SunUp and Sunset genomes revealed impact of particle bombardment mediated transformation and domestication history in papaya

Transgenic papaya is widely publicized for controlling papaya ringspot virus. However, the impact of particle bombardment on the genome remains unknown. The transgenic SunUp and its progenitor Sunset genomes were assembled into 351.5 and 350.3 Mb in nine chromosomes, respectively. We identified a 1.64 Mb insertion containing three transgenic insertions in SunUp chromosome 5, consisting of 52 nuclear-plastid, 21 nuclear-mitochondrial and 1 nuclear genomic fragments. A 591.9 kb fragment in chromosome 5 was translocated into the 1.64 Mb insertion. We assembled a gapless 9.8 Mb hermaphrodite-specific region of the Y-h chromosome and its 6.0 Mb X counterpart. Resequencing 86 genomes revealed three distinct groups, validating their geographic origin and breeding history. We identified 147 selective sweeps and defined the essential role of zeta-carotene desaturase in carotenoid accumulation during domestication. Our findings elucidated the impact of particle bombardment and improved our understanding of sex chromosomes and domestication to expedite papaya improvement. Genome assemblies for the SunUp transgenic papaya and its progenitor Sunset identify three transgene-insertions in SunUp. Resequencing of 86 papaya genomes highlights the impacts of breeding and geographic origin.

Automated summary

This study investigated the genome structure of transgenic papaya and the impact of particle bombardment on the genome. The results revealed that the genomes of transgenic papaya SunUp and its progenitor Sunset consist of nine chromosomes. A segment containing three transgenic insertions was identified in one of the chromosomes of SunUp. Additionally, the study discovered the genome structure of the hermaphrodite-specific region and its X counterpart. Resequencing analysis demonstrated the geographic origin and breeding history of papaya.