PXD006375

PXD006375 is an original dataset announced via ProteomeXchange.

Title	Identification and quantification of allele specific proteins and homeolog expression bias in an allopolyploid non-model crop by integrating transcriptomics and proteomics.
Description	The fate of doubled genes, from allopolyploid or autopolyploid origin, is controlled at multiple levels within the central dogma: gene loss or silencing, neo- and/or sub functionalization, inter genomic transfer, allele dominance/co-dominance, differences in transcription/translation efficiency, post translational modifications… These regulatory processes through evolution have caused a plethora of genotype x environment interactions displayed in the modern day phenotypes. The study of non-model crops is challenging but solutions are emerging. More and more, one gets insight into the tolerance mechanisms of a specific genotype. By integrating transcriptomics into our proteomic data, we studied the genetic diversity of an allopolyploid ABB banana, a tolerant genotype, and compared it to two different sensitive AAA genotypes. The root growth of the ABB cultivar was 60 % higher under mild osmotic stress. 234,000 spectra were aligned and quantified, resulting in 2,753 identified root proteins. 383 gene loci displayed genotype specific differential expression whereof 252 showed at least one Single Amino Acid Polymorphism (SAAP). The homeoallelic contribution was assessed using transcriptome read alignment, thus revealing each allele contribution at the RNA level. This provides insight in the structure and the organization of the triploid genome. In the ABB cultivar, allele expressions are supposed to follow a 1/3 and 2/3 pattern. We found that many genes deviated from this expectation and we show that 32 gene loci even displayed a 100% read preference for the allele that was unique for the ABB tolerant genotype , suggesting that the presence of unique alleles and homoelog expression bias is correlated to the observed phenotype.
HostingRepository	PRIDE
AnnounceDate	2018-01-31
AnnouncementXML	Submission_2018-01-31_00:31:29.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD006375
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Jelle van Wesemael
SpeciesList	scientific name: Musa acuminata subsp. malaccensis; NCBI TaxID: 214687;
ModificationList	Ammonia-loss; Glu->pyro-Glu; Oxidation; Acetyl; Carbamidomethyl; Gln->pyro-Glu
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2017-04-25 05:31:04	ID requested
⏵ 1	2018-01-31 00:31:31	announced

van Wesemael J, Hueber Y, Kissel E, Campos N, Swennen R, Carpentier S, Homeolog expression analysis in an allotriploid non-model crop via integration of transcriptomics and proteomics. Sci Rep, 8(1):1353(2018) [pubmed]

curator keyword: Biological

submitter keyword: Integration transcriptomics and proteomics, allele specificity, Musa acuminata, non-model crop

Sebastien Carpentier
contact affiliation	Laboratory of Tropical Crop Improvement, Division of Crop Biotechnics, KU Leuven, B-3001, Leuven, Belgium FAcility for System Biology based Mass Spectrometry (SYBIOMA), KU Leuven, B-3001, Leuven, Belgium
contact email	sebastien.carpentier@kuleuven.be
lab head
Jelle van Wesemael
contact affiliation	Division Crop Biotechnics, KU Leuven, Belgium
contact email	jelle.vanwesemael@kuleuven.be
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2018/01/PXD006375

PRIDE project URI

• PRIDE
  1. PXD006375
     1. Label: PRIDE project
     2. Name: Identification and quantification of allele specific proteins and homeolog expression bias in an allopolyploid non-model crop by integrating transcriptomics and proteomics.