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A Draft Genome Sequence of Nicotiana benthamiana to Enhance Molecular Plant-Microbe Biology Research

December 2012 , Volume 25 , Number  12
Pages  1,523 - 1,530

Aureliano Bombarely,1 Hernan G. Rosli,1 Julia Vrebalov,1 Peter Moffett,1,2 Lukas A. Mueller,1 and Gregory B. Martin1,3,4

1Boyce Thompson Institute for Plant Research, Ithaca, NY 14853, USA; 2Département de Biologie, Université de Sherbrooke, Sherbrooke, Quebec J1K 2R1, Canada; 3Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, NY 14853, USA; 4Genomics and Biotechnology Section, Department of Biological Sciences, Faculty of Science, King Abdulaziz University, P.O. Box 80203 Jeddah 21589, Saudi Arabia

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Accepted 28 July 2012.

Nicotiana benthamiana is a widely used model plant species for the study of fundamental questions in molecular plant-microbe interactions and other areas of plant biology. This popularity derives from its well-characterized susceptibility to diverse pathogens and, especially, its amenability to virus-induced gene silencing and transient protein expression methods. Here, we report the generation of a 63-fold coverage draft genome sequence of N. benthamiana and its availability on the Sol Genomics Network for both BLAST searches and for downloading to local servers. The estimated genome size of N. benthamiana is 3 Gb (gigabases). The current assembly consists of approximately 141,000 scaffolds, spanning 2.6 Gb with 50% of the genome sequence contained within scaffolds >89 kilobases. Of the approximately 16,000 N. benthamiana unigenes available in GenBank, >90% are represented in the assembly. The usefulness of the sequence was demonstrated by the retrieval of N. benthamiana orthologs for 24 immunity-associated genes from other species including Ago2, Ago7, Bak1, Bik1, Crt1, Fls2, Pto, Prf, Rar1, and mitogen-activated protein kinases. The sequence will also be useful for comparative genomics in the Solanaceae family as shown here by the discovery of microsynteny between N. benthamiana and tomato in the region encompassing the Pto and Prf genes.

© 2012 The American Phytopathological Society