Genome-wide analysis of Carica papaya reveals a small NBS resistance gene family
- 910 Downloads
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.
KeywordsCarica papaya Resistance genes NBS-LRR genes TIR domain CC motif Alternative splicing
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).
- Deslandes L, Olivier J, Peeters N, Feng DX, Khounlotham M, Boucher C, Somssich I, Genin S, Marco Y (2003) Physical interaction between RRS1-R, a protein conferring resistance to bacterial wilt, and PopP2, a type III effector targeted to the plant nucleus. Proc Natl Acad Sci USA 100:8024–8029PubMedCrossRefGoogle Scholar
- Dodds PN, Lawrence GJ, Pryor A, Ellis JG (2000) Genetic analysis and evolution of plant disease resistance genes. In: Dickinson M, Beynon J (eds) Molecular plant pathology. Annual plant reviews, vol 4 M. Sheffield Academic Press, Sheffield, pp 88–107Google Scholar
- Jones DA, Jones JDG (1996) The roles of leucine-rich repeats in plant defences. Adv Bot Res Adv Plant Pathol 24:90–167Google Scholar
- Kim KC, Lai Z, Fan B, Chen Z (2008) Arabidopsis WRKY38 and WRKY62 transcription factors interact with Histone Deacetylase 19 in basal defense. Plant Cell [Epub ahead of print]Google Scholar
- Marchler-Bauer A, Anderson JB, Derbyshire MK, DeWeese-Scott C, Gonzales NR, Gwadz M, Hao L, He S, Hurwitz DI, Jackson JD, Ke Z, Krylov D, Lanczycki CJ, Liebert CA, Liu C, Lu F, Lu S, Marchler GH, Mullokandov M, Song JS, Thanki N, Yamashita RA, Yin JJ, Zhang D, Bryant SH (2007) CDD: a conserved domain database for interactive domain family analysis. Nucleic Acids Res 35:D237–D240PubMedCrossRefGoogle Scholar
- Mukhtar MS, Deslandes L, Auriac MC, Marco Y, Somssich IE (2008) The Arabidopsis transcription factor WRKY27 influences wilt disease symptom development caused by Ralstonia solanacearum. Plant J [Epub ahead of print]Google Scholar
- Nishijima W (2002) A new disease hits papaya. Agric Hawaii 3:26Google Scholar
- Opassiri R, Pomthong B, Akiyama T, Nakphaichit M, Onkoksoong T, Ketudat Cairns M, Ketudat Cairns JR (2007) A stress-induced rice (Oryza sativa L.) beta-glucosidase represents a new subfamily of glycosyl hydrolase family 5 containing a fascin-like domain. Biochem J 408:241–249PubMedCrossRefGoogle Scholar