Detection and molecular characterization of the Iris severe mosaic virus-Ir isolate from Iran

Nateqi, Masoud; Habibi, Mina Koohi; Dizadji, Akbar; Parizad, Shirin

doi:10.1515/jppr-2015-0032

Cited by 8 publications

(3 citation statements)

References 20 publications

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“…In this context, use of reverse transcriptase PCR (RT-PCR), which works on the principle of cDNA synthesis from RNA, is one of the most promising approaches in plant viral diagnosis [ 39 ]. Using RT-PCR, Nateqi and coworkers [ 77 ] identified Iris severe mosaic virus (ISMV) using specific primers. A one-step RT-PCR is more sensitive, reliable, and cost-effective and has been employed on a wide variety of the RNA genome-based viruses in plants.…”

Section: Methods For Plant Viral Diagnosticmentioning

confidence: 99%

Current Developments and Challenges in Plant Viral Diagnostics: A Systematic Review

Mehetre

Leo

Singh³

et al. 2021

Viruses

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Plant viral diseases are the foremost threat to sustainable agriculture, leading to several billion dollars in losses every year. Many viruses infecting several crops have been described in the literature; however, new infectious viruses are emerging frequently through outbreaks. For the effective treatment and prevention of viral diseases, there is great demand for new techniques that can provide accurate identification on the causative agents. With the advancements in biochemical and molecular biology techniques, several diagnostic methods with improved sensitivity and specificity for the detection of prevalent and/or unknown plant viruses are being continuously developed. Currently, serological and nucleic acid methods are the most widely used for plant viral diagnosis. Nucleic acid-based techniques that amplify target DNA/RNA have been evolved with many variants. However, there is growing interest in developing techniques that can be based in real-time and thus facilitate in-field diagnosis. Next-generation sequencing (NGS)-based innovative methods have shown great potential to detect multiple viruses simultaneously; however, such techniques are in the preliminary stages in plant viral disease diagnostics. This review discusses the recent progress in the use of NGS-based techniques for the detection, diagnosis, and identification of plant viral diseases. New portable devices and technologies that could provide real-time analyses in a relatively short period of time are prime important for in-field diagnostics. Current development and application of such tools and techniques along with their potential limitations in plant virology are likewise discussed in detail.

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Section: Methods For Plant Viral Diagnosticmentioning

confidence: 99%

Current Developments and Challenges in Plant Viral Diagnostics: A Systematic Review

Mehetre

Leo

Singh³

et al. 2021

Viruses

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“…Transcripts from the soybean mosaic virus was found abundantly expressed in all five tissues analyzed. Although, these viruses have been isolated from these plants (and the related species Iris) previously [18][19][20][21][22], recent studies have shown the threat posed by these viruses to saffron cultivation is seriously underestimated. Several bacterial and fungal genera incorporating known pathogen species have also been identified.…”

Section: Discussionmentioning

confidence: 99%

“…Previously, saffron has been shown to be infected with bean yellow MV [18] and Narcissus MV [19]. Iris, which belong to the same Iridaceae family as saffron, was shown to be infected with Iris severe MV [20,21] and Narcissus MV [22]. A recent study highlights that the threat from these MVs is seriously underestimated [23].…”

Section: Viral Transcriptsmentioning

confidence: 99%

Transcriptome from saffron (Crocus sativus) plants in Jammu and Kashmir reveals abundant soybean mosaic virus transcripts and several putative pathogen bacterial and fungal genera

Chakraborty¹

2016

Preprint

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Saffron (Crocus sativus) is a spice with immense economic and medicinal relevance, due to its anticancer and chemopreventive properties. Although the genomic sequence of saffron is not publicly available, the RNA-seq based transcriptome of saffron from Jammu and Kashmir provides several, yet explored, insights into the metagenome of the plant from that region. In the current work, sequence databases were created in the YeATS suite from the NCBI and Ensembl databases to enable faster comparisons. These were used to determine the metagenome of saffron. Soybean mosaic virus, a potyvirus, was found to be abundantly expressed in all five tissues analyzed. Recent studies have highlighted that issues arising from latent potyvirus infections in saffron is severely underestimated. Bacterial and fungal identification is made complex due to symbiogenesis, especially in the absence of the endogenous genome. Symbiogenesis results in transcripts having significant homology to bacterial genomes and eukaryotic genomes. A stringent criterion based on homology comparison was used to identify bacterial and fungal transcripts, and inferences were constrained to the genus level. Leifsonia, Elizabethkingia and Staphylococcus were some of the identified bacteria, while Mycosphaerella and Pyrenophora were among the fungi detected. Among the bacterial genera, L. xyli is the causal agent for ratoon stunting disease in sugarcane, while E. meningoseptica and S. haemolyticus, having acquired multiresistance against available antimicrobial agents, are important in clinical settings. Mycosphaerella and Pyrenophora incorporate several pathogenic species. It is shown that a transcript from heat shock protein of the fungi Cladosporium cladosporioides has been erroneously annotated as a saffron gene. The detection of these pathogens should enable proper strategies for ensuring better yields. The functional annotation of proteins in the absence of a genome is subject to errors due to the existence of significantly homologous proteins in organisms from different branches of life. Obtaining the bacterial genomes:"ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/bacteria/ assembly summary.txt" provides details of available bacteria genomes. This was parsed, and the first occuring species of a genus was chosen randomly (getBacterialGenomes.csh:n=1355 in Dataset1).Obtaining plant mitochondrial, chloroplast and ribosomal sequences:The NCBI database was queried for : Plants, RefSeq, Mitochondrion/Chloroplast/Ribosomal rRNA/Ribosomal mRNA. These were combined in a single file (DB.list CHLORO MITO MRIBO RRIBO, n=40049 in Dataset1). Obtaining plant mitochondrial, chloroplast and ribosomal sequences:The fungal sequences were obtained from the Ensembl site [16]. A random species was chosen for each genus (list.ensembl.fungi.txt in Dataset1, n=222).The YeATS suite was used extensively to query these databases using the BLAST command-line interface [17]. The BLAST bitscore was used as a comparison metric instead of the Evalue since it allows differentiation for high ho...

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Iris spp. (Iris)

Sastry¹,

Mandal²,

Scott³

et al. 2019

Encyclopedia of Plant Viruses and Viroids

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Detection and molecular characterization of the Iris severe mosaic virus-Ir isolate from Iran

Cited by 8 publications

References 20 publications

Current Developments and Challenges in Plant Viral Diagnostics: A Systematic Review

Current Developments and Challenges in Plant Viral Diagnostics: A Systematic Review

Transcriptome from saffron (Crocus sativus) plants in Jammu and Kashmir reveals abundant soybean mosaic virus transcripts and several putative pathogen bacterial and fungal genera

Iris spp. (Iris)

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