RT Journal Article SR Electronic T1 Homology-guided re-annotation improves the gene models of the alloploid Nicotiana benthamiana JF bioRxiv FD Cold Spring Harbor Laboratory SP 373506 DO 10.1101/373506 A1 Jiorgos Kourelis A1 Farnusch Kaschani A1 Friederike M. Grosse-Holz A1 Felix Homma A1 Markus Kaiser A1 Renier A. L. van der Hoorn YR 2019 UL http://biorxiv.org/content/early/2019/03/27/373506.abstract AB 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. Here we present an improved re-annotation of the Niben1.0.1 draft genome assembly guided by gene models from other Nicotiana species. 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% completeness; only 53,411 protein-encoding genes; and improved protein lengths and functional annotations, this new predicted proteome is better than the preceding proteome annotations. This dataset is more sensitive and accurate in proteomics applications, clarifying the detection by activity-based proteomics of proteins that were previously mis-annotated to be inactive. Phylogenetic analysis of the subtilase family of hydrolases reveal a pseudogenisation of likely homeologs, associated with a contraction of the functional genome in this alloploid plant species. We use this gene annotation to assign extracellular proteins in comparison to a total leaf proteome, to display the enrichment of hydrolases in the apoplast.