A multi-omic Nicotiana benthamiana resource for fundamental research and biotechnology

Abstract

Nicotiana benthamiana is currently the most globally important plant biotechnology platform and a widely adopted plant research tool. Its progenitors have been allotetraploid for ~ 6MY during which the genome has experienced transposable element (TE) proliferation, chromosome and gene loss, and rearrangement. We have developed a multi-omics reference set, including platinum quality genome assemblies for the LAB and QLD ecotypes, and identified their microRNA complements, epigenetic landscapes, subgenomic memberships, metabolic composition and the regions favoured for transgene and TE integration. Genomic analysis revealed intergenic region expansion and long range synteny with the chromosomes of other Solanaceae. The 19-chromosome ~3Gb N. benthamiana genome shows advanced diploidization with the preservation of only ~45% of both functional homoeologous genes, 8 homeologous chromosome pairs, loss of 5 chromosomes, and 3 orphan chromosomes. Massive segmental autopolyploidization, presumably through repeated and extensive “duplication/deletion” homoeologous recombination, has produced highly chimeric chromosomes comprised of genes from the putative ancestral parents N. sylvestris and N. glauca. Two recent bursts of Copia mobility, 750 kYA and 75kYA. These relatively recent events likely contributed to ecotype diversification and genome diploidization, while an earlier Gypsy proliferation is common to the whole Nicotiana genus and contributed mainly to the intergenic expansion. QLD appears to have a higher gene number and more functional pathways than LAB which, combined with their inter-fertility, high-quality genome assemblies, easy transient and stable transformation and editing, make this a powerful resource partnership.