PXD065205

PXD065205 is an original dataset announced via ProteomeXchange.

Title	High conservation of translationally significant RNA editing sites in hyper-editing ferns implies they are not selectively neutral
Description	RNA editing is essential for processing transcripts in plant chloroplasts and mitochondria. Levels of RNA editing vary between lineages, but some hornworts, lycophytes and ferns have an extraordinary abundance of RNA editing. A feature of ‘hyper-editing’ species is the prevalence of RNA editing events which influence translation by affecting start codons and stop codons via C-to-U editing and U-to-C editing respectively. These ‘translationally significant’ RNA editing events may play roles in regulating organelle gene expression. To investigate the importance of translationally significant RNA editing events, we generated DNA and RNA sequence libraries for four Salviniales water ferns: Azolla rubra, Azolla pinnata, Marsilea mutica and Salvinia molesta. We assembled chloroplast genomes, mitochondrial genes and transcriptomes, and identified RNA editing sites and candidate RNA editing factors. We re-analysed sequence data of Azolla filiculoides and conducted a comparative analysis of RNA editing in chloroplasts and mitochondrial transcripts. Estimates of pyrimidine transition rates show that translationally significant RNA editing sites are more conserved than other non-synonymous editing sites, suggesting an emergent role in organelle gene expression that is not selectively neutral. Shotgun proteomics of Marsilea mutica chloroplast thylakoid fractions verified the expected consequences of RNA editing on translation of chloroplast transcripts and implies that mechanisms exist to avoid translation of partially edited transcripts. Start codon editing may be one of those mechanisms.
HostingRepository	PRIDE
AnnounceDate	2025-10-27
AnnouncementXML	Submission_2025-10-26_17:12:32.104.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Owen Duncan
SpeciesList	scientific name: Marsilea mutica; NCBI TaxID: NEWT:167748;
ModificationList	No PTMs are included in the dataset
Instrument	6550 iFunnel Q-TOF LC/MS

Revision	Datetime	Status	ChangeLog Entry
0	2025-06-19 00:23:30	ID requested
⏵ 1	2025-10-26 17:12:33	announced

10.1093/molbev/msaf241;

Kwok van der Giezen FM, McDowell R, Duncan O, Zumkeller S, Colas des Francs-Small C, Small I, High Conservation of Translation-Enabling RNA Editing Sites in Hyper-editing Ferns Implies They Are Not Selectively Neutral. Mol Biol Evol, 42(10):(2025) [pubmed]

submitter keyword: RNA Editing,Masrsieal

Ian Small
contact affiliation	School of Molecular Sciences, The University of Western Australia, Perth, WA 6009, Australia
contact email	ian.small@uwa.edu.au
lab head
Owen Duncan
contact affiliation	UWA
contact email	owen.duncan@uwa.edu.au
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/2025/10/PXD065205

PRIDE project URI

• PRIDE
  1. PXD065205
     1. Label: PRIDE project
     2. Name: High conservation of translationally significant RNA editing sites in hyper-editing ferns implies they are not selectively neutral