Variability studies on pigeonpea sterility mosaic emaraviruses in Tamil Nadu reveals rampant mixed infections and interspecies recombination

Abstract

Sterility Mosaic Disease (SMD) is one of the most important diseases of pigeonpea in the Indian subcontinent. SMD of pigeonpea is associated with two distinct emaravirus species, Pigeonpea sterility mosaic emaravirus 1 (PPSMV-1) and Pigeonpea sterility mosaic emaravirus 2 (PPSMV-2). Both the emaravirus species consist of six negative-sense RNA segments referred to as RNA1, RNA2, RNA3, RNA4, RNA5 and RNA6. In this study, we analysed the variability among 12 isolates of PPSMV from 12 locations of major pigeonpea growing regions of the south Indian state Tamil Nadu. Reverse Transcription -Polymerase Chain Reaction (RT-PCR) analysis showed that both PPSMV-1 and PPSMV-2 were present in all the 12 locations as mixed infections and the segment RNA6 was present in all the isolates of PPSMV-1 and -2. Phylogenetic analysis with the nucleotide sequence of Nucleocapsid Protein (NP) and Movement Protein (MP) revealed that PPSMV-1 is more closely related to Redbud yellow ringspot virus than PPSMV-2. Whereas, PPSMV-2 is more closely related to Fig mosaic virus than PPSMV-1. Sequence identity analysis of the RNA1 segment of PPSMV-1 isolates revealed that the lowest sequence identity of 83.2% was with the Bihar isolate. Recombination analysis of NP sequences revealed that the Coimbatore-5 isolate of PPSMV-1 showed inter-species recombination with Bidar isolate of PPSMV-1 and Patancheru isolate of PPSMV2. Likewise, the MP sequence of Trichy-1 isolate of PPSMV-1 showed interspecies recombination with PPSMV-1 Mahagaon isolate and Raspberry leaf blotch virus isolate (NCBI Acc. No. FR823301).