Date: 17 Jul 2013

Sequencing and Assembly of the Transgenic Papaya Genome

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Abstract

Papaya is an excellent model for studying fruit tree genomics. Papaya has a short generation time of 9–12 months, a small genome of 372 Mbp, and little residual within genome heterozygosity, and it produces an abundance of offspring. Papaya is also significant agriculturally, as it produces one of the world’s most nutritious fruits, and it has a pair of incipient sex chromosomes that are well suited for studying sex chromosome evolution. These features spurred the papaya genome sequencing project. The papaya genome was sequenced using 2.8 million whole-genome shotgun reads from a female transgenic SunUp cultivar. The shotgun assembly and physical maps were integrated with a genetic map to generate the draft genome. Analysis of the draft genome revealed fewer genes than any other sequenced plant genome, making it an excellent candidate for studying biosynthesis pathways. Synteny analysis suggests that papaya has no recent genome-wide duplications, which could potentially make it a good model of the ancient angiosperm genome. Most gene families have fewer members in papaya, with several exceptions, including drastic expansion in the MADs-box family. The draft genome sequence of papaya accelerated papaya sex chromosome research and facilitated comparative genomic studies in angiosperm.