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Genome of papaya, a fast growing tropical fruit tree

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Abstract

Papaya is a major fruit crop in tropical and subtropical regions worldwide. It has long been recognized as a nutritious and healthy fruit rich in vitamins A and C. Its small genome, unique aspects of nascent sex chromosomes, and agricultural importance are justifications for sequencing the genome. A female plant of the transgenic variety SunUp was selected for sequencing its genome to avoid the complication of assembling the XY chromosomes in a male or hermaphrodite plant. The draft genome revealed fewer genes than sequenced genomes of flowering plants, partly due to its lack of genome wide duplication since the ancient triplication event shared by eudicots. Most gene families have fewer members in papaya, including significantly fewer disease resistance genes. However, striking amplifications in gene number were found in some functional groups, including MADS-box genes, starch synthases, and volatiles that might affect the speciation and adaptation of papaya. The draft genome was used to clone a gene controlling fruit flesh color and to accelerate the construction of physical maps of sex chromosomes in papaya. Finishing the papaya genome and re-sequencing selected genomes in the family will further facilitate papaya improvement and the study of genome and sex chromosome evolution in angiosperms, particularly in Caricaceae.

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Acknowledgments

We thank Fanchang Zeng for assistance. This work is partly supported by a grant from the National Science Foundation (NSF) (award no. DBI-0922545).

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Authors and Affiliations

  1. Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA

    Ray Ming & Mary A. Schuler

  2. Texas Agrilife Research Center, Texas A&M University, Weslaco, TX, 78596, USA

    Qingyi Yu

  3. Hawaii Agriculture Research Center, P.O. Box 100, Kunia, HI, 96759, USA

    Paul H. Moore, Ming-Li Wang & Yun J. Zhu

  4. Department of Tropical Plant and Soil Sciences, University of Hawaii, Honolulu, HI, 96822, USA

    Robert E. Paull & Nancy J. Chen

  5. Department of Horticulture, University of Wisconsin, Madison, WI, 53706, USA

    Jiming Jiang

  6. Plant Genome Mapping Laboratory, University of Georgia, Athens, GA, 30602, USA

    Andrew H. Paterson

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  1. Ray Ming
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  2. Qingyi Yu
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Correspondence to Ray Ming.

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Communicated by A. Abbott

A contribution to the Special Issue ‘‘The genomes of the giants: a walk through the forest of tree genomes’’

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Ming, R., Yu, Q., Moore, P.H. et al. Genome of papaya, a fast growing tropical fruit tree. Tree Genetics & Genomes 8, 445–462 (2012). https://doi.org/10.1007/s11295-012-0490-y

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