Biology subjects

Reddy, C. N. L.

Publications and source records attributed to Reddy, C. N. L..

3 recordsLinked to original sources

bioRxiv2023

Genetic diversity and evidence of recombination of Horsegram yellow mosaic virus infecting pole bean (Phaseolus vulgaris L.) from South India

The yellow mosaic disease (YMD) caused by begomoviruses is a major constraint for the production of pole bean (Phaseolus vulgaris L.) in India. Survey was carried out in the eastern dry zone of Karnataka during 2019-20 to record the incidence of yellow mosaic disease in pole bean which revealed the ubiquitous prevalence of YMD in pole bean ranging from 6.02 to 80.74 per cent. Leaf samples collected (symptomatic and asymptomatic) were subjected for begomovirus detection using specific primers. Twelve samples, representing all the 12 taluks in the surveyed region were considered for full genome amplification by RCA, cloned and sequenced. Genome length of 12 current isolates ranged from 2718 - 2744 and 2668 - 2671 nucleotides for DNA-A and DNA-B, respectively. Sequence analysis using Sequence Demarcation Tool (SDT) showed >91 per cent nucleotide identity of current isolates (DNA-A) with other horsegram yellow mosaic virus (HgYMV) isolates available in the GenBank. As per existing ICTV criteria, all the current isolates can be considered as strains of HgYMV. Further, DNA-B associated with all the 12 isolates also shared >91 per cent nucleotide identity with DNA-B of HgYMV isolates, indicating absence of component re-assortment in HgYMV. Variation in the pairwise nucleotide identity and phylogenetic analysis confirmed the existence of new strains within the current HgYMV isolates. GC plot analysis reveals potential recombination in the low GC rich regions. Further, recombination breakpoint analysis indicated intra-species recombination in both DNA-A and DNA-B, which might have driven the origin of new strains in HgYMV. This is the first comprehensive study on begomoviruses ioslates associated with the yellow mosaic disease of pole bean based on complete genome sequencing in the world.

molecular biology↗

bioRxiv2023

Virome analyses by next-generation sequencing (NGS) in chilli (Capsicum anuum L.) presented with diverse symptoms phenotype revealed the association of seven plant viruses

Chilli is an important vegetable and spice crop, is known to be infected by several viruses. Techniques used in diagnosis of plant viral diseases before Next-generation sequencing (NGS) are having limitation of identifying the only known viruses. In the present study, virome analyses in infected chilli leaf samples was carried out using NGS to know the diversity of both known and unknown viruses associated with diseased symptoms. For virome profiling, samples from 19 fields were collected from chilli plants showing leaf curling, vein banding, mosaic, mottling, shoestring/rat tail/filiform/leathery and dull coloured leaves. Viral disease incidence in the surveyed fields varied from 26.66% to 47.50%. Total RNA was extracted from the 19 chilli leaf samples collected from fields and were pooled at equimolar concentration for virome profiling. From the rRNA-depleted pooled total RNA, mRNA and sRNA libraries were prepared and sequenced using Illumina NOVASEQ 6000 platform. Raw sequence data obtained was de novo assembled using three approaches; mRNAome with Trinity, sRNAome with Velvet and whole transcriptome (WT) with SPAdes assembly. Chilli virome, pairwise sequence identity and phylogenetic analyses revealed the presence of seven different viruses; chilli leaf curl virus (ChiLCV) along with its associated alpha and betasatellites, cucumber mosaic virus (CMV), groundnut bud necrosis orthotospovirus (GBNV), pepper cryptic virus-2 (PCV-2), pepper vein yellows virus (PeVYV), bell pepper alphaendornavirus (BPEV) and tobacco vein clearing virus (TVCV). From the virus associated contigs, complete/near-complete genomes for ChiLCV, CMV, PCV-2, PeVYV and BPEV and, partial genomes for GBNV and TVCV were reconstructed from the RNAome. Recombination breakpoint analyses revealed presence of recombination breakpoints in ChiLCV (coat protein and AC4 regions), CMV RNA2 (2a protein region) and P0, P3 and P5 protein regions of PeVYV. viruses identified in the current study are known to be originated from intra and interspecific recombination. Further, all the viruses detected in the pooled RNA sample were validated by PCR and loop mediated isothermal amplification (LAMP) using specific primers designed. Among the seven viruses identified in the study in chilli, PeVYV and BPEV are the first reports from India.

molecular biology↗

bioRxiv2022

Detection and molecular characterization of a phytoplasma associated with Cucumber (Cucumis sativus) and its first report from India

Cucumber (Cucumis sativus) plants exhibiting typical phyllody symptoms were collected from farmers field of Chintamani, Chickballapur districts of Karnataka (India). Disease incidence of phyllody was 2-3%. The etiology of the cucumber phyllody phytoplasma (CuPP) was confirmed by amplifying 16S rRNA gene from symptomatic plants using PCR followed by nested PCR using universal primers pairs P1/P7 and R16F2n/R16R2. After general detection the non-ribosomal SecY and rp (ribosomal protein) genes was amplified using specific primers. The PCR amplified products 16SrRNA (1.2 kb), SecY (1.6 kb) rp gene (1.2 kb) was cloned and sequenced. Sequence and phylogenetic analyses of 16S rRNA, secY and rp genes revealed that the detected phytoplasma is a member of the 16SrI group (Candidatus Phytoplasma asteris). Further on the basis of computer-simulated RFLP (= in silico RFLP) analysis of amplified F2n/R2 region of 16S rRNA gene indicates that, the detected phytoplasma was belongs to the subgroup X (16SrII-X). This is the first report on phytoplasma associated with phyllody disease of cucumber in India.

molecular biology↗