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PXD010435 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleRe-annotated Nicotiana benthamiana gene models for improved proteomics and reverse genetics
DescriptionNicotiana 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.
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterFarnusch Kaschani
SpeciesList scientific name: Nicotiana benthamiana; NCBI TaxID: 4100;
ModificationListmonohydroxylated residue; acetylated residue; iodoacetamide derivatized residue
InstrumentLTQ Orbitrap Elite
Dataset History
RevisionDatetimeStatusChangeLog Entry
02018-07-16 03:21:32ID requested
12019-10-09 00:24:31announced
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 affiliationAnalytics Core Facility Essen (ACE), Chemische Biologie, Universit├Ąt Duisburg-Essen, ZMB, Germany
contact emailfarnusch.kaschani@uni-due.de
lab head
Farnusch Kaschani
contact affiliationUniversity Duisburg-Essen
contact emailfarnusch.kaschani@uni-due.de
dataset submitter
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