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Resistance gene analogs involved in tolerant cassava–geminivirus interaction that shows a recovery phenotype

Abstract

The current literature describes recovery from virus-induced symptoms as a RNA silencing defense, but immunity-related genes, including the structurally specific resistance gene analogs (RGAs) that may play a key role in tolerance and recovery is not yet reported. In this study, the transcriptome data of tolerant cassava TME3 (which exhibits a recovery phenotype) and susceptible cassava T200 infected with South African cassava mosaic virus were explored for RGAs. Putative resistance protein analogs (RPAs) with amide-like indole-3-acetic acid–Ile-Leu-Arg (IAA-ILR) and leucine-rich repeat (LRR)-kinase conserved domains were unique to TME3. Common responsive RPAs in TME3 and T200 were the dirigent-like protein, coil–coil nucleotide-binding site (NBS) and toll-interleukin-resistance, disease resistance zinc finger chromosome condensation-like protein (DZC), and NBS-apoptosis repressor with caspase recruitment (ARC)–LRR domains. Mutations in RPAs in the MHD motif of the NBS-ARC2 subdomain associated with the recovery phase in TME3 were observed. Additionally, a cohort of 25 RGAs mined solely during the recovery process in TME3 was identified. Phylogenetic and expression analyses support that diverse RGAs are differentially expressed during tolerance and recovery. This study reveals that in cassava, a perennial crop, RGAs participate in tolerance and differentially accumulate during recovery as a complementary defense mechanism to natural occurring RNA silencing to impair viral replication.

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Acknowledgments

L. Bengyella was supported by URC post-doctoral funding from the School of Molecular and Cell Biology (CESM:130203), the University of the Witwatersrand, Johannesburg, South Africa, and the National Research Foundation (NRF) for funding. We thank Farhahna Allie, Michal J Okoniewski, and Erica J Pierce who participated in generating the primary transcriptome data based on SACMV infection of cassava T200 and TME3 as part of a study in the Plant Biotechology Programme of Prof. Chrissie Rey.

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Correspondence to Bengyella Louis.

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Edited by Seung-Kook Choi.

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11262_2015_1246_MOESM1_ESM.tif

Fig. S1 Details of micro-propagation of cassava, growth conditions, and infection of plants with infection clones of SACMV DNA-A and DNA-B cloned wild-type Agrobacterium tumefaciens Agl1 (TIFF 836 kb)

11262_2015_1246_MOESM2_ESM.tif

Fig. S2 Multiple sequence alignment of mined resistance protein analogs from SACMV-infected tolerant cassava TME3. The results depict the conserved core NBS domain with GxPL motif (indicated by an arrow) and mutations in MHD motifs of the C-terminal ARC2 subdomain indicated by two arrows (TIFF 137 kb)

11262_2015_1246_MOESM3_ESM.tif

Fig. S3 Multiple sequence alignment of mined resistance protein analogs from SACMV-infected susceptible cassava T200. The results depicts the conserved core NBS domain with GxPL motif (indicated by an arrow) and duplications of MHD motifs of the C-terminal ARC2 subdomain are highlighted (TIFF 106 kb)

11262_2015_1246_MOESM4_ESM.xlsx

Table S1 A) Details of primers set used, B) List of common resistance gene analogs responsive to SACMV in susceptible cassava T200 and tolerant cassava TME3, C) Details of mined SACMV responsive resistance gene analogs in T200 at log2 fold change ≥ 1.0, and D) Details of mined SACMV responsive resistance gene analogs in TME3 at log2 fold change ≥ 1.0 (XLSX 30 kb)

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Louis, B., Rey, C. Resistance gene analogs involved in tolerant cassava–geminivirus interaction that shows a recovery phenotype. Virus Genes 51, 393–407 (2015). https://doi.org/10.1007/s11262-015-1246-1

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Keywords

  • Recovery
  • Tolerance
  • Cassava
  • Transcriptome
  • R gene analogs
  • MHD motif mutations
  • South African cassava mosaic virus