Syed Shan-e-Ali Zaidi

CRISPR/Cas9-Mediated Immunity to Geminiviruses: Differential Interference and Evasion

The CRISPR/Cas9 system has recently been used to confer molecular immunity against several eukaryotic viruses, including plant DNA geminiviruses. Here, we provide a detailed analysis of the efficiencies of targeting different coding and non-coding sequences in the genomes of multiple geminiviruses. Moreover, we analyze the ability of geminiviruses to evade the CRISPR/Cas9 machinery. Our results demonstrate that the CRISPR/Cas9 machinery can efficiently target coding and non-coding sequences and interfere with various geminiviruses. Furthermore, targeting the coding sequences of different geminiviruses resulted in the generation of viral variants capable of replication and systemic movement. By contrast, targeting the noncoding intergenic region sequences of geminiviruses resulted in interference, but with inefficient recovery of mutated viral variants, which thus limited the generation of variants capable of replication and movement. Taken together, our results indicate that targeting noncoding, intergenic sequences provides viral interference activity and significantly limits the generation of viral variants capable of replication and systemic infection, which is essential for developing durable resistance strategies for long-term virus control.

CRISPR-Cpf1: A New Tool for Plant Genome Editing

Clustered regularly interspaced palindromic repeats (CRISPR)-CRISPR-associated proteins (CRISPR-Cas), a groundbreaking genome-engineering tool, has facilitated targeted trait improvement in plants. Recently, CRISPR-CRISPR from Prevotella and Francisella 1 (Cpf1) has emerged as a new tool for efficient genome editing, including DNA-free editing in plants, with higher efficiency, specificity, and potentially wider applications than CRISPR-Cas9.

Tomato leaf curl New Delhi virus; a widespread bipartite begomovirus in the territory of monopartite begomoviruses.

Tomato leaf curl New Delhi virus (ToLCNDV) is an exceptional Old World bipartite begomovirus. On the Indian subcontinent, a region in which monopartite DNA satellite-associated begomoviruses with mostly narrow geographical ranges predominate, it is widespread, with a geographical range also including the Far East, Middle East, North Africa and Europe. The success of ToLCNDV probably derives from its broad host range and highly flexible genomic configuration: its DNA-A component is capable of productively interacting with, and trans-replicating, diverse DNA-B components and betasatellites. An understanding of the capacity of ToLCNDV to infect a variety of hosts and spread across a broad and ecologically variable geographical range could illuminate the potential economic threats associated with similar begomoviral invasions. Towards this end, we used available ToLCNDV sequences to reconstruct the history of ToLCNDV spread. TAXONOMY Family Geminiviridae, Genus Begomovirus. ToLCNDV is a bipartite begomovirus. Following the revised begomovirus taxonomic criteria of 91% and 94% nucleotide identity for species and strain demarcation, respectively, ToLCNDV is a distinct species with two strains: ToLCNDV and ToLCNDV-Spain. HOST RANGE The primary cultivated host of ToLCNDV is tomato (Solanum lycopersicum), but the virus is also known to infect 43 other plant species from a range of families, including Cucurbitaceae, Euphorbiaceae, Solanaceae, Malvaceae and Fabaceae. DISEASE SYMPTOMS Typical symptoms of ToLCNDV infection in its various hosts include leaf curling, vein thickening, puckering, purpling/darkening of leaf margins, leaf area reduction, internode shortening and severe stunting.

Viral Vectors for Plant Genome Engineering

Recent advances in genome engineering (GE) has made it possible to precisely alter DNA sequences in plant cells, providing specifically engineered plants with traits of interest. Gene targeting efficiency depends on the delivery-method of both sequence-specific nucleases and repair templates, to plant cells. Typically, this is achieved using Agrobacterium mediated transformation or particle bombardment, both of which transform only a subset of cells in treated tissues. The alternate in planta approaches, stably integrating nuclease-encoding cassettes and repair templates into the plant genome, are time consuming, expensive and require extra regulations. More efficient GE reagents delivery methods are clearly needed if GE is to become routine, especially in economically important crops that are difficult to transform. Recently, autonomously replicating virus-based vectors have been demonstrated as efficient means of delivering GE reagents in plants. Both DNA viruses (Bean yellow dwarf virus, Wheat dwarf virus and Cabbage leaf curl virus) and RNA virus (Tobacco rattle virus) have demonstrated efficient gene targeting frequencies in model plants (Nicotiana benthamiana) and crops (potato, tomato, rice, and wheat). Here we discuss the recent advances using viral vectors for plant genome engineering, the current limitations and future directions.

Engineering Dual Begomovirus-Bemisia tabaci Resistance in Plants

The whitefly Bemisia tabaci is an important pest of many economically important crops and the vector of begomoviruses (family Geminiviridae). Recently, the expression of insecticidal proteins and/or toxins or double-stranded (ds)RNA homologous to B. tabaci genes has been demonstrated to provide the plant with protection against B. tabaci and the viruses that it transmits.

Sesbania bispinosa, a new host of a begomovirus-betasatellite complex in Pakistan

Abstract Symptoms of severe leaf curling, yellowing and vein thickening, typical of begomovirus infection, were observed on Sesbania bispinosa grown in cotton leaf curl disease affected cotton fields in Pakistan. A begomovirus and its associated betasatellite were amplified and sequenced from these affected plants. Complete nucleotide sequence showed that a monopartite begomovirus named Pedilanthus leaf curl virus (PeLCV) is associated with the disease and it shared highest sequence identity (98.73%) with a clone previously reported from soybean. Characterization of the betasatellite showed that it had highest sequence identity (96–97%) with Tobacco leaf curl betasatellite (TbLCB), previously isolated from soybean. Our data shows the expansion of the host range of begomovirus-betasatellite complexes. To the best of our knowledge, this is the first occurrence of PeLCV and TbLCB on S. bispinosa.

Transcriptomics reveals multiple resistance mechanisms against cotton leaf curl disease in a naturally immune cotton species, Gossypium arboreum

Cotton leaf curl disease (CLCuD), caused by cotton leaf curl viruses (CLCuVs), is among the most devastating diseases in cotton. While the widely cultivated cotton species Gossypium hirsutum is generally susceptible, the diploid species G. arboreum is a natural source for resistance against CLCuD. However, the influence of CLCuD on the G. arboreum transcriptome and the interaction of CLCuD with G. arboreum remains to be elucidated. Here we have used an RNA-Seq based study to analyze differential gene expression in G. arboreum under CLCuD infestation. G. arboreum plants were infested by graft inoculation using a CLCuD infected scion of G. hirsutum. CLCuD infested asymptomatic and symptomatic plants were analyzed with RNA-seq using an Illumina HiSeq. 2500. Data analysis revealed 1062 differentially expressed genes (DEGs) in G. arboreum. We selected 17 genes for qPCR to validate RNA-Seq data. We identified several genes involved in disease resistance and pathogen defense. Furthermore, a weighted gene co-expression network was constructed from the RNA-Seq dataset that indicated 50 hub genes, most of which are involved in transport processes and might have a role in the defense response of G. arboreum against CLCuD. This fundamental study will improve the understanding of virus-host interaction and identification of important genes involved in G. arboreum tolerance against CLCuD.

Corrigendum: CRISPR/Cas9-Mediated Immunity to Geminiviruses: Differential Interference and Evasion

Scientific Reports 6: Article number: 26912; published online: 26 May 2016; updated: 26 August 2016 This Article contains an error in Figure 5 where Figure 5D and 5E were published as Figure 5E and 5D respectively. The correct Figure 5 and correct figure legend appears below as Figure 1.

The Rise of Cotton Genomics

Cotton is the most important fiber crop, but its polyploid genome is complex and difficult to improve. Recent advances in obtaining high-quality genome sequences of cultivated tetraploid and diploid cotton species may now overcome this hurdle, as well as provide new insights on important fiber quality and disease resistance genes.

NextGen VOICES: A postdoc's purpose

We gave young scientists this challenge: What is the purpose of a postdoc? Address this question by writing a job advertisement for the perfect postdoc position. We received responses from scientists around the world representing a variety of fields. Some wrote advertisements for their ideal postdoc