Abstract
BackgroundThe allotetraploid tobacco species Nicotiana benthamiana native to Australia has become a popular host for recombinant protein production. Although its usage grows every year, little is known on this plant’s genomic and transcriptomic features. Most N. benthamiana accessions currently used in research lack proper documentation of their breeding history and provenance. One of these, the glycoengineered N. benthamiana line ΔXT/FT is increasingly used for the production of biopharmaceutical proteins.ResultsBased on an existing draft assembly of the N. benthamiana genome we predict 50,516 protein –encoding genes (62,216 transcripts) supported by expression data derived from 2.35 billion mRNA-seq reads. Using single-copy core genes we show high completeness of the predicted gene set. We functionally annotate more than two thirds of the gene set through sequence homology to genes from other Nicotiana species. We demonstrate that the expression profiles from leaf tissue of ΔXT/FT and its wild type progenitor only show minimal differences. We identify the transgene insertion sites in ΔXT/FT and show that one of the transgenes was inserted inside another predicted gene that most likely lost its function upon insertion. Based on publicly available mRNA-seq data, we confirm that the N. benthamiana accessions used by different research institutions most likely derive from a single source.ConclusionsThis work provides gene annotation of the N. benthamiana genome, a genomic and transcriptomic characterization of a transgenic N. benthamiana line in comparison to its wild-type progenitor, and sheds light onto the relatedness of N. benthamiana accessions that are used in laboratories around the world.
Highlights
The allotetraploid tobacco species Nicotiana benthamiana native to Australia has become a popular host for recombinant protein production
We identified 60.7% of the sequence being composed of transposable elements (TEs) of which the majority belonged to the class of LTR retrotransposons (Additional file 1: Table S1), as expected for plant genomes [24, 25]
As transcriptomic evidence a total of 2.35 billion mRNA-seq reads from eight different N. benthamiana accessions were used, corresponding to 151.6 Gb of sequencing data; of these, 126 million reads (31.5 Gb) were generated in this study (Additional file 2)
Summary
The allotetraploid tobacco species Nicotiana benthamiana native to Australia has become a popular host for recombinant protein production. The glycoengineered N. benthamiana line ΔXT/FT is increasingly used for the production of biopharmaceutical proteins. Nicotiana benthamiana is an allotetraploid plant indigenous to Australia. During the last two decades this plant emerged as a very promising host for recombinant protein production, in. The transgenic N. benthamiana line ΔXT/FT has been engineered [8] to act as a production system for therapeutic proteins and has been successfully used to produce antibodies at an industrial scale [5, 9, 10]. Its main feature is the knockdown of genes encoding fucosyl-transferases (FT) and xylosyl-transferases (XT) through RNA interference, a procedure that enables the production of recombinant glycoproteins with human glycan profiles in planta. A linkage between core fucosylation and monoclonal antibody potency has been described [17]
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