST ID, length, and annotation of the top BLASTx hit, including accession number, length, description, E value, bit score, frame, query_start, query_end, hit_start, hit_end, positives, and identities.

Format: XLS Size: 102KB Download file

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Additional file 5:

GOassignment. Summary of GO assignment of H. bacteriophora distinct ESTs. The table describes the GO assignment for each of 10,886 H. bacteriophora distinct ESTs, of which 4,201 have "no GO assignment". The GO terms separated by semicolons include accession numbers, term descriptions, and term types.

Format: XLS Size: 1.2MB Download file

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Additional file 6:

msat. Summary of microsatellite loci identified in H. bacteriophora distinct ESTs. The table describes the microsatellite loci identified in H. bacteriophora distinct ESTs, including the ID and length of H. bacteriophora distinct EST ID, the start and stop coordinates and motif units of the microsatellite loci, GC contents of the distinct ESTs and the flanking sequences, primer sequence, length, and Tm of the left and right primers, and the size of the amplification product from these primers. The asterisk (*) marking H. bacteriophora distinct EST IDs denotes that the primers designed for these loci amplify other adjacent loci too.

Format: XLS Size: 66KB Download file

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