SRA

Nematodes are the most numerous animals in soil. Insect parasitic nematodes of the genus Heterorhabditis are capable of selectively seeking, infecting and killing their insect hosts in 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 soil. H. indica is the most prevalent species of Heterorhabditis in India. To understand the genes and molecular processes that govern the the biology of the IJ stage of H. indica, and to create the foundation for genetic exploration of H. indica, we sequenced the transcriptome of H. indica IJs. The de-novo sequence assembly using velvet - oases pipeline resulted in 18,710 contigs with N50 of 909 bp. However, after using cd-hit-est and filtering out <300bp transcripts, 13,592 unique transcripts were identified, and N50 increased to 1371. Orthologs of the genes expressing in IJ stage of the H indica were identified by comparing these 13,592 protein sequences with complete genomes of other closely related rhabditid nematodes through reciprocal blast approach which revealed 3364 orthologs with C. elegans, 3103 with C. briggsae, 2164 with Pristionchus pacificus, 346 with H. bacteriophora, and 3171 orthologs with C. remanei. Further, H. indica transcriptome was compared with the available plant, animal and human parasitic nematode genome sequences. We found 9906 and 8892 protein matches with Meloidogyne hapla and M. incognita respectively, 9685 with Ascaris suum, 9051 with Brugia malayi, 8188 with Strongyloides ratti and 7588 with Trichinella spiralis. Similar to C. elegans, all the four dauer formation pathways - cGMP - PKG signaling pathway, Insulin signaling pathway, Dafachronic acid pathway and TGF-ß are were conserved and active in the IJ stage H. indica. Several important signaling pathways were found active in the IJs indicating that in-spite of being a developmentally arrested stage, IJs are a hot bed of signalling and are actively interacting with their environment. Similarly, glycolysis and fatty acid degradation pathways were highly active in IJs indicating breakdown of food reserves. Twenty four orthologs of C. elegans RNAi pathway effector genes were found in H. indica IJ transcriptome, including nrde-3 which has been identified for the first time in any of the parasitic worms.