Genome and transcriptome characterization of the glycoengineered Nicotiana benthamiana line ΔXT/FT
Abstract Background The 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 curr...
Main Authors: | , , , , |
---|---|
Format: | Article |
Language: | English |
Published: |
BMC
2019-07-01
|
Series: | BMC Genomics |
Subjects: | |
Online Access: | http://link.springer.com/article/10.1186/s12864-019-5960-2 |
id |
doaj-ce9c03a379664af79bcbaab3fd9e6854 |
---|---|
record_format |
Article |
spelling |
doaj-ce9c03a379664af79bcbaab3fd9e68542020-11-25T03:01:33ZengBMCBMC Genomics1471-21642019-07-0120111610.1186/s12864-019-5960-2Genome and transcriptome characterization of the glycoengineered Nicotiana benthamiana line ΔXT/FTMatteo Schiavinato0Richard Strasser1Lukas Mach2Juliane C. Dohm3Heinz Himmelbauer4Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU)Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences (BOKU)Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences (BOKU)Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU)Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU)Abstract Background The 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. Results Based 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. Conclusions This 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.http://link.springer.com/article/10.1186/s12864-019-5960-2Nicotiana benthamianaGenomeGene predictionTransgeneIntraspecific variationAccession history |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Matteo Schiavinato Richard Strasser Lukas Mach Juliane C. Dohm Heinz Himmelbauer |
spellingShingle |
Matteo Schiavinato Richard Strasser Lukas Mach Juliane C. Dohm Heinz Himmelbauer Genome and transcriptome characterization of the glycoengineered Nicotiana benthamiana line ΔXT/FT BMC Genomics Nicotiana benthamiana Genome Gene prediction Transgene Intraspecific variation Accession history |
author_facet |
Matteo Schiavinato Richard Strasser Lukas Mach Juliane C. Dohm Heinz Himmelbauer |
author_sort |
Matteo Schiavinato |
title |
Genome and transcriptome characterization of the glycoengineered Nicotiana benthamiana line ΔXT/FT |
title_short |
Genome and transcriptome characterization of the glycoengineered Nicotiana benthamiana line ΔXT/FT |
title_full |
Genome and transcriptome characterization of the glycoengineered Nicotiana benthamiana line ΔXT/FT |
title_fullStr |
Genome and transcriptome characterization of the glycoengineered Nicotiana benthamiana line ΔXT/FT |
title_full_unstemmed |
Genome and transcriptome characterization of the glycoengineered Nicotiana benthamiana line ΔXT/FT |
title_sort |
genome and transcriptome characterization of the glycoengineered nicotiana benthamiana line δxt/ft |
publisher |
BMC |
series |
BMC Genomics |
issn |
1471-2164 |
publishDate |
2019-07-01 |
description |
Abstract Background The 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. Results Based 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. Conclusions This 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. |
topic |
Nicotiana benthamiana Genome Gene prediction Transgene Intraspecific variation Accession history |
url |
http://link.springer.com/article/10.1186/s12864-019-5960-2 |
work_keys_str_mv |
AT matteoschiavinato genomeandtranscriptomecharacterizationoftheglycoengineerednicotianabenthamianalinedxtft AT richardstrasser genomeandtranscriptomecharacterizationoftheglycoengineerednicotianabenthamianalinedxtft AT lukasmach genomeandtranscriptomecharacterizationoftheglycoengineerednicotianabenthamianalinedxtft AT julianecdohm genomeandtranscriptomecharacterizationoftheglycoengineerednicotianabenthamianalinedxtft AT heinzhimmelbauer genomeandtranscriptomecharacterizationoftheglycoengineerednicotianabenthamianalinedxtft |
_version_ |
1724693283879256064 |