PXD003129 is an
original dataset announced via ProteomeXchange.
Dataset Summary
Title | Protein markers of Bursaphelenchus xylophilus Steiner & Buhrer, 1934 (Nickle, 1970) populations using quantitative proteomics and character compatibility |
Description | The Pine Wood Nematode (PWN) Bursaphelenchus xylophilus is a severe forest pathogen in countries where it has been introduced and is considered a worldwide quarantine organism. In this study, protein markers for differentiating populations of this nematode were identified by studying differences among four selected Iberian and one American population. These populations were compared by quantitative proteomics (iTRAQ), which considers the level of protein expression. From a total of 2862 proteins identified using the public database from the B. xylophilus genome project, 216 were unambiguous and significantly differentially expressed in the studied populations. Comparisons of their pairwise ratio were statistically treated and supported in order to convert them into discrete character states, suggesting that 141 proteins were not informative as population specific markers. Application of the Character Compatibility methodology on the remaining 75 proteins (belonging to families with different biological functions) excludes 27 which are incompatible among them. Considering only the compatible proteins, the method selects a subset of 34 specific unique protein markers which allowed the compared classification of the Iberian isolates. This approach makes it easier search for diagnostic tools and phylogenetic inference within species and populations of a pathogen exhibiting a high level of genetic diversity. |
HostingRepository | PRIDE |
AnnounceDate | 2018-07-05 |
AnnouncementXML | Submission_2018-07-05_03:32:06.xml |
DigitalObjectIdentifier | https://dx.doi.org/10.6019/PXD003129 |
ReviewLevel | Peer-reviewed dataset |
DatasetOrigin | Original dataset |
RepositorySupport | Supported dataset by repository |
PrimarySubmitter | Sergio Ciordia |
SpeciesList | scientific name: Bursaphelenchus xylophilus (Pinewood nematode worm) (Aphelenchoides xylophilus); NCBI TaxID: 6326; |
ModificationList | iTRAQ4plex-116 reporter+balance reagent acylated residue; methylthiolated residue; monohydroxylated residue; acetylated residue; deamidated residue |
Instrument | TripleTOF 5600 |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
0 | 2015-11-02 02:23:14 | ID requested | |
⏵ 1 | 2018-07-05 03:32:07 | announced | |
Publication List
Ciordia S, Robertson L, Arcos SC, Gonz, รก, lez MR, Mena Mdel C, Zamora P, Vieira P, Abrantes I, Mota M, Castagnone-Sereno P, Navas A, Buhrer, 1934 (Nickle, 1970) populations using quantitative proteomics and character compatibility. Proteomics, 16(6):1006-14(2016) [pubmed] |
Keyword List
curator keyword: Biological |
submitter keyword: Bursaphelenchus xylophilus, Quantitative Proteomics, iTRAQ, Proteins population biomarkers, Character Compatibility |
Contact List
Alfonso Navas |
contact affiliation | Museo Nacional de Ciencias Naturales (MNCN-CSIC) |
contact email | alfonsons@mncn.csic.es |
lab head | |
Sergio Ciordia |
contact affiliation | National Center for Biotechnology |
contact email | sciordia@cnb.csic.es |
dataset submitter | |
Full Dataset Link List
Dataset FTP location
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PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD003129
- Label: PRIDE project
- Name: Protein markers of Bursaphelenchus xylophilus Steiner & Buhrer, 1934 (Nickle, 1970) populations using quantitative proteomics and character compatibility