A1 Journal article (refereed)
De novo transcriptome assembly of a facultative parasitic nematode Pelodera (syn. Rhabditis) strongyloides (2019)

Zhang, M., Heikkinen, L., Knott, E., & Wong, G. (2019). De novo transcriptome assembly of a facultative parasitic nematode Pelodera (syn. Rhabditis) strongyloides. Gene, 710, 30-38. https://doi.org/10.1016/j.gene.2019.05.041

JYU authors or editors

Publication details

All authors or editors: Zhang, Menglei; Heikkinen, Liisa; Knott, Emily; Wong, Garry

Journal or series: Gene

ISSN: 0378-1119

eISSN: 1879-0038

Publication year: 2019

Volume: 710

Issue number: 0

Pages range: 30-38

Publisher: Elsevier BV

Publication country: Netherlands

Publication language: English

DOI: https://doi.org/10.1016/j.gene.2019.05.041

Publication open access: Not open

Publication channel open access: 

Publication is parallel published (JYX): https://jyx.jyu.fi/handle/123456789/64434

Abstract

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.

Keywords: parasites; nematodes; RNA; transcription (biological events)

Free keywords: dauer; facultative parasite; Pelodera strongyloides; starvation; transcriptome assembly

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Ministry reporting: Yes

Reporting Year: 2019

JUFO rating: 1