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Transcriptomic analysis of the entomopathogenic nematode Heterorhabditis bacteriophora TTO1

Bai, Xiaodong and Adams, Byron J. and Ciche, Todd A. and Clifton, Sandra and Gaugler, Randy and Hogenhout, Saskia A. and Spieth, John and Sternberg, Paul W. and Wilson, Richard K. and Grewal, Parwinder S. (2009) Transcriptomic analysis of the entomopathogenic nematode Heterorhabditis bacteriophora TTO1. BMC Genomics, 10 . Art. No. 205. ISSN 1471-2164. PMCID PMC2686736. https://resolver.caltech.edu/CaltechAUTHORS:20090706-113251763

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Abstract

Background: The entomopathogenic nematode Heterorhabditis bacteriophora and its symbiotic bacterium, Photorhabdus luminescens, are important biological control agents of insect pests. This nematode-bacterium-insect association represents an emerging tripartite model for research on mutualistic and parasitic symbioses. Elucidation of mechanisms underlying these biological processes may serve as a foundation for improving the biological control potential of the nematode-bacterium complex. This large-scale expressed sequence tag (EST) analysis effort enables gene discovery and development of microsatellite markers. These ESTs will also aid in the annotation of the upcoming complete genome sequence of H. bacteriophora. Results: A total of 31,485 high quality ESTs were generated from cDNA libraries of the adult H. bacteriophora TTO1 strain. Cluster analysis revealed the presence of 3,051 contigs and 7,835 singletons, representing 10,886 distinct EST sequences. About 72% of the distinct EST sequences had significant matches (E value < 1e-5) to proteins in GenBank's non-redundant (nr) and Wormpep190 databases. We have identified 12 ESTs corresponding to 8 genes potentially involved in RNA interference, 22 ESTs corresponding to 14 genes potentially involved in dauer-related processes, and 51 ESTs corresponding to 27 genes potentially involved in defense and stress responses. Comparison to ESTs and proteins of free-living nematodes led to the identification of 554 parasitic nematode-specific ESTs in H. bacteriophora, among which are those encoding F-box-like/WD-repeat protein theromacin, Bax inhibitor-1-like protein, and PAZ domain containing protein. Gene Ontology terms were assigned to 6,685 of the 10,886 ESTs. A total of 168 microsatellite loci were identified with primers designable for 141 loci. Conclusion: A total of 10,886 distinct EST sequences were identified from adult H. bacteriophora cDNA libraries. BLAST searches revealed ESTs potentially involved in parasitism, RNA interference, defense responses, stress responses, and dauer-related processes. The putative microsatellite markers identified in H. bacteriophora ESTs will enable genetic mapping and population genetic studies. These genomic resources provide the material base necessary for genome annotation, microarray development, and in-depth gene functional analysis.


Item Type:Article
Related URLs:
URLURL TypeDescription
http://dx.doi.org/10.1186/1471-2164-10-205DOIArticle
http://www.biomedcentral.com/1471-2164/10/205PublisherArticle
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2686736PubMed CentralArticle
ORCID:
AuthorORCID
Sternberg, Paul W.0000-0002-7699-0173
Additional Information:© Bai et al; licensee BioMed Central Ltd. 2009. This article is published under license to 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. Received: 21 July 2008; accepted: 30 April 2009; published: 30 April 2009. This project was supported by grants from the United States Department of Agriculture (USDA)/National Science Foundation (NSF) Microbial Genome Sequence Program and National Human Genome Research Institute (NHGRI) awarded to PSG, BJA, TAC, RG, and PWS. We thank teams of scientists led by Lucinda Fulton, Makedonka Mitreva, Kimberly Delehaunty, Michael Becker, and Brenda Theising at the Genome Center at Washington University School of Medicine in St. Louis, MO who produced and curated EST data.
Funders:
Funding AgencyGrant Number
Department of AgricultureUNSPECIFIED
NSFUNSPECIFIED
National Human Genome Research InstituteUNSPECIFIED
PubMed Central ID:PMC2686736
Record Number:CaltechAUTHORS:20090706-113251763
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20090706-113251763
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:14496
Collection:CaltechAUTHORS
Deposited By: Jason Perez
Deposited On:08 Jul 2009 16:21
Last Modified:03 Oct 2019 00:50

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