Nicotiana benthamiana is a model organism widely adopted in plant biology. Its complete assembly remains unavailable despite several recent improvements. To further improve its usefulness, we generate and phase the complete 2.85 Gb genome assembly of allotetraploid N. benthamiana. 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 which CENH3 protein more preferentially occupies, suggestive of their crucial roles in centromere function. We demonstrate that ribosomal DNA is a major origin of centromeric satellites, and mitochondrial DNA could be employed as a core component of the centromere. Subgenome analysis indicates that the emergence of satellite arrays probably drives new centromere formation. Altogether, we propose that N. benthamiana centromeres evolved via neocentromere formation, satellite expansion, retrotransposon enrichment and mtDNA integration.

Nicotiana benthamiana 是一种在植物生物学中广泛采用的模式生物。尽管最近进行了几项改进，但其完整的程序集仍然不可用。为了进一步提高其实用性，我们生成并分相了本氏异体四倍体 N. benthamiana 的完整 2.85 Gb 基因组组装。我们发现，尽管茄科着丝粒广泛以 Ty3/吉普赛反转录转座子为主，但基于卫星的着丝粒在本氏猪笼草中出奇地常见，19 个着丝粒中有 11 个以兆碱基尺度的卫星阵列为特征。有趣的是，富含卫星和无卫星的着丝粒被不同的吉普赛反转录转座子广泛侵入，CENH3 蛋白更优先占据这些转座子，这表明它们在着丝粒功能中起着关键作用。我们证明核糖体 DNA 是着丝粒卫星的主要来源，线粒体 DNA 可用作着丝粒的核心成分。亚基因组分析表明，卫星阵列的出现可能推动了新的着丝粒形成。总而言之，我们提出本氏烟草着丝粒是通过新着丝粒形成、卫星扩增、反转录转座子富集和 mtDNA 整合进化而来的。