Plant & Animal Genomes XVI Conference

January 12-16, 2008
Town & Country Convention Center
San Diego, CA

Hunting Down The Papaya Transgenes

Michael Schatz

  Center for Bioinformatics and Computational Biology, University of Maryland,College Park, MD 20742, USA

In the middle of the last century, the Papaya ringspot potyvirus (PRSV) devastated the papaya industry on the island of Oahu in Hawaii and in other fields throughout the world. With the eminent threat of the disease spreading to the fields in the Puna district of Hawaii island, researchers in the mid 1980s developed PRSV-resistant transgenic lines of papaya using the pathogen-derived resistance approach, in which genes from PRSV were inserted into the papaya genome using a gene gun. The commercialization of these transgenic lines in the late 1990s virtually saved the Hawaiian papaya industry, but without a full genome sequence, there was lingering concern as to the exact nature of the transgenic insertions.
In my presentation, I will report on the draft genome sequence of the virus-resistant ‘SunUp’ papaya, created in collaboration with the University of Hawaii, the University of Illinois at Urbana-Champaign, and other institutions. I will focus on the computational methods used for assembling the genome, validating its correctness, and the subsequent search for transgenic inserts. Our genome wide analysis, combined with Southern blot analysis and directed PCR, confirms the efficiency of the gene gun technology, with only 3 conclusive transgenic insertions. In addition, even though the papaya genome is nearly twice the size
of the Arabidopsis genome, it contains fewer genes, and thus makes it an excellent candidate for further study of biosynthetic pathways and networks.