Release of a draft genome sequence for Nicotiana benthamianaScientists 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]. Sequencing approachSeedlings 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 sequencedThe accession sequenced is referred to as "Nb-BTI". Seeds can be obtained by contacting Gregory Martin at gbm7@cornell.edu.Assembly StatisticsN. 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 ========================================================== N. benthamiana Genome v0.3 Contigs Contigs for Nicotiana benthamiana draft genome assembly version 0.3. This assembly was made with the run 1: 5 lanes of PE-500bp, 1 lane of MP-2Kb and 1 lane of MP-5Kb, using SOAPdeNovo as assembler (Kmer 63). Statistics: ========================================================== = REPORT: Niben.genome.v0.3.contigs = ========================================================== Sequence Count: 3010735 sequences Total Length: 2899410662 bp Longest sequence: 103554 bp (ID = Niben.v0.3.Ctg25014514) Shortest sequence: 201 bp (ID = Niben.v0.3.Ctg6458060) Average length: 963.024199074312 bp N95 length: 233 bp N95 index: 2338365 sequences N90 length: 274 bp N90 index: 1763126 sequences N75 length: 619 bp N75 index: 606395 sequences N50 length: 4140 bp N50 index: 156329 sequences N25 length: 10316 bp N25 index: 43823 sequences ========================================================== N. benthamiana Genome v0.3 Scaffolds + NrContigs Scaffolds and contigs that are not contained in any scaffold for Nicotiana benthamiana draft genome assembly version 0.3 ========================================================== = REPORT: Niben.genome.v0.3.scaffolds.nrcontigs = ========================================================== Sequence Count: 2770496 sequences Total Length: 2951043762 bp Longest sequence: 104967 bp (ID = Niben.v0.3.Scf25287388) Shortest sequence: 201 bp (ID = Niben.v0.3.Ctg6458060) Average length: 1065.16802839636 bp N95 length: 233 bp N95 index: 2087056 sequences N90 length: 276 bp N90 index: 1504209 sequences N75 length: 667 bp N75 index: 349603 sequences N50 length: 9243 bp N50 index: 94013 sequences N25 length: 15951 bp N25 index: 32376 sequences ========================================================== ToolsThe 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
AcknowledgmentsSequencing 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 tutorialAn on-line tutorial of the VIGS procedure is available on the JOVE site.
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