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Symbiosis

, Volume 55, Issue 3, pp 111–118 | Cite as

Applications of high-throughput sequencing to symbiotic nematodes of the genus Heterorhabditis

  • Hillel T. Schwartz
  • Igor Antoshechkin
  • Paul W. SternbergEmail author
Article

Abstract

Entomopathogenic nematodes of the genus Heterorhabditis live in symbiosis with pathogenic Photorhabdus bacteria. Heterorhabditis nematodes are entirely dependent on these bacteria for their food source; in return, the nematodes offer the bacteria a way to infect and kill insects. For their part, Photorhabdus bacteria are lethal to a broad range of insect hosts, to other nematodes, and to other microorganisms, but not to their Heterorhabditis hosts. These nematodes offer the potential to provide a robust experimental system for the in•depth study of a mutually beneficial symbiotic relationship, with both members of the partnership accessible to molecular and genetic studies. New genomic technologies offer the possibility for this potential to be realized, and for Heterorhabditis nematodes to become a standard model system for the investigation of host•symbiote relationships. We present a perspective on the application of these technologies to nematode•bacterial symbiosis and an update on our efforts to sequence three Heterorhabditis species reported at the recent NemaSym meeting.

Keywords

Genome Assembly Read Length Illumina Sequencing Insect Host Recombinant Line 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

References

  1. Akhurst RJ, Mourant RG, Baud L, Boemare NE (1996) Phenotypic and DNA relatedness between nematode symbionts and clinical strains of the genus Photorhabdus (Enterobacteriaceae). Int J Syst Bacteriol 46:1034–1041PubMedCrossRefGoogle Scholar
  2. Baird NA, Etter PD, Atwood TS, Currey MC, Shiver AL, Lewis ZA, Selker EU, Cresko WA, Johnson EA (2008) Rapid SNP discovery and genetic mapping using sequenced RAD markers. PLoS One 3:e3376PubMedCrossRefGoogle Scholar
  3. Baugh LR, Demodena J, Sternberg PW (2009) RNA Pol II accumulates at promoters of growth genes during developmental arrest. Science 324:92–94PubMedCrossRefGoogle Scholar
  4. Bennett HP, Clarke DJ (2005) The pbgPE operon in Photorhabdus luminescens is required for pathogenicity and symbiosis. J Bacteriol 187:77–84PubMedCrossRefGoogle Scholar
  5. Bentley DR, Balasubramanian S, Swerdlow HP, Smith GP, Milton J, Brown CG, Hall KP, Evers DJ, Barnes CL, Bignell HR et al (2008) Accurate whole human genome sequencing using reversible terminator chemistry. Nature 456:53–59PubMedCrossRefGoogle Scholar
  6. C. elegans sequencing consortium (1998) Genome sequence of the nematode C. elegans: a platform for investigating biology. Science 282:2012–2018Google Scholar
  7. Ciche TA, Ensign JC (2003) For the insect pathogen Photorhabdus luminescens, which end of a nematode is out? Appl Environ Microbiol 69:1890–1897PubMedCrossRefGoogle Scholar
  8. Ciche TA, Sternberg PW (2007) Postembryonic RNAi in Heterorhabditis bacteriophora: a nematode insect parasite and host for insect pathogenic symbionts. BMC Dev Biol 7:101PubMedCrossRefGoogle Scholar
  9. Ciche TA, Kim KS, Kaufmann-Daszczuk B, Nguyen KC, Hall DH (2008) Cell Invasion and Matricide during Photorhabdus luminescens Transmission by Heterorhabditis bacteriophora Nematodes. Appl Environ Microbiol 74:2275–2287PubMedCrossRefGoogle Scholar
  10. Clarke DJ (2008) Photorhabdus: a model for the analysis of pathogenicity and mutualism. Cell Microbiol 10:2159–2167PubMedCrossRefGoogle Scholar
  11. Doitsidou M, Poole RJ, Sarin S, Bigelow H, Hobert O (2010) C. elegans mutant identification with a one-step whole-genome-sequencing and SNP mapping strategy. PloS one 5:e15435PubMedCrossRefGoogle Scholar
  12. Duchaud E, Rusniok C, Frangeul L, Buchrieser C, Givaudan A, Taourit S, Bocs S, Boursaux-Eude C, Chandler M, Charles JF et al (2003) The genome sequence of the entomopathogenic bacterium Photorhabdus luminescens. Nat Biotechnol 21:1307–1313PubMedCrossRefGoogle Scholar
  13. Enright MR, Griffin CT (2004) Specificity of association between Paenibacillus spp. and the entomopathogenic nematodes, Heterorhabditis spp. Microb Ecol 48:414–423PubMedCrossRefGoogle Scholar
  14. Enright MR, McInerney JO, Griffin CT (2003) Characterization of endospore-forming bacteria associated with entomopathogenic nematodes, Heterorhabditis spp., and description of Paenibacillus nematophilus sp. nov. Int J Syst Evol Microbiol 53:435–441PubMedCrossRefGoogle Scholar
  15. Forst S, Nealson K (1996) Molecular biology of the symbiotic-pathogenic bacteria Xenorhabdus spp. and Photorhabdus spp. Microbiol Rev 60:21–43PubMedGoogle Scholar
  16. Gnerre S, Maccallum I, Przybylski D, Ribeiro FJ, Burton JN, Walker BJ, Sharpe T, Hall G, Shea TP, Sykes S et al (2011) High-quality draft assemblies of mammalian genomes from massively parallel sequence data. Proc Natl Acad Sci U S A 108:1513–1518PubMedCrossRefGoogle Scholar
  17. Hallem EA, Dillman AR, Hong AV, Zhang Y, Yano JM, DeMarco SF, Sternberg PW (2011) A sensory code for host seeking in parasitic nematodes. Current biology: CB 21:377–383PubMedCrossRefGoogle Scholar
  18. Han R, Ehlers R (1999) Trans-specific nematicidal activity of Photorhabdus luminescens. Nematology 1:687–693CrossRefGoogle Scholar
  19. Han R, Ehlers RU (2000) Pathogenicity, development, and reproduction of Heterorhabditis bacteriophora and Steinernema carpocapsae under axenic in vivo conditions. J Invertebr Pathol 75:55–58PubMedCrossRefGoogle Scholar
  20. Hashmi S, Hashmi G, Glazer I, Gaugler R (1998) Thermal response of Heterorhabditis bacteriophora transformed with the Caenorhabditis elegans hsp70 encoding gene. J Exp Zool 281:164–170PubMedCrossRefGoogle Scholar
  21. Hu PJ (2007) Dauer. WormBook, ed. The C. elegans Research Community, doi/ 10.1895/wormbook.1.144.1, http://www.wormbook.org.
  22. Hu KJ, Li JX, Webster JM (1999) Nematicidal metabolites produced by Photorhabdus luminescens (Enterobacteriaceae), bacterial symbiont of entomopathogenic nematodes. Nematology 1:457–469CrossRefGoogle Scholar
  23. Koltai H, Glazer I, Segal D (1994) Phenotypic and genetic characterization of two new mutants of Heterorhabditis bacteriophora. J Nematol 26:32–39PubMedGoogle Scholar
  24. Li J, Chen G, Webster JM, Czyzewska E (1995) Antimicrobial metabolites from a bacterial symbiont. J Nat Prod 58:1081–1086PubMedCrossRefGoogle Scholar
  25. Li L, Stoeckert CJ Jr, Roos DS (2003) OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Res 13:2178–2189PubMedCrossRefGoogle Scholar
  26. Li G, Fullwood MJ, Xu H, Mulawadi FH, Velkov S, Vega V, Ariyaratne PN, Mohamed YB, Ooi HS, Tennakoon C et al (2010) ChIA-PET tool for comprehensive chromatin interaction analysis with paired-end tag sequencing. Genome Biol 11:R22PubMedCrossRefGoogle Scholar
  27. Loewenstein Y, Raimondo D, Redfern OC, Watson J, Frishman D, Linial M, Orengo C, Thornton J, Tramontano A (2009) Protein function annotation by homology-based inference. Genome Biol 10:207PubMedCrossRefGoogle Scholar
  28. Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Bemben LA, Berka J, Braverman MS, Chen YJ, Chen Z et al (2005) Genome sequencing in microfabricated high-density picolitre reactors. Nature 437:376–380PubMedGoogle Scholar
  29. Metzker ML (2010) Sequencing technologies - the next generation. Nat Rev Genet 11:31–46PubMedCrossRefGoogle Scholar
  30. Miller JR, Koren S, Sutton G (2010) Assembly algorithms for next-generation sequencing data. Genomics 95:315–327PubMedCrossRefGoogle Scholar
  31. Milstead JE (1979) Heterorhabditis bacteriophora as a vector for introducing its associated bacterium into the hemocoel of galleria-mellonella larvae. J Invertebr Pathol 33:324–327CrossRefGoogle Scholar
  32. Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B (2008) Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nature methods 5:621–628PubMedCrossRefGoogle Scholar
  33. Mortazavi A, Schwarz EM, Williams B, Schaeffer L, Antoshechkin I, Wold BJ, Sternberg PW (2010) Scaffolding a Caenorhabditis nematode genome with RNA-seq. Genome Res 20:1740–1747PubMedCrossRefGoogle Scholar
  34. Neely RK, Deen J, Hofkens J (2011) Optical mapping of DNA: single-molecule-based methods for mapping genomes. Biopolymers 95:298–311PubMedCrossRefGoogle Scholar
  35. Neiman M, Lundin S, Savolainen P, Ahmadian A (2011) Decoding a substantial set of samples in parallel by massive sequencing. PLoS One 6:e17785PubMedCrossRefGoogle Scholar
  36. Nikoloski Z, Grimbs S, Klie S, Selbig J (2011) Complexity of automated gene annotation. Bio Systems 104:1–8PubMedCrossRefGoogle Scholar
  37. Oh SW, Mukhopadhyay A, Dixit BL, Raha T, Green MR, Tissenbaum HA (2006) Identification of direct DAF-16 targets controlling longevity, metabolism and diapause by chromatin immunoprecipitation. Nat Genet 38:251–257PubMedCrossRefGoogle Scholar
  38. Popiel I, Vasquez EM (1991) Cryopreservation of Steinernema carpocapsae and Heterorhabditis bacteriophora. J Nematol 23:432–437PubMedGoogle Scholar
  39. Qiu X, Han R, Yan X, Liu M, Cao L, Yoshiga T, Kondo E (2009) Identification and characterization of a novel gene involved in the trans-specific nematicidal activity of Photorhabdus luminescens LN2. Appl Environ Microbiol 75:4221–4223PubMedCrossRefGoogle Scholar
  40. Rockman MV, Kruglyak L (2008) Breeding designs for recombinant inbred advanced intercross lines. Genetics 179:1069–1078PubMedCrossRefGoogle Scholar
  41. Roy PJ, Stuart JM, Lund J, Kim SK (2002) Chromosomal clustering of muscle-expressed genes in Caenorhabditis elegans. Nature 418:975–979PubMedGoogle Scholar
  42. Somvanshi VS, Kaufmann-Daszczuk B, Kim KS, Mallon S, Ciche TA (2010) Photorhabdus phase variants express a novel fimbrial locus, mad, essential for symbiosis. Mol MicrobiolGoogle Scholar
  43. Stanke M, Waack S (2003) Gene prediction with a hidden Markov model and a new intron submodel. Bioinformatics 19(Suppl 2):ii215–ii225PubMedCrossRefGoogle Scholar
  44. Stanke M, Diekhans M, Baertsch R, Haussler D (2008) Using native and syntenically mapped cDNA alignments to improve de novo gene finding. Bioinformatics 24:637–644PubMedCrossRefGoogle Scholar
  45. Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, van Baren MJ, Salzberg SL, Wold BJ, Pachter L (2010) Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol 28:511–515PubMedCrossRefGoogle Scholar
  46. Valouev A, Ichikawa J, Tonthat T, Stuart J, Ranade S, Peckham H, Zeng K, Malek JA, Costa G, McKernan K et al (2008) A high-resolution, nucleosome position map of C. elegans reveals a lack of universal sequence-dictated positioning. Genome Res 18:1051–1063PubMedCrossRefGoogle Scholar
  47. Waterfield NR, Ciche T, Clarke D (2009) Photorhabdus and a host of hosts. Annu Rev Microbiol 63:557–574PubMedCrossRefGoogle Scholar
  48. Watson RJ, Joyce SA, Spencer GV, Clarke DJ (2005) The exbD gene of Photorhabdus temperata is required for full virulence in insects and symbiosis with the nematode Heterorhabditis. Mol Microbiol 56:763–773PubMedCrossRefGoogle Scholar
  49. Zhang Y, Ma C, Delohery T, Nasipak B, Foat BC, Bounoutas A, Bussemaker HJ, Kim SK, Chalfie M (2002) Identification of genes expressed in C. elegans touch receptor neurons. Nature 418:331–335PubMedCrossRefGoogle Scholar
  50. Zhou X, Kaya HK, Heungens K, Goodrich-Blair H (2002) Response of ants to a deterrent factor(s) produced by the symbiotic bacteria of entomopathogenic nematodes. Appl Environ Microbiol 68:6202–6209PubMedCrossRefGoogle Scholar
  51. Zhou X, Ren L, Meng Q, Li Y, Yu Y, Yu J (2010) The next-generation sequencing technology and application. Protein Cell 1:520–536PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media B.V. 2012

Authors and Affiliations

  • Hillel T. Schwartz
    • 1
  • Igor Antoshechkin
    • 2
  • Paul W. Sternberg
    • 1
    Email author
  1. 1.Howard Hughes Medical Institute and Division of Biology, California Institute of TechnologyPasadenaUSA
  2. 2.Division of Biology, California Institute of TechnologyPasadenaUSA

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