PXD050500

PXD050500 is an original dataset announced via ProteomeXchange.

Title	A complete telomere-to-telomere genome of bread wheat presents insights into the evolution, transcriptome, and proteome of a hexaploid genome
Description	The complete assembly of vast and complex plant genomes, like the hexaploid wheat genome, remains challenging. Here, we present CS-IAAS, a comprehensive telomere-to-telomere (T2T) gap-free Triticum aestivum L. reference genome, encompassing 14.51 billion base pairs and featuring all 21 centromeres and 42 telomeres. Annotation revealed 90.8 Mb additional centromeric satellite arrays and 5,611 ribosomal DNA(rDNA) units. Genome-wide rearrangements, centromeric elements, TE expansion, and segmental duplications were deciphered during tetraploidization and hexaploidization, providing a comprehensive understanding of wheat subgenome evolution. Among them, TE insertions during hexaploidization greatly influenced gene expression balances, thus increasing the genome plasticity of transcriptional levels. Additionally, we generated 163,329 full-length cDNA sequences and proteomic data that helped annotate 141,035 high-confidence (HC) protein-coding genes. However, in such a hexaploidy genome, 20.05%, 33.43%, and 42.76% of gene transcript levels, alternative splicing events, and protein levels were detected unbalancing among subgenomes. The complete T2T reference genome (CS-IAAS), along with its transcriptome and proteome, represents a significant step in our understanding of wheat genome complexity, and provides insights for future wheat research and breeding.
HostingRepository	PRIDE
AnnounceDate	2024-12-29
AnnouncementXML	Submission_2024-12-29_04:22:44.487.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	guochen qin
SpeciesList	scientific name: Triticum aestivum (Wheat); NCBI TaxID: 4565;
ModificationList	No PTMs are included in the dataset
Instrument	timsTOF Pro 2

Revision	Datetime	Status	ChangeLog Entry
0	2024-03-09 15:33:58	ID requested
⏵ 1	2024-12-29 04:22:44	announced

Dataset with its publication pending

submitter keyword: bread wheat,gap-free genome, proteome

Guochen Qin
contact affiliation	Pku-iaas, Shandong,China
contact email	guochen.qin@pku-iaas.edu.cn
lab head
guochen qin
contact affiliation	Peking University Institute of Advanced Agricultural Sciences
contact email	guochen.qin@pku-iaas.edu.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/2024/12/PXD050500

PRIDE project URI

• PRIDE
  1. PXD050500
     1. Label: PRIDE project
     2. Name: A complete telomere-to-telomere genome of bread wheat presents insights into the evolution, transcriptome, and proteome of a hexaploid genome