PXD010435-1

PXD010435 is an original dataset announced via ProteomeXchange.

Title	Re-annotated Nicotiana benthamiana gene models for improved proteomics and reverse genetics
Description	Nicotiana benthamiana is an important model organism and representative of the Solanaceae (Nightshade) family. N. benthamiana has a complex ancient allopolyploid genome with 19 chromosomes, and an estimated genome size of 3.1Gb. Several draft assemblies of the N. benthamiana genome have been generated, however, many of the gene-models in these draft assemblies appear incorrect. Here we present a nearly non-redundant database of improved N. benthamiana gene-models based on gene annotations from well-annotated genomes in the Nicotiana genus. We show that the new predicted proteome is more complete than the previous proteomes and more sensitive and accurate in proteomics applications, while maintaining a reasonable low gene number (~43,000). As a proof-of-concept we use this proteome to compare the leaf extracellular (apoplastic) proteome to a total extract of leaves. Several gene families are more abundant in the apoplast. For one of these apoplastic protein families, the subtilases, we present a phylogenetic analysis illustrating the utility of this database. Besides proteome annotation, this database will aid the research community with improved target gene selection for genome editing and off-target prediction for gene silencing.
HostingRepository	PRIDE
AnnounceDate	2019-10-09
AnnouncementXML	Submission_2019-10-09_00:24:30.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Farnusch Kaschani
SpeciesList	scientific name: Nicotiana benthamiana; NCBI TaxID: 4100;
ModificationList	monohydroxylated residue; acetylated residue; iodoacetamide derivatized residue
Instrument	LTQ Orbitrap Elite

Revision	Datetime	Status	ChangeLog Entry
0	2018-07-16 03:21:32	ID requested
⏵ 1	2019-10-09 00:24:31	announced

Kourelis J, Kaschani F, Grosse-Holz FM, Homma F, Kaiser M, van der Hoorn RAL, A homology-guided, genome-based proteome for improved proteomics in the alloploid Nicotiana benthamiana. BMC Genomics, 20(1):722(2019) [pubmed]

curator keyword: Biological

submitter keyword: Solanaceae, Plant Innate Immunity, Nicotiana benthamiana, Proteomics, Subtilases

Farnusch Kaschani
contact affiliation	Analytics Core Facility Essen (ACE), Chemische Biologie, Universität Duisburg-Essen, ZMB, Germany
contact email	farnusch.kaschani@uni-due.de
lab head
Farnusch Kaschani
contact affiliation	University Duisburg-Essen
contact email	farnusch.kaschani@uni-due.de
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/2019/10/PXD010435

PRIDE project URI

• PRIDE
  1. PXD010435
     1. Label: PRIDE project
     2. Name: Re-annotated Nicotiana benthamiana gene models for improved proteomics and reverse genetics