PXD006375 is an
original dataset announced via ProteomeXchange.
Dataset Summary
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 |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
0 | 2017-04-25 05:31:04 | ID requested | |
⏵ 1 | 2018-01-31 00:31:31 | announced | |
Publication List
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] |
Zorrilla-Fontanesi Y, Rouard M, Cenci A, Kissel E, Do H, Dubois E, Nidelet S, Roux N, Swennen R, Carpentier SC, Differential root transcriptomics in a polyploid non-model crop: the importance of respiration during osmotic stress. Sci Rep, 6():22583(2016) [pubmed] |
Keyword List
curator keyword: Biological |
submitter keyword: Integration transcriptomics and proteomics, allele specificity, Musa acuminata, non-model crop |
Contact List
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 | |
Full Dataset Link List
Dataset FTP location
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PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD006375
- Label: PRIDE project
- Name: Identification and quantification of allele specific proteins and homeolog expression bias in an allopolyploid non-model crop by integrating transcriptomics and proteomics.