Release of a Draft Genome Sequence for Nicotiana benthamiana

BTI scientists have released a draft sequence of the Nicotiana benthamiana genome which is accessible through the SGN BLAST tool and can be downloaded by ftp (see:http://solgenomics.net/). The work was supported by BTI and NSF 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].

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. For more information about the genome sequence, please see:http://solgenomics.net/.

Accession sequenced

The accession sequenced is referred to as ‘Nb-BTI’. Seeds can be obtained by contacting Gregory Martin [gbm7@cornell.edu].

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).

References

1. Gomez A. B., J. Vrebalov, P. Moffett, L. A. Mueller, and G. B. Martin (2012). A draft genome sequence ofNicotiana benthamiana and web-based tools for its use in plant-microbe biology research. In preparation.

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.