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Background  Nematodes are the most numerous animals in the soil. Insect parasitic nematodes of the genus  Heterorhabditis  are capable of selectively seeking, infecting and killing their insect-hosts in the soil. The infective juvenile (IJ) stage of the  Heterorhabditis  nematodes is analogous to  Caenorhabditis elegans  dauer juvenile stage, which remains in ‘arrested development’ till it finds and infects a new insect-host in the soil.  H. indica  is the most prevalent species of  Heterorhabditis  in India. To understand the genes and molecular processes that govern the biology of the IJ stage, and to create a resource to facilitate functional genomics and genetic exploration, we sequenced the transcriptome of  H. indica  IJs.    Results  The de-novo sequence assembly using Velvet-Oases pipeline resulted in 13,593 unique transcripts at N50 of 1,371 bp, of which 53 % were annotated by blastx.  H. indica  transcripts showed higher orthology with parasitic nematodes as compared to free living nematodes.  In-silico  expression analysis showed 30 % of transcripts expressing with ≥100 FPKM value. All the four canonical dauer formation pathways like cGMP-PKG, insulin, dafachronic acid and TGF-β were active in the IJ stage. Several other signaling pathways were highly represented in the transcriptome. Twenty-four orthologs of  C. elegans  RNAi pathway effector genes were discovered in  H. indica,  including  nrde-3  that is reported for the first time in any of the parasitic nematodes. An ortholog of  C. elegans tol-1  was also identified. Further, 272 kinases belonging to 137 groups, and several previously unidentified members of important gene classes were identified.    Conclusions  We generated high-quality transcriptome sequence data from  H. indica  IJs for the first time. The transcripts showed high similarity with the parasitic nematodes,  M. hapla,  and  A. suum  as opposed to  C. elegans , a species to which  H. indica  is more closely related. The high representation of transcripts from several signaling pathways in the IJs indicates that despite being a developmentally arrested stage; IJs are a hotbed of signaling and are actively interacting with their environment.    Electronic supplementary material  The online version of this article (doi:10.1186/s12864-016-2510-z) contains supplementary material, which is available to authorized users.

A transcriptomic insight into the infective juvenile stage of the insect parasitic nematode, Heterorhabditis indica