Resistance gene analogs involved in tolerant cassava–geminivirus interaction that shows a recovery phenotype Bengyella Louis 1 • Chrissie Rey 1 Received: 10 June 2015 / Accepted: 2 September 2015 Ó Springer Science+Business Media New York 2015 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 ana- logs (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 chro- mosome 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 com- plementary defense mechanism to natural occurring RNA silencing to impair viral replication. Keywords Recovery Á Tolerance Á Cassava Á Transcriptome Á R gene analogs Á MHD motif mutations Á South African cassava mosaic virus Introduction Cassava (Manihot esculenta Crantz) has a diploid chro- mosome number (2n = 36), and was introduced to Africa from tropical Latin America [1] by the Portuguese in the 16th century [2]. Currently, 262 million tonnes of cassava is cultivated on 20 million hectares worldwide [3]. Irre- spective of this output, most of the cassava landraces have lost their resistance to cassava mosaic geminiviruses (CMG) and cassava brown streak viruses (CBSV) which cause cassava mosaic disease (CMD) and cassava brown streak disease (CBSD), respectively. Resistance is defined as the ability to limit parasite burden to non-detectable levels of virus replication [4]. Ideally, a fully resistant plant would not be infected by a virus and would not show any symptoms [5] and no detectable viral titer [6]. Conversely, tolerance to virus infection leads to reduced crop damage [5, 7] and is associated with persistent virus replication at low levels [6, 8]. Remarkably, CMG are the most important economic constraint to cassava farming in Sub-Saharan Africa and the Indian sub-continent [9], and yield losses in some cases amount to 100 % [10]. Thus, the search for immunity-related genes (IRGs), and structurally specific Edited by Seung-Kook Choi. Electronic supplementary material The online version of this article (doi:10.1007/s11262-015-1246-1) contains supplementary material, which is available to authorized users. & Bengyella Louis bengyellalouis@gmail.com Chrissie Rey chrissie.rey@wits.ac.za 1 School of Molecular and Cell Biology, University of the Witwatersrand, 1, Jan Smuts, Ave, Braamfontein, Johannesburg 2000, South Africa 123 Virus Genes DOI 10.1007/s11262-015-1246-1