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Analysis of papaya BAC end sequences reveals first insights into the organization of a fruit tree genome

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Abstract

Papaya (Carica papaya L.) is a major tree fruit crop of tropical and subtropical regions with an estimated genome size of 372 Mbp. We present the analysis of 4.7% of the papaya genome based on BAC end sequences (BESs) representing 17 million high-quality bases. Microsatellites discovered in 5,452 BESs and flanking primer sequences are available to papaya breeding programs at http://www.genomics.hawaii.edu/papaya/BES. Sixteen percent of BESs contain plant repeat elements, the vast majority (83.3%) of which are class I retrotransposons. Several novel papaya-specific repeats were identified. Approximately 19.1% of the BESs have homology to Arabidopsis cDNA. Increasing numbers of completely sequenced plant genomes and BES projects enable novel approaches to comparative plant genomics. Paired BESs of Carica, Arabidopsis, Populus, Brassica and Lycopersicon were mapped onto the completed genomes of Arabidopsis and Populus. In general the level of microsynteny was highest between closely related organisms. However, papaya revealed a higher degree of apparent synteny with the more distantly related poplar than with the more closely related Arabidopsis. This, as well as significant colinearity observed between peach and poplar genome sequences, support recent observations of frequent genome rearrangements in the Arabidopsis lineage and suggest that the poplar genome sequence may be more useful for elucidating the papaya and other rosid genomes. These insights will play a critical role in selecting species and sequencing strategies that will optimally represent crop genomes in sequence databases.

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Abbreviations

BAC:

Bacterial artificial chromosome

BES:

BAC end sequence

kb:

Kilobase

Mbp:

Megabase pairs

MYA:

Million years ago

nt:

Nucleotide

SSR:

Simple sequence repeat

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Acknowledgements

The Center for Genomics, Proteomics and Bioinformatics Research Initiative at the University of Hawai’i contributed 11,013 of the BAC end sequence chromatograms that are described here, using funds provided by the University of Hawai’i. The remainder of the BES data was generated with funds from the United States Department of Agriculture (USDA) Tropical and Subtropical Agriculture Research Program (grant HAW00557G) and a USDA-Agricultural Research Service Cooperative Agreement (CA 58-3020-8-134) with the Hawai’i Agriculture Research Center.

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Authors and Affiliations

  1. Department of Molecular Biosciences and Bioengineering, University of Hawai‘i, 1955 East-West Road, Agricultural Sciences Building Room 218, Honolulu, HI, 96822, USA

    Chun Wan J. Lai, Moriah Eustice, Peizhu Guan, Ricelle Agbayani & Gernot G. Presting

  2. Hawaii Agriculture Research Center, Aiea, HI, 96701, USA

    Qingyi Yu, Rachel L. Skelton, Meghan R. Jones, Jan Murray, Moriah Eustice, Peizhu Guan, Ricelle Agbayani & Ray Ming

  3. Center for Genomics, Proteomics and Bioinformatics Research Initiative, University of Hawai‘i, Honolulu, HI, 96822, USA

    Shaobin Hou & Kanako L. T. Lewis

  4. USDA-ARS, Pacific Basin Agricultural Research Center, Hilo, HI, 96720, USA

    Paul H. Moore

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

    Ray Ming

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  1. Chun Wan J. Lai
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  2. Qingyi Yu
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  9. Peizhu Guan
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  10. Ricelle Agbayani
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  11. Paul H. Moore
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  12. Ray Ming
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  13. Gernot G. Presting
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Corresponding author

Correspondence to Gernot G. Presting.

Additional information

Communicated by R. Hagemann

Chun Wan J. Lai and Qingyi Yu have contributed equally to this work.

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Lai, C.W.J., Yu, Q., Hou, S. et al. Analysis of papaya BAC end sequences reveals first insights into the organization of a fruit tree genome. Mol Genet Genomics 276, 1–12 (2006). https://doi.org/10.1007/s00438-006-0122-z

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  • DOI: https://doi.org/10.1007/s00438-006-0122-z

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