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Genome-Wide Analysis of Repetitive Elements in Papaya

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Abstract

Papaya (Carica papaya L.) is an important fruit crop cultivated in tropical and subtropical regions worldwide. A first draft of its genome sequence has been recently released. Together with Arabidopsis, rice, poplar, grapevine and other genomes in the pipeline, it represents a good opportunity to gain insight into the organization of plant genomes. Here we report a detailed analysis of repetitive elements in the papaya genome, including transposable elements (TEs), tandemly-arrayed sequences, and high copy number genes. These repetitive sequences account for ∼56% of the papaya genome with TEs being the most abundant at 52%, tandem repeats at 1.3% and high copy number genes at 3%. Most common types of TEs are represented in the papaya genome with retrotransposons being the dominant class, accounting for 40% of the genome. The most prevalent retrotransposons are Ty3-gypsy (27.8%) and Ty1-copia (5.5%). Among the tandem repeats, microsatellites are the most abundant in number, but represent only 0.19% of the genome. Minisatellites and satellites are less abundant, but represent 0.68% and 0.43% of the genome, respectively, due to greater repeat length. Despite an overall smaller gene repertoire in papaya than many other angiosperms, a significant fraction of genes (>2%) are present in large gene families with copy number greater than 20. This repeat database clarified a major part of the papaya genome organization and partly explained the lower gene repertoire in papaya than in Arabidopsis.

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Notes

  1. We use the estimate from Table 2 as a large fraction of the Retrotransposon matches in Table 1 have not been classified.

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Acknowledgements

We thank Ning Jiang for suggestions and discussion on construction and characterization of the papaya repeat database. We appreciate financial support from the U.S. National Institutes of Health (R01-GM083873 to S.S.), the U.S. National Science Foundation (DBI-0553417 to R.M. and A.H.P.), the U. Hawaii and U.S. Department of Defense (W81XWH0520013 to M.A).

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Authors and Affiliations

  1. Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD, 20742, USA

    Niranjan Nagarajan, Mihai Pop & Steven L. Salzberg

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

    Rafael Navajas-Pérez & Andrew H. Paterson

  3. Department of Microbiology, University of Hawaii, Honolulu, HI, 96822, USA

    Maqsudul Alam

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

    Ray Ming

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  1. Niranjan Nagarajan
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Correspondence to Niranjan Nagarajan.

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Nagarajan and Navajas-Pérez contributed equally to this work.

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Nagarajan, N., Navajas-Pérez, R., Pop, M. et al. Genome-Wide Analysis of Repetitive Elements in Papaya. Tropical Plant Biol. 1, 191–201 (2008). https://doi.org/10.1007/s12042-008-9015-0

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