The complete genome assembly of Nicotiana benthamiana reveals genetic and epigenetic landscape of centromeres

Nicotiana benthamiana is a model organism widely adopted in plant biology and biotechnology. Its genomic research has lagged since its initial release in 2012. To further improve its usefulness, we generate and phase the complete 2.85 Gb genome assembly of allotetraploid N. benthamiana with all 19 centromeres and 38 telomeres fully resolved. We find that although Solanaceae centromeres are widely dominated by Ty3/Gypsy retrotransposons, satellite-based centromeres are surprisingly common in N. benthamiana with 11 of 19 centromeres featured by megabase-scale satellite arrays. Interestingly, the satellite-enriched and satellite-free centromeres are extensively invaded by distinct Gypsy retrotransposons where CENH3 protein more preferentially occupies, suggestive of their crucial roles in centromere function. We demonstrate that rDNA is a major origin of centromeric satellites, and mitochondrial DNA could be employed as core component of centromere. Subgenome analysis indicate emergence of satellite arrays likely drives the centromere formation and maturation during genomic shock after polyploidization. Altogether, we propose N. benthamiana centromeres evolves via neocentromere formation, satellite expansion, retrotransposon enrichment, and mtDNA integration.