PXD015806

PXD015806 is an original dataset announced via ProteomeXchange.

Title	Seed comparative genomics in three coffee species evidence desiccation tolerance mechanisms among intermediate seeds
Description	In contrast to the desiccation tolerant (DT) ‘orthodox’ seeds, the so-called ‘intermediate’ seeds cannot survive complete drying and are short-lived. All species of the genus Coffea produce intermediate seeds but show a considerable variability for the seed DT level, which may help to decipher the molecular basis of seed DT in plants. We thus led a comparative transcriptome analysis of developing seeds in three coffee species with contrasting seed DT levels. Seeds of all species shared a major transcriptional switch during late maturation that governs a general slow-down of metabolism. However, numerous key stress-related genes, including those coding for the late embryogenesis abundant protein EM6 and the osmosensitive calcium channel ERD4, were upregulated during DT acquisition in the two species with high seed DT, C. arabica and C. eugenioides. By contrast, an upregulation of numerous players of the metabolism, transport and perception of auxin was observed in C. canephora seeds with low DT. Moreover, species with high DT showed a stronger down-regulation of the mitochondrial machinery dedicated to the tricarboxylic acid cycle and oxidative phosphorylation. Accordingly, respiration measurements during seed dehydration demonstrated that intermediate seeds with the highest DT levels are better prepared to cease respiration and avoid oxidative stresses.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_05:05:25.525.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	sonia hem
SpeciesList	scientific name: Coffea arabica (Arabian coffee); NCBI TaxID: 13443; scientific name: Coffea eugenioides; NCBI TaxID: 49369; scientific name: Coffea canephora; NCBI TaxID: 49390;
ModificationList	2-pyrrolidone-5-carboxylic acid (Glu); 2-pyrrolidone-5-carboxylic acid (Gln); monohydroxylated residue; acetylated residue; iodoacetamide derivatized residue; deamidated residue
Instrument	Q Exactive Plus

Revision	Datetime	Status	ChangeLog Entry
0	2019-10-14 02:04:50	ID requested
1	2020-05-26 14:44:48	announced
⏵ 2	2024-10-22 05:05:26	announced	2024-10-22: Updated project metadata.

10.1093/jxb/erz508;

Stavrinides AK, Dussert S, Combes MC, Fock-Bastide I, Severac D, Minier J, Bastos-Siqueira A, Demolombe V, Hem S, Lashermes P, Jo, ë, t T, Seed comparative genomics in three coffee species identify desiccation tolerance mechanisms in intermediate seeds. J Exp Bot, 71(4):1418-1433(2020) [pubmed]

submitter keyword: dehydration, transcriptome., intermediate seeds, respiration,Coffea, late maturation, desiccation tolerance, metabolic quiescence, seed development

Thierry Joët
contact affiliation	IRD, Université Montpellier, UMR DIADE, BP 64501, F-34394 Montpellier, France
contact email	thierry.joet@ird.fr
lab head
sonia hem
contact affiliation	INRA
contact email	sonia.hem@supagro.inra.fr
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD015806
     1. Label: PRIDE project
     2. Name: Seed comparative genomics in three coffee species evidence desiccation tolerance mechanisms among intermediate seeds