Following a BAC by BAC sequencing approach, MSY and the corresponding X region is being currently sequenced in papaya. Candidate MSY BACs were first validated by FISH mapping and/or by comparison with shotgun WGS data. Then, clones were sequenced using the shotgun approach with at least 10X coverage.

Storage and visualization of all these data is utilizing software from the Generic Model Organism Database (GMOD) project (Stein et al. 2002- http://www.gmod.org). A key component of the GMOD project is the generic genome browser, GBrowse (a CGI application for displaying genome annotations). This web-based application retrieves and displays genomic annotation and raw sequence from a relational or flat-file database. Currently, our data is stored as GFF flat files that are corrected for updated coordinate systems as the BAC scaffold assembly evolves, but as the annotation datasets become unstable or become too large for this format, we intend to store the data in a MySQL database using the Chado database schema. The GBROWSE config file has been manually adjusted for track names and attributes specific to the MSY-DB. The reader is referred to GMOD documentation for details on the GBROWSE implementation. All this information is currently accessible at our GBrowse site.

Separately from our NSF-funded project, a total of 2.8 million WGS sequencing reads generated from a female plant of transgenic cultivar SunUp (Ming et al., 2008) and 31,488 EST sequences assembled in 8,571 unigenes (unpublished data) were analyzed. EST sequences and unigenes were anchored to the WGS by BLAST. Best hits at 0.01 were considered. These data are available at the Hawaii Papaya Genome Project at the University of Hawaii.

References:

Ming R, Hou S, Feng Y, Yu QY, Dionne-Laporte A, Saw J, Senin P, Wang W, Salzberg SL, Tang H, Lyons E, Rice D, Riley M, Skelton R, Murray J, Chen C, Eustice M, Tong E, Albert H, Paull RE, Wang ML, Zhu Y, Schatz M, Nagarajan N, Agbayani R, Guan P, Blas A, Wang J, Na JK, Michael T, Shakirov EV, Haas B, Thimmapuram J, Nelson D, Wang X, Bowers JE, Suzuki J, Tripathi S, Neupane K, Wei H, Singh R, Irikura B, Jiang N, Zhang W, Wall K, Presting G, Gschwend A, Li Y, Windsor AJ, Navajas-Perez R, Torres MJ, Feltus FA, Porter B, Paidi M, Luo MC, Liu L, Christopher D, Moore PH, Sugimura T, dePamphilis C, Jiang J, Schuler M, Mitchell-Olds T, Shippen D, Palmer JD, Freeling M, Paterson AH, Gonsalves D, Wang L, Alam M (2008) The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus). Nature 452:991-997

Stein LD, Mungall C, Shu SQ, Caudy M, Mangone M, Day A, Nickerson E, Stajich JE, Harris TW, Arva A, Lewis S (2002) The Generic Genome Browser: A building block for a model organism system database. Genome Research 12:1599-1610.