High-throughput RNA sequencing and genetic structure studies of turnip mosaic virus infecting black and yellow mustard revealing emergence of world-B3 pathotype in India

Abstract

The RNA viruses are marked by high genetic diversity, which allows them to quickly adapt to new and resistant hosts. The pathogenic turnip mosaic virus (TuMV) infects Brassicaceae plant species all over the world.Aim: To study the evolution and host expansion of a TuMV for the first time in India using molecular population genetic framework. Materials and Results: Here, we decipher the complete genome sequences of two TuMV world-B3 strains infecting yellow and black mustard in India through highthroughput RNA sequencing subjecting ribosomal RNA depleted mRNA isolated from leaves exhibiting puckering and mosaic symptoms with 100% incidence and high severity in the experimental field. The viral genomes of the two isolates were 9817 and 9829 nucleotides long. They featured two open reading frames (ORFs), one of which encoded a polyprotein comprised of 3164 amino acids and the other of which encoded a PIPO protein of 62 amino acids. Conclusions:The two TuMV strains from New Delhi region shared identity with the world-B pathotype and subpathotype world B3 showcasing its emergence first time in South Asia. In contrast, other isolates reported previously from South Asia were all Asian-BR pathotypes.Significance and Impact of the Study: According to our knowledge, this is the first instance of TuMV association with black mustard naturally. Their geographical prevalence justifies a lower degree of genetic differentiation and higher rate of gene flow calculated between the world-B and Asian-BR pathotypes. This study provides insights on population structuring, expansions and evolution, level of genetic heterogeneity and variability of worldwide prevalent isolates of TuMV which will further aid in understanding virus epidemiology and help prevent losses.

Genomic characterization of recombinant cucumber mosaic virus isolates infecting mustard species via HTS in India

“…Here, we report the host shift of CMV to infect black and yellow‐seeded mustard in India. The plants exhibiting severe mosaic, puckering and stunting were found to be infected by both CMV and TuMV while the samples exhibiting puckering symptoms were infected with only TuMV (Singhal et al, 2022). The genomic sequences of two CMV isolates i.e., CMV YM and CMV BM‐ in this investigation shared their highest levels of identity with isolates from South‐East Asian nations that belong to the subgroup IB (India, Taiwan, China and Italy).…”

“…On observation of symptoms of severe mosaic, puckering and stunting in mustard experimental fields of Indian Council of Agricultural Research-Indian Agricultural Research Institute (ICAR-IARI), New Delhi, the association of viruses was hypothesized for which leaf sample collection was done and sent for virome analysis via high-throughput RNAseq approach. Our study indicated invariable association of turnip mosaic virus (TuMV) with the diseased mustard plant but association of cucumber mosaic virus (CMV) was also observed along with TuMV by electron microscopy and reverse transcriptase-polymerase chain reaction (RT-PCR; Singhal et al, 2022). Several CMV isolates are known to cause symptoms ranging from minor mosaic to severe stunting and necrosis (Lee et al, 2007).…”

“…The leaf samples from various yellow-seeded mustard (Pusa Gold), black-seeded mustard (BN-3), brown-seeded conventional (Pusa Vijay) and quality mustard (single zero type [PM-30 and Pusa Karishma] and double zero type [JC-21, JC-33 and PDZ1, PDZ-5, PDZM-33]) varieties were analysed in this study. EM analysis revealed the presence of flexuous particles (Singhal et al, 2022), but the presence of spherical particles indicated mixed infection of viruses as well (Figure S1).…”

“…trilocularis ), thought to have Mediterranean origin; brown mustard, sometimes known as Indian mustard ( Brassica juncea ); and black mustard ( B. nigra ), thought to have Asia Minor‐Iran origin. Several viruses have been found to infect mustard in India, including turnip yellows virus (TuYV) (Sharma et al, 2013), turnip mosaic virus (TuMV) (Singhal et al, 2022), croton yellow vein mosaic virus (CYVMV) (Roy et al, 2013).…”

“…The viruses that have recently "jumped host species" cause the worst virus infections (Villarreal et al, 2000). The identification of plant viruses and their mixed infections has increased significantly due to high-throughput sequencing coupled with bioinformatics analysis (Nabi et al, 2022;Prajapati et al, 2022;Singhal et al, 2021Singhal et al, , 2022Villamor et al, 2019). The purpose of this study was to examine the viral spectrum of this essential oilseed plant.…”