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Genome-wide analysis of Carica papaya reveals a small NBS resistance gene family

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Abstract

The majority of plant disease resistance proteins identified to date belong to a limited number of structural classes, of which those containing nucleotide-binding site (NBS) motifs are the most common. This study provides a detailed analysis of the NBS-encoding genes of the fifth sequenced angiosperm, Carica papaya. Despite having a significantly larger genome than Arabidopsis thaliana, papaya has fewer NBS genes. Nevertheless, papaya maintains genes belonging to both Toll/interleukin-1 receptor (TIR) and non-TIR subclasses. Papaya’s NBS gene family shares most similarity with Vitis vinifera homologs, but seven non-TIR members with distinct motif sequence represent a novel subgroup. Transcript splice variants and adjacent genes encoding resistance-associated proteins may provide functional compensation for the apparent scarcity of NBS class resistance genes. Looking forward, the papaya NBS gene family is uniquely small in size but structurally diverse, making it suitable for functional studies aimed at a broader understanding of plant resistance genes.

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Acknowledgments

We thank Dr. Paul H. Moore for critical review of the manuscript and Mr. Ratnesh Singh and Dr. Ming-Li Wang at the Hawai’i Agriculture Research Center (HARC) for providing bioinformatics technical assistance. Funding for this project was provided by the United States Department of Agriculture (USDA), Cooperative State Research Education and Extension Service (CSREES), and Tropical and Subtropical Agriculture Research (T-STAR).

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Authors and Affiliations

  1. Department of Molecular Biosciences and Bioengineering, University of Hawai’i at Mānoa, Honolulu, HI, 96822, USA

    Brad W. Porter

  2. Hawai’i Agriculture Research Center, 99-193 Aiea Heights Drive, Aiea, HI, 96701, USA

    Maya Paidi & Yun J. Zhu

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

    Ray Ming

  4. Department of Microbiology, University of Hawai’i at Mānoa, Honolulu, HI, 96822, USA

    Maqsudul Alam

  5. Department of Plant and Environmental Protection Sciences, University of Hawai’i at Mānoa, Honolulu, HI, 96822, USA

    Wayne T. Nishijima

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  1. Brad W. Porter
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Correspondence to Yun J. Zhu.

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Communicated by K. Shirasu.

B. W. Porter and M. Paidi contributed equally to this work.

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Porter, B.W., Paidi, M., Ming, R. et al. Genome-wide analysis of Carica papaya reveals a small NBS resistance gene family. Mol Genet Genomics 281, 609–626 (2009). https://doi.org/10.1007/s00438-009-0434-x

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