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De novo transcriptome assembly of a facultative parasitic nematode Pelodera (syn. Rhabditis) strongyloides
Menglei Zhang1; Liisa Heikkinen2; K. Emily Knott2; Garry Wong1
2019-08
Source PublicationGENE
ISSN0378-1119
Volume710Pages:30-38
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.

KeywordDauer Facultative Parasite Pelodera Strongyloides Starvation Transcriptome Assembly
DOI10.1016/j.gene.2019.05.041
Indexed BySCIE
Language英語English
WOS Research AreaGenetics & Heredity
WOS SubjectGenetics & Heredity
WOS IDWOS:00483423500005
Scopus ID2-s2.0-85066394960
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Document TypeJournal article
CollectionFaculty of Health Sciences
Affiliation1.Centre of Reproduction, Development and Aging, Faculty of Health Sciences, University of Macau, Macau, SAR, China
2.University of Jyväskylä, Finland
First Author AffilicationCentre of Reproduction, Development and Aging
Recommended Citation
GB/T 7714
Menglei Zhang,Liisa Heikkinen,K. Emily Knott,et al. De novo transcriptome assembly of a facultative parasitic nematode Pelodera (syn. Rhabditis) strongyloides[J]. GENE,2019,710:30-38.
APA Menglei Zhang,Liisa Heikkinen,K. Emily Knott,&Garry Wong.(2019).De novo transcriptome assembly of a facultative parasitic nematode Pelodera (syn. Rhabditis) strongyloides.GENE,710,30-38.
MLA Menglei Zhang,et al."De novo transcriptome assembly of a facultative parasitic nematode Pelodera (syn. Rhabditis) strongyloides".GENE 710(2019):30-38.
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