PXD003129

PXD003129 is an original dataset announced via ProteomeXchange.

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

Revision	Datetime	Status	ChangeLog Entry
0	2015-11-02 02:23:14	ID requested
⏵ 1	2018-07-05 03:32:07	announced

Ciordia S, Robertson L, Arcos SC, Gonz, á, 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]

curator keyword: Biological

submitter keyword: Bursaphelenchus xylophilus, Quantitative Proteomics, iTRAQ, Proteins population biomarkers, Character Compatibility

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

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PRIDE project URI

• PRIDE
  1. PXD003129
     1. Label: PRIDE project
     2. Name: Protein markers of Bursaphelenchus xylophilus Steiner & Buhrer, 1934 (Nickle, 1970) populations using quantitative proteomics and character compatibility