Release of a draft genome sequence for Nicotiana benthamiana

Scientists at the Boyce Thompson Institute for Plant Research (BTI) have released a draft sequence of the Nicotiana benthamiana genome which is accessible through the SGN BLAST tool and can be downloaded from an ftp site (see: http://solgenomics.net/). The project was funded by BTI and National Science Foundation grants IOS-1025642 and IOS-0343327.

N. benthamiana is a widely used model for plant-microbe biology and other research applications. It is particularly useful because it is related to tomato and potato and is amenable to virus-induced gene silencing (VIGS) which facilitates the efficient functional study of plant genes.

The draft sequence of N. benthamiana will allow better design of constructs for virus-induced gene-silencing (VIGS) in order to reduce the possibility of 'off-target' gene silencing [1]. The sequence will also be useful for identifying orthologs of tomato and potato genes, for comparative genomics with other Solanaceae species, and for the retrieval of promoter sequences.

N. benthamiana has a very complex genome consisting of n=19 chromosomes that is estimated at over 3.5GB in size. Taxonomically, it is an old allotetraploid of the section Suaveolentes that formed from diploid parents from the section Sylvestres and the section Noctiflorae. It is native to Australia [2, 3].


BLAST N. benthamiana genome  FTP Site

Sequencing approach

Seedlings were grown in the greenhouse and nuclear DNA was extracted from etiolated leaves. From the DNA, three distinct libraries were synthesized for use in a Illumina HiSeq-2000 sequencer: 1) a paired end library with an insert size of approximately 500 bp insert size; 2) a mate-pair type library with an insert size of 2kb; and 3) a mate pair with an insert size of 5kb. Sequencing was performed using a full run with 4 lanes of the paired end library and 1 lane each of the mate pair libraries.

Accession sequenced

The accession sequenced is referred to as "Nb-1". Seeds can be obtained by contacting Gregory Martin at gbm7@cornell.edu.

Assembly Statistics

N. benthamiana Genome v0.42 Contigs


==========================================================
= REPORT: Niben.genome.v0.4.2.scaffolds.nrcontigs.fasta =
==========================================================
Sequence Count: 141339 sequences
Total Length: 2630346647 bp
Longest sequence: 615591 bp (ID = Niben.v0.4.1.Scf588)
Shortest sequence: 201 bp (ID = Niben.v0.4.1.Ctg23127767)
Average length: 18610.1970935128 bp
N95 length: 12828 bp
N95 index: 37713 sequences
N90 length: 23201 bp
N90 index: 30261 sequences
N75 length: 48209 bp
N75 index: 18834 sequences
N50 length: 89778 bp
N50 index: 8897 sequences
N25 length: 148847 bp
N25 index: 3141 sequences
==========================================================

==========================================================
= REPORT: Niben.genome.v0.4.2.contigs.fasta =
==========================================================
Sequence Count: 461463 sequences
Total Length: 2462490758 bp
Longest sequence: 208210 bp (ID = Niben.v0.4.1.Scf14070.Ctg1)
Shortest sequence: 201 bp (ID = Niben.v0.4.1.Ctg23128323)
Average length: 5336.26912233483 bp
N95 length: 1564 bp
N95 index: 215459 sequences
N90 length: 3403 bp
N90 index: 163811 sequences
N75 length: 8068 bp
N75 index: 96046 sequences
N50 length: 16480 bp
N50 index: 42984 sequences
N25 length: 29264 bp
N25 index: 14540 sequences
==========================================================

Tools

The draft assembly can be analyzed using the SGN BLAST tool. There are no restrictions on the use of these data except that full genome analyses cannot be published.

References

  1. Bombarely, A., H. G. Rosli, J. Vrebalov, P. Moffett, L. A. Mueller, and G. B. Martin (2012). A draft genome sequence of Nicotiana benthamiana to enhance molecular plant-microbe biology research. Molecular Plant-Microbe Interactions 25:1523-1530.
  2. Knapp, S. M. W. Chase and J. J. Clarkson (2004). Nomenclatural changes and a new sectional classification in Nicotiana (Solanaceae). Taxon 53:73-82.
  3. Goodin, M. M., D. Zaitlin, R. A. Naidu, and S. A. Lommel (2008). Nicotiana benthamiana: Its history and future as a model for plant-pathogen interactions. Molecular Plant-Microbe Interactions 21:1026.

Data Agreement

By downloading the Nicotiana benthamiana genome information in this directory you accept the following terms: The sequence information can be used freely with the only restriction that a full genome analysis cannot be published based on this data before publication by the sequencing collaborators.

Please contact Greg Martin (gbm7@cornell.edu) if you have any questions.

Acknowledgments

Sequencing of the N. benthamiana genome was supported by funds from the Boyce Thompson Institute for Plant Research and National Science Foundation grants IOS-1025642 (A. Collmer and G. Martin), and IOS-0343327 (P. Moffett).

Online tutorial

An on-line tutorial of the VIGS procedure is available on the JOVE site.

Links

The Nicotiana benthamiana sequencing project in Austrialia/New Zealand can be accessed throught their website.

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