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

Abstract

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 (VIGS) 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 (http://solgenomics.net/) for both BLAST searches and for downloading to local servers. The estimated genome size of N. benthamiana is ~3 gigabases (Gb). The current assembly consists of ~141,000 scaffolds, spanning 2.6 Gb of which >50% are longer than 89 kilobases. Of the ~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 MAP kinases. The sequence will also be useful for comparative genomics in the Solanaceae as shown here by the discovery of microsynteny between N. benthamiana and tomato in the region encompassing the Pto/Prf genes.