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dc.contributor.authorZhang, Menglei
dc.contributor.authorHeikkinen, Liisa
dc.contributor.authorKnott, Emily
dc.contributor.authorWong, Garry
dc.date.accessioned2019-06-07T11:42:34Z
dc.date.available2020-09-01T21:35:10Z
dc.date.issued2019
dc.identifier.citationZhang, M., Heikkinen, L., Knott, E., & Wong, G. (2019). De novo transcriptome assembly of a facultative parasitic nematode Pelodera (syn. Rhabditis) strongyloides. <i>Gene</i>, <i>710</i>, 30-38. <a href="https://doi.org/10.1016/j.gene.2019.05.041" target="_blank">https://doi.org/10.1016/j.gene.2019.05.041</a>
dc.identifier.otherCONVID_30879062
dc.identifier.otherTUTKAID_81565
dc.identifier.urihttps://jyx.jyu.fi/handle/123456789/64434
dc.description.abstractPelodera 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.en
dc.format.mimetypeapplication/pdf
dc.language.isoeng
dc.publisherElsevier BV
dc.relation.ispartofseriesGene
dc.rightsCC BY-NC-ND 4.0
dc.subject.otherdauer
dc.subject.otherfacultative parasite
dc.subject.otherPelodera strongyloides
dc.subject.otherstarvation
dc.subject.othertranscriptome assembly
dc.titleDe novo transcriptome assembly of a facultative parasitic nematode Pelodera (syn. Rhabditis) strongyloides
dc.typearticle
dc.identifier.urnURN:NBN:fi:jyu-201906052990
dc.contributor.laitosBio- ja ympäristötieteiden laitosfi
dc.contributor.laitosDepartment of Biological and Environmental Scienceen
dc.contributor.oppiaineEkologia ja evoluutiobiologiafi
dc.contributor.oppiaineEcology and Evolutionary Biologyen
dc.type.urihttp://purl.org/eprint/type/JournalArticle
dc.date.updated2019-06-05T12:15:18Z
dc.description.reviewstatuspeerReviewed
dc.format.pagerange30-38
dc.relation.issn0378-1119
dc.relation.numberinseries0
dc.relation.volume710
dc.type.versionacceptedVersion
dc.rights.copyright© 2019 Elsevier B.V.
dc.rights.accesslevelopenAccessfi
dc.relation.grantnumber258365
dc.subject.ysoRNA
dc.subject.ysoloiset
dc.subject.ysotranskriptio (biologia)
dc.subject.ysosukkulamadot
dc.format.contentfulltext
jyx.subject.urihttp://www.yso.fi/onto/yso/p7689
jyx.subject.urihttp://www.yso.fi/onto/yso/p4493
jyx.subject.urihttp://www.yso.fi/onto/yso/p2788
jyx.subject.urihttp://www.yso.fi/onto/yso/p8726
dc.rights.urlhttps://creativecommons.org/licenses/by-nc-nd/4.0/
dc.relation.doi10.1016/j.gene.2019.05.041
dc.relation.funderSuomen Akatemiafi
dc.relation.funderAcademy of Finlanden
jyx.fundingprogramAkatemiatutkijan tehtävä, SAfi
jyx.fundingprogramResearch post as Academy Research Fellow, AoFen
jyx.fundinginformationThis research was supported by the Faculty of Health Sciences, Universidade de Macau (MYRG2016-00101-FHS) and the Academy of Finland (Project 258365 to KEK). Computational analyses were supported by High Performance Computing Cluster (HPC Cluster) in University of Macau and super cluster taito in CSC, Finnish IT Center for Science.


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