PXD024720

PXD024720 is an original dataset announced via ProteomeXchange.

Title	The evolution of Proteomics in the genus Flaveria
Description	C4 photosynthesis overpasses C3 by a higher photosynthetic rate, along with a higher water and nitrogen use efficiency. The establishment of C4 photosynthesis requires modification of ancestral C3 in both anatomical and metabolic aspects, both are involved in many functional pathways which have not been fully demonstrated. This study aims to illustrate overall functional changes along the evolution of C4 photosynthesis, with a purpose to gain an overall view of what are required for C4 photosynthesis. To achieve this, this study assembled chromosome scale of genome sequencing of five Flaveria species, representing gradual evolutionary stages of C4 photosynthesis from C3 to C3-C4 and to C4. Here, result showed that the genome size gradually increases from C3 to intermediate to C4 species, which ranges from 0.5 G to 1.87 G. The enlarged genomes are mainly from transposable elements, with the number of protein coding gene are comparable along evolution. The copy of C4 version CA1 and PEPC1, as well as PEPC-k gained extra one, two and five copies in C4 species F. trinervia as a result of tandem duplication, which plays a positive role for the emergency of C4 photosynthesis. Besides, the evolutionary pattern of C4 gene on transcript abundance are consistent with that on protein abundance, suggesting transcriptional regulation is a key factor for establishing C4 photosynthesis.
HostingRepository	PRIDE
AnnounceDate	2025-01-21
AnnouncementXML	Submission_2025-01-21_01:56:55.416.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Amy Lyu
SpeciesList	scientific name: Flaveria ramosissima; NCBI TaxID: 41578;
ModificationList	No PTMs are included in the dataset
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2021-03-15 00:04:38	ID requested
⏵ 1	2025-01-21 01:56:55	announced

Dataset with its publication pending

submitter keyword: Flaveria,C4 photosynthesis, Evolution, Proteomics

Xin-Guang Zhu
contact affiliation	CAS Center for Excellence in Molecular Plant Science, Chinese Academic on Science
contact email	zhuxg@cemps.ac.cn
lab head
Amy Lyu
contact affiliation	CAS Center for Excellence in Molecular Plant Sciences
contact email	lvmj@cemps.ac.cn
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/2025/01/PXD024720

PRIDE project URI

• PRIDE
  1. PXD024720
     1. Label: PRIDE project
     2. Name: The evolution of Proteomics in the genus Flaveria