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

ABSTRACT:

Background

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.

Results

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 missing or partial. We complement these missing proteins by similarly annotating other draft genome assemblies. This approach overcomes problems caused by mis-annotated exon-intron boundaries and mis-assigned short read transcripts to homeologs in polyploid genomes. With an estimated 98.1% complete

SUBMITTER: Kourelis J 

PROVIDER: S-EPMC6778390 | biostudies-literature | 2019 Oct

REPOSITORIES: biostudies-literature