Comparison of Pepper and Tomato Pseudomolecule Revealed Differentiation Mechanisms of Genome Size and Structure in Pepper

Pepper is a unique species among Solanaceous plants due to its large genome size. The genome size of pepper is measured as 3090 Mbp, which is approximately three times larger than that of tomato (950 Mbp). Recently, the research group involved in pepper genome sequencing project generated pepper pseudomolecules in draft state. By comparing the pepper pseudomolecules against corresponding tomato chromosomes, we could elucidate differentiation of the pepper genome size and structure in Solanaceous plants. The overall comparison of pepper and tomato chromosomes revealed well conserved genic regions but different repeat region. The pepper chromosomes were highly expanded in heterochromatic regions. Comparison of repeat contents revealed that Ty3/Gypsy elements were most abundant in pepper. In pepper genome, the Ty3/Gypsy elements were accumulated in both heterochromatic and euchromatic regions but mainly in heterochromatic regions. Ty1/Copia in pepper genome was accumulated in both heterochromatic and euchromatic regions. In contrast, both Ty3/Gypsy and Ty1/Copia elements in tomato genome were accumulated in heterochromatic regions. This indicates that accumulation of Ty3/Gypsy elements in pepper played an important role in heterochromatin expansion. Both pepper and tomato genome revealed traces of whole genome duplication, and this occurred before speciation. The pepper LTR-retrotransposons were actively accumulated after the whole genome duplication, and the peak was close to speciation time. The insertion pattern of pepper LTR-retrotransposons revealed the different insertion time in different regions. The LTR-retrotransposons in heterochromatic regions were older than those in euchromatic regions. These results show a characteristic expansion mechanism of genome expansion in plant kingdom.