De novo transcriptome assembly of a facultative parasitic nematode Pelodera (syn. Rhabditis) strongyloides

• Published in: Gene Vol. 710; pp. 30 - 38
• Main Authors: Zhang, Menglei, Heikkinen, Liisa, Knott, K. Emily, Wong, Garry
• Format: Journal Article
• Language: English
• Published: Netherlands Elsevier B.V 20.08.2019
• Subjects: Dauer; evolution; Facultative parasite; genes; larvae; light microscopy; Necator americanus; nucleotide sequences; parasitism; parasitoses; Pelodera strongyloides; Rhabditis; ribosomal RNA; RNA interference; RNA transport; RNA-directed RNA polymerase; sequence analysis; Starvation; Strongyloides stercoralis; transcriptome; Transcriptome assembly; transport proteins; Trichuris trichiura; dsRNA; DE; Starvation; Pelodera strongyloides; GO; Dauer; Facultative parasite; FPKM; N; RSEM; TPM; Transcriptome assembly; S; FDR; NGM; PE; RdRP; W; KEGG
• ISSN: 0378-1119; 1879-0038; 1879-0038
• DOI: 10.1016/j.gene.2019.05.041

Pelodera strongyloides is a generally free-living gonochoristic facultative nematode. The whole genomic sequence of P. strongyloides remains unknown but 4 small subunit ribosomal RNA (ssrRNA) gene sequences are available. This project launched a de novo transcriptome assembly with 100 bp paired-end RNA-seq reads from normal, starved and wet-plate cultured animals. Trinity assembly tool generated 104,634 transcript contigs with N50 contig being 2195 bp and average contig length at 1103 bp. Transcriptome BLASTX matching results of five nematodes (C. elegans, Strongyloides stercoralis, Necator americanus, Trichuris trichiura, and Pristionchus pacificus) were consistent with their evolutionary relationships. Sixteen genes were identified to be homologous to key elements of the C. elegans RNA interference system, such as Dicer, Argonaute, RNA-dependent RNA polymerase and double strand RNA transport proteins. In starved samples, we observed up-regulation of cuticle related genes and 3 dauer formation genes. Dauer morphology was captured with enlarged phasmid under light microscopy, and dauer and normal larvae counts in clumps had a Pearson's product-moment correlation of 0.805 with P-value = 0.0088. Our results demonstrate that P. strongyloides could be used for studying nematode-related human or pet parasitic diseases. The sequenced assembled transcriptome reported here may be useful to understand the evolution of parasitism in Nematoda. •The transcriptome of a facultative nematode Pelodera strongyloides was sequenced.•The transcriptome BLASTX alignments with 1 free-living and 4 parasitic nematodes were consistent with their phylogeny.•A total of 104,634 transcript contigs with N50 contig length of 2,195 nucleotides were obtained.•Starving conditions resulted in up-regulation of cuticle related and dauer formation genes.