Devang Mehta


Last Name

Mehta

First Name

Devang

ORCID

0000-0002-8911-1174

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2016 - 201952020 - 20211
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Publications 1 - 6 of 6
  • Linking CRISPR-Cas9 interference in cassava to the evolution of editing-resistant geminiviruses
    Item type: Journal Article
    Mehta, Devang; Stürchler, Alessandra; Anjanappa, Ravi B.; et al. (2019)
    Genome Biology
    Background Geminiviruses cause damaging diseases in several important crop species. However, limited progress has been made in developing crop varieties resistant to these highly diverse DNA viruses. Recently, the bacterial CRISPR/Cas9 system has been transferred to plants to target and confer immunity to geminiviruses. In this study, we use CRISPR-Cas9 interference in the staple food crop cassava with the aim of engineering resistance to African cassava mosaic virus, a member of a widespread and important family (Geminiviridae) of plant-pathogenic DNA viruses. Results Our results show that the CRISPR system fails to confer effective resistance to the virus during glasshouse inoculations. Further, we find that between 33 and 48% of edited virus genomes evolve a conserved single-nucleotide mutation that confers resistance to CRISPR-Cas9 cleavage. We also find that in the model plant Nicotiana benthamiana the replication of the novel, mutant virus is dependent on the presence of the wild-type virus. Conclusions Our study highlights the risks associated with CRISPR-Cas9 virus immunity in eukaryotes given that the mutagenic nature of the system generates viral escapes in a short time period. Our in-depth analysis of virus populations also represents a template for future studies analyzing virus escape from anti-viral CRISPR transgenics. This is especially important for informing regulation of such actively mutagenic applications of CRISPR-Cas9 technology in agriculture.
  • Characterization of Brown Streak Virus–Resistant Cassava
    Item type: Journal Article
    Anjanappa, Ravi B.; Mehta, Devang; Maruthi, M.N.; et al. (2016)
    Molecular Plant-Microbe Interactions
    Cassava brown streak disease (CBSD) has become a major constraint to cassava production in East and Central Africa. The identification of new sources of CBSD resistance is essential to deploy CBSD mitigation strategies, as the disease is progressing westwards to new geographical areas. A stringent infection method based on top cleft–grafting combined with precise virus titer quantitation was utilized to screen 14 cassava cultivars and elite breeding lines. When inoculated with mixed infections of Cassava brown streak virus (CBSV) and Ugandan cassava brown streak virus (UCBSV), the scions of elite breeding lines KBH 2006/18 and KBH 2006/26 remained symptom-free during a 16-week period of virus graft inoculation, while susceptible varieties displayed typical CBSD infection symptoms at 4 weeks after grafting. The identified CBSD resistance was stable under the coinoculation of CBSV and UCBSV with cassava geminiviruses. Double-grafting experiments revealed that transmission of CBSV and UCBSV to CBSD-susceptible top scions was delayed when using intermediate scions of elite breeding lines KBH 2006/18 and KBH 2006/26. Nonetheless, comparison of virus systemic movement using scions from KBH2006/18 and a transgenic CBSD resistant 60444 line (60444-Hp9 line) showed that both CBSV and UCBSV move at undetectable levels through the stems. Further, protoplast-based assays of virus titers showed that the replication of CBSV is inhibited in the resistant line KBH2006/18, suggesting that the identified CBSD resistance is at least partially based on inhibition of virus replication. Our molecular characterization of CBSD resistance in cassava offers a robust virus-host system to further investigate the molecular determinants of CBSD resistance.
  • A new full-length circular DNA sequencing method for viral-sized genomes reveals that RNAi transgenic plants provoke a shift in geminivirus populations in the field
    Item type: Journal Article
    Mehta, Devang; Hirsch-Hoffmann, Matthias; Were, Mariam; et al. (2019)
    Nucleic Acids Research
    We present a new method, CIDER-Seq (Circular DNA Enrichment sequencing) for the unbiased enrichment and long-read sequencing of viral-sized circular DNA molecules. We used CIDER-Seq to produce single-read full-length virus genomes for the first time. CIDER-Seq combines PCR-free virus enrichment with Single Molecule Real Time sequencing and a new sequence de-concatenation algorithm. We apply our technique to produce >1200 full-length, highly accurate geminivirus genomes from RNAi-transgenic and control plants in a field trial in Kenya. Using CIDER-Seq we can demonstrate for the first time that the expression of antiviral double-stranded RNA (dsRNA) in transgenic plants causes a consistent shift in virus populations towards species sharing low homology to the transgene derived dsRNA. Our method and its application in an economically important crop plant opens new possibilities in periodic virus sequence surveillance and accurate profiling of diverse circular DNA elements.
  • DomainViz: intuitive visualization of consensus domain distributions across groups of proteins
    Item type: Journal Article
    Schläpfer, Pascal; Mehta, Devang; Ridderikhoff, Cameron; et al. (2021)
    Nucleic Acids Research
    The prediction of functional domains is typically among the first steps towards understanding the function of new proteins and protein families. There are numerous databases of annotated protein domains that permit researchers to identify domains on individual proteins of interest. However, it is necessary to perform high-throughput domain searches to gain evolutionary insight into the functions of proteins and protein families. Unfortunately, at present, it is difficult to search for, and visualize domain conservation across multiple proteins and/or multiple groups of proteins in an intuitive manner. Here we present DomainViz, a new web-server that streamlines the identification and visualization of domains across multiple protein sequences. Currently, DomainViz uses the well-established PFAM and Prosite databases for domain searching and assembles intuitive, publication-ready ‘monument valley’ plots (mv-plots) that display the extent of domain conservation along two dimensions: positionality and frequency of occurrence in the input protein sequences. In addition, DomainViz produces a conventional domain-ordering figure. DomainViz can be used to explore the conservation of domains within a single protein family, across multiple families, and across families from different species to support studies into protein function and evolution. The web-server is publicly available at: https://uhrigprotools.biology.ualberta.ca/domainviz.
  • Accelerated ex situ breeding of GBSS- and PTST1-edited cassava for modified starch
    Item type: Journal Article
    Bull, Simon; Seung, David; Chanez, Christelle; et al. (2018)
    Science Advances
    Crop diversification required to meet demands for food security and industrial use is often challenged by breeding time and amenability of varieties to genome modification. Cassava is one such crop. Grown for its large starch-rich storage roots, it serves as a staple food and a commodity in the multibillion-dollar starch industry. Starch is composed of the glucose polymers amylopectin and amylose, with the latter strongly influencing the physicochemical properties of starch during cooking and processing. We demonstrate that CRISPR-Cas9 (clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9)–mediated targeted mutagenesis of two genes involved in amylose biosynthesis, PROTEIN TARGETING TO STARCH (PTST1) or GRANULE BOUND STARCH SYNTHASE (GBSS), can reduce or eliminate amylose content in root starch. Integration of the Arabidopsis FLOWERING LOCUS T gene in the genome-editing cassette allowed us to accelerate flowering—an event seldom seen under glasshouse conditions. Germinated seeds yielded S1, a transgene-free progeny that inherited edited genes. This attractive new plant breeding technique for modified cassava could be extended to other crops to provide a suite of novel varieties with useful traits for food and industrial applications.
Publications 1 - 6 of 6