PXD013606

PXD013606 is an original dataset announced via ProteomeXchange.

Title	Comparative proteome analysis across moss, monocots and dicots unveils the evolutionary dynamics of core processes
Description	Comparative functional genomics offers a powerful approach to study species evolution. To date, the majority of these studies have focused on the transcriptome in mammalian and yeast phylogenies. Here we present a novel multi-species proteomic dataset and a computational pipeline to compare the protein levels across multiple plant species systematically. Globally we find that protein levels diverge according to phylogenetic distance, but is more constrained than at the mRNA level. Module-level comparative analysis of groups of proteins shows that proteins that are more highly expressed tend to be more conserved. To interpret the evolutionary patterns of conservation and divergence, we develop a novel integrative analysis pipeline that combines publicly available transcriptomic datasets to define co-expression modules. Our analysis pipeline can be used to relate the changes in protein levels to different species-specific phenotypic traits. We present a case study with the rhizobia-legume symbiosis process that supports the important role of autophagy and redox management processes in this symbiotic association.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_05:14:37.219.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Harald Marx
SpeciesList	scientific name: Pinus taeda; NCBI TaxID: 3352; scientific name: Arabidopsis thaliana (Mouse-ear cress); NCBI TaxID: 3702; scientific name: Solanum tuberosum (Potato); NCBI TaxID: 4113; scientific name: Medicago truncatula (Barrel medic) (Medicago tribuloides); NCBI TaxID: 3880; scientific name: Oryza sativa (Rice); NCBI TaxID: 4530; scientific name: Physcomitrella patens subsp. patens (Moss); NCBI TaxID: 3218; scientific name: Zea mays (Maize); NCBI TaxID: 4577;
ModificationList	No PTMs are included in the dataset
Instrument	LTQ Orbitrap

Revision	Datetime	Status	ChangeLog Entry
0	2019-04-23 06:03:43	ID requested
1	2020-11-04 02:28:40	announced
⏵ 2	2024-10-22 05:14:37	announced	2024-10-22: Updated project metadata.

Dataset with its publication pending

curator keyword: Biological

submitter keyword: LC-MS/MS, Plants, Phylogeny, DDA

Joshua J. Coon
contact affiliation	Thomas and Margaret Pyle Chair at the Morgridge Institute for Research Professor, Biomolecular Chemistry and Chemistry University of Wisconsin, Madison Director, NIH National Center for Quantitative Biology of Complex Systems
contact email	jcoon@chem.wisc.edu
lab head
Harald Marx
contact affiliation	University of Vienna
contact email	harald.marx@univie.ac.at
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/2020/11/PXD013606

PRIDE project URI

• PRIDE
  1. PXD013606
     1. Label: PRIDE project
     2. Name: Comparative proteome analysis across moss, monocots and dicots unveils the evolutionary dynamics of core processes