1. Hawaii Agriculture Research Center, Aiea, Hawaii 96701, USA
2. Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
3. Advanced Studies in Genomics, Proteomics and Bioinformatics, University of Hawaii, Honolulu, Hawaii 96822, USA
4. TEDA School of Biological Sciences and Biotechnology, Nankai University, Tianjin Economic-Technological Development Area, Tianjin 300457, China
5. Tianjin Research Center for Functional Genomics and Biochip, Tianjin Economic-Technological Development Area, Tianjin 300457, China
6. Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, College of Life Sciences, Nankai University, Tianjin 300071, China
7. Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland 20742, USA
8. Department of Molecular Bioscience and Bioengineering, University of Hawaii, Honolulu, Hawaii 96822, USA
9. Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30602, USA
10. Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA
11. Department of Tropical Plant and Soil Sciences, University of Hawaii, Honolulu, Hawaii 96822, USA
12. Waksman Institute of Microbiology and Department of Plant Biology and Pathology, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, USA
13. Department of Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
14. Department of Biology, Indiana University, Bloomington, Indiana 47405, USA
15. USDA-ARS, Pacific Basin Agricultural Research Center, Hilo, Hawaii 96720, USA
16. Department of Biochemistry and Biophysics, 2128 TAMU, Texas A&M University, College Station, Texas 77843, USA
17. The Institute for Genomic Research, Rockville, Maryland 20850, USA
18. W.M. Keck Center for Comparative and Functional Genomics, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
19. Department of Molecular Sciences, University of Tennessee, Memphis, Tennessee 38163, USA
20. Leeward Community College, University of Hawaii, Pearl City, Hawaii 96782, USA
21. Wicell Research Institute, Madison, Wisconsin 53707, USA
22. Department of Horticulture, Michigan State University, East Lansing, Michigan 48824, USA
23. Department of Horticulture, University of Wisconsin, Madison, Wisconsin 53706, USA
24. Department of Biology, Duke University, Durham, North Carolina 27708, USA
25. Department of Plant Sciences, University of California, Davis, California 95616, USA
26. Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland 20742, USA
27. Maui High Performance Computing Center, Kihei, Hawaii 96753, USA
28. Departments of Cell and Developmental Biology, Biochemistry and Plant Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
29. Applied Biosystems, 850 Lincoln Centre Drive, Foster City, California 94404, USA
30. Department of Microbiology, University of Hawaii, Honolulu, Hawaii 96822, USA
31. These authors contributed equally to this work.

Correspondence to: Lei Wang^4,5,6Maqsudul Alam^3,30 Correspondence and requests for materials should be addressed to M.A. (Email: alam@hawaii.edu) or L.W. (Email: wanglei@nankai.edu.cn).

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Papaya, a fruit crop cultivated in tropical and subtropical regions, is known for its nutritional benefits and medicinal applications. Here we report a 3 draft genome sequence of 'SunUp' papaya, the first commercial virus-resistant transgenic fruit tree¹ to be sequenced. The papaya genome is three times the size of the Arabidopsis genome, but contains fewer genes, including significantly fewer disease-resistance gene analogues. Comparison of the five sequenced genomes suggests a minimal angiosperm gene set of 13,311. A lack of recent genome duplication, atypical of other angiosperm genomes sequenced so far^{2, 3, 4, 5}, may account for the smaller papaya gene number in most functional groups. Nonetheless, striking amplifications in gene number within particular functional groups suggest roles in the evolution of tree-like habit, deposition and remobilization of starch reserves, attraction of seed dispersal agents, and adaptation to tropical daylengths. Transgenesis at three locations is closely associated with chloroplast insertions into the nuclear genome, and with topoisomerase I recognition sites. Papaya offers numerous advantages as a system for fruit-tree functional genomics, and this draft genome sequence provides the foundation for revealing the basis of Carica's distinguishing morpho-physiological, medicinal and nutritional properties.

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