Dataset Information

Re-annotated Nicotiana benthamiana gene models for improved proteomics and reverse genetics

ABSTRACT: 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.

INSTRUMENT(S): LTQ Orbitrap Elite

ORGANISM(S): Nicotiana Benthamiana

SUBMITTER: Farnusch Kaschani

LAB HEAD: Farnusch Kaschani

PROVIDER: PXD010435 | Pride | 2019-10-09

REPOSITORIES: Pride

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Publications

A homology-guided, genome-based proteome for improved proteomics in the alloploid Nicotiana benthamiana.

Kourelis Jiorgos J Kaschani Farnusch F Grosse-Holz Friederike M FM Homma Felix F Kaiser Markus M van der Hoorn Renier A L RAL

BMC genomics 20191004 1

<h4>Background</h4>Nicotiana benthamiana is an important model organism of the Solanaceae (Nightshade) family. Several draft assemblies of the N. benthamiana genome have been generated, but many of the gene-models in these draft assemblies appear incorrect.<h4>Results</h4>Here we present an improved proteome based on the Niben1.0.1 draft genome assembly guided by gene models from other Nicotiana species. Due to the fragmented nature of the Niben1.0.1 draft genome, many protein-encoding genes are ...[more]

PMID: 31585525

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