Variability of Emaravirus Species Associated with Sterility Mosaic Disease of Pigeonpea in India Provides Evidence of Segment Reassortment

Abstract

Sterility mosaic disease (SMD) of pigeonpea is a serious constraint for cultivation of pigeonpea in India and other South Asian countries. SMD of pigeonpea is associated with two distinct emaraviruses, Pigeonpea sterility mosaic virus 1 (PPSMV-1) and Pigeonpea sterility mosaic virus 2 (PPSMV-2), with genomes consisting of five and six negative-sense RNA segments, respectively. The recently published genome sequences of both PPSMV-1 and PPSMV-2 are from a single location, Patancheru from the state of Telangana in India. However, here we present the first report of sequence variability among 23 isolates of PPSMV-1 and PPSMV-2, collected from ten locations representing six states of India. Both PPSMV-1 and PPSMV-2 are shown to be present across India and to exhibit considerable sequence variability. Variability of RNA3 sequences was higher than the RNA4 sequences for both PPSMV-1 and PPSMV-2. Additionally, the sixth RNA segment (RNA6), previously reported to be associated with only PPSMV-2, is also associated with isolates of PPSMV-1. Multiplex reverse transcription PCR (RT-PCR) analyses show that PPSMV-1 and PPSMV-2 frequently occur as mixed infections. Further sequence analyses indicated the presence of reassortment of RNA4 between isolates of PPSMV-1 and PPSMV-2.

The population structure of Rose rosette virus in the USA

“…Similar findings have also been observed in pigeon pea sterility mosaic virus-2 isolates, with 5 % variability seen in the RNA 5 segment [54]. In addition, diversity in RNA 3 and RNA 4 was similar to that previously observed for RRV and other emaraviruses [55][56][57][58][59][60][61].…”

Population structure, evolution and detection of blackberry leaf mottle‐associated virus, an emerging emaravirus

“…Recombination in negative‐sense RNA viruses is reported to be rare, in contrast to positive‐sense RNA and DNA viruses (Chare & Holmes, ). However, such events were detected within RNA4, similar to other emaraviruses (Walia et al ., ; Patil et al ., ). On the other hand, reassortants occur naturally in populations of plant viruses with segmented genomes (Martín et al ., ; Jonson et al ., ; Tentchev et al ., ; Bergua et al ., ).…”

“…Such events can be detected using RDP4 software if the genomic segments are concatenated and breakpoints occur in the vicinity of the region where different genes have been joined (Stainton et al ., ; Savory & Ramakrishnan, ). In emaraviruses, reassortment has been reported in FMV, pigeonpea sterility mosaic virus 1 (PPSMV1) and PPSMV2 (Walia et al ., ; Patil et al ., ). Phylogenetic incongruence of the NP and MP genes and the potential recombination and reassortment events detected in the BLMaV population indicate that genetic exchange may also play an important role in shaping BLMaV populations.…”

First Complete Genome Sequence of a Distinct Papaya Ringspot Virus Isolate from the Northeastern Region of India

“…In 2015, leaf samples from a PRSV-infected papaya plant were collected from Umiam (erstwhile Barapani) in the state of Meghalaya, located in the NER of India. Total RNA extraction and cDNA synthesis were done as described by Patil et al ( 12 ). Later, the cDNA was used for PCR amplification with potyvirus universal primers ( 13 ) and degenerate primers from this study.…”

“…Later, degenerate primers were designed at conserved regions of PRSV, and the entire PRSV-Meghalaya genome was real-time PCR (RT-PCR) amplified as 5 segments of ∼1.8 to 2.5 kb in size. These amplicons were cloned and sequenced as described by Patil et al ( 12 ). The assembly of the contigs resulted in a complete genome size of 10,343 nt for the PRSV-Meghalaya isolate.…”