PXD024750
PXD024750 is an original dataset announced via ProteomeXchange.
Dataset Summary
| Title | The ancient Salicoid genome duplication event: A platform for reconstruction of de novo gene evolution in Populus trichocarp |
| Description | Orphan genes are characteristic genomic features that have no detectable homology to genes in any other species and represent an important attribute of genome evolution as sources of novel genetic functions. Here, we identified 445 genes specific to Populus trichocarpa. Of these, we performed deeper reconstruction of 13 orphan genes to provide evidence of de novo gene evolution. Populus and its sister genera Salix are particularly well suited for the study of orphan gene evolution because of the Salicoid whole-genome duplication event (WGD) which resulted in highly syntenic sister chromosomal segments across the Salicaceae. We leveraged this genomic feature to reconstruct de novo gene evolution from inter-genera, inter-species, and intra-genomic perspectives by comparing the syntenic regions within the P. trichocarpa reference, then P. deltoides, and finally Salix purpurea. Furthermore, we demonstrated that 86.5% of the putative orphan genes had evidence of transcription. Additionally, we also utilized the Populus genome-wide association mapping panel (GWAS), a collection of 1,084 undomesticated P. trichocarpa genotypes to further determine putative regulatory networks of orphan genes using expression quantitative trait loci (eQTL) mapping. Collectively, we provide novel insights into the processes of de novo gene evolution in the context of a long-lived eukaryote. |
| HostingRepository | MassIVE |
| AnnounceDate | 2022-09-28 |
| AnnouncementXML | Submission_2022-09-28_05:47:15.314.xml |
| DigitalObjectIdentifier | |
| ReviewLevel | Non peer-reviewed dataset |
| DatasetOrigin | Original dataset |
| RepositorySupport | Unsupported dataset by repository |
| PrimarySubmitter | Paul Abraham |
| SpeciesList | scientific name: Populus trichocarpa; common name: black cottonwood; NCBI TaxID: 3694; |
| ModificationList | Oxidation; Carbamidomethyl |
| Instrument | Q Exactive Plus |
Dataset History
| Revision | Datetime | Status | ChangeLog Entry |
|---|---|---|---|
| 0 | 2021-03-15 10:09:02 | ID requested | |
| ⏵ 1 | 2022-09-28 05:47:15 | announced |
Publication List
| no publication |
Keyword List
| submitter keyword: plant, proteome, orphan genes |
Contact List
| Wellington Muchero | |
|---|---|
| contact affiliation | Oak Ridge National Laboratory |
| contact email | mucherow@ornl.gov |
| lab head | |
| Paul Abraham | |
| contact affiliation | ORNL |
| contact email | pav@ornl.gov |
| dataset submitter | |
Full Dataset Link List
| MassIVE dataset URI |
| 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://massive.ucsd.edu/MSV000087050/ |
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