PXD010435 is an
original dataset announced via ProteomeXchange.
Dataset Summary
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 |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
0 | 2018-07-16 03:21:32 | ID requested | |
⏵ 1 | 2019-10-09 00:24:31 | announced | |
Publication List
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] |
Keyword List
curator keyword: Biological |
submitter keyword: Solanaceae, Plant Innate Immunity, Nicotiana benthamiana, Proteomics, Subtilases |
Contact List
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 | |
Full Dataset Link List
Dataset FTP location
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PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD010435
- Label: PRIDE project
- Name: Re-annotated Nicotiana benthamiana gene models for improved proteomics and reverse genetics