The papaya physical map is displayed using the WebFPC software, a web based java program to view the contigs of FPC database (Pampanwar et al., 2005- Arizona Genomics Computional Laboratory). Data are curated at the University of Georgia's Plant Genome Mapping laboratory.

The papaya BAC library used for fingerprinting was constructed from hermaphrodite 'SunUp', the original transgenic cultivar (Ming et al. 2001). This BAC library includes 39,168 BAC clones with average insert size of 132kb, providing 13.7x genome equivalents. All 39,168 BAC clones were fingerprinted using high information content fingerprinting (Luo et al. 2003) and the failed clones were repeated two rounds, obtaining successful fingerprints for 38,522 BAC clones (98.4% of the BAC library). After excluding the clones with empty and small inserts, highly repetitive sequences, cross-well contamination, and incomplete restriction enzyme digestion, the remaining 30,824 fingerprints (78.7% of the BAC library) were input to FPC for fingerprinted contig map assembly.

A total of 2,277 overgo probes representing conserved sequences in Arabidopsis and genetically mapped Brassica loci were tested against 36,864 Papaya BACs. A total of 1,329 overgos (58% of overgos designed) detected positive BACs in papaya BAC library. After eliminating low quality data, the remaining 1,122 overgos were anchored on the papaya FPC map. Among these overgos, 759 (67.7%) overgos hit single contigs and the average number of clones per overgo is 4.5.

References:

Luo, M.-C., Thomas, C., You, F.M., Hsiao, J., Ouyang S., Buell, C.R., Malandro, M., McGuire, P.E., Anderson, O.D., and Dvorak, J. 2003. High-throughput fingerprinting of bacterial artificial chromosomes using the SNaPshot labeling kit and sizing of restriction fragments by capillary electrophoresis. Genomics 82: 378-389.

Ming, R., Hou, S., Feng, Y., Yu, Q., Dionne-Laporte, A., Saw, J.H., Senin, P., Wang, W., Ly, B.V., Lewis, K.L., et al. 2008. The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus). Nature 452: 991-6.

Ming, R., Moore, P.H., Zee, F., Abbey, C.A., Ma, H., and Paterson, A.H. 2001. Construction and characterization of a papaya BAC library as a foundation for molecular dissection of a tree-fruit genome. Theoretical and Applied Genetics 102: 1432-2243.