Geminiviruses: Taxonomic Structure and Diversity in Genomic Organization

2020 ◽  
Vol 14 (2) ◽  
pp. 86-98
Author(s):  
Saurabh Kulshrestha ◽  
Abhishek Bhardwaj ◽  
Vanshika
Keyword(s):  
Transgenic Plants ◽  
Genomic Organization ◽  
Genomic Structure ◽  
Taxonomic Status ◽  
Relevant Information ◽  
Plant Viruses ◽  
Monopartite Begomoviruses ◽  
Taxonomic Structure ◽  
New Horizons ◽  
Circular Ssdna

Background: Geminiviridae is one of the best-characterized and hence, one of the largest plant-virus families with the highest economic importance. Its members characteristically have a circular ssDNA genome within the encapsidation of twinned quasi-icosaheadral virions (18-38 nm size-range). Objective: Construction of a narrative review on geminiviruses, to have a clearer picture of their genomic structure and taxonomic status. Methods: A thorough search was conducted for papers and patents regarding geminiviruses, where relevant information was used to study their genomic organization, diversity and taxonomic structure. Results: Geminiviruses have been classified into nine genera (viz., genus Begomovirus, Mastrevirus, Curtovirus, Topocuvirus, Becurtovirus, Turncurtovirus, Capulavirus, Eragrovirus and Grablovirus) having distinct genomic organizations, host ranges and insect vectors. Genomic organization of all genera generally shows the presence of 4-6 ORFs encoding for various proteins. For now, Citrus chlorotic dwarf-associated virus (CCDaV), Camellia chlorotic dwarf-associated virus (CaCDaV) and few other geminiviruses are still unassigned to any genera. The monopartite begomoviruses (and few mastreviruses) have been found associated with aplhasatellites and betasatellites (viz., ~1.3 kb circular ssDNA satellites). Recent reports suggest that deltasatellites potentially reduce the accumulation of helper-Begomovirus species in host plants. Some patents have revealed the methods to generate transgenic plants resistant to geminiviruses. Conclusion: Geminiviruses rapidly evolve and are a highly diverse group of plant-viruses. However, research has shown new horizons in tackling the acute begomoviral diseases in plants by generating a novel bio-control methodology in which deltasatellites can be used as bio-control agents and generate transgenic plants resistant to geminiviruses.

Strategies for Research

1990 ◽  
Author(s):  
Steven Kim
Keyword(s):  
Industrial Development ◽  
Research Effort ◽  
Planning Horizon ◽  
Relevant Information ◽  
First Year ◽  
New Horizons ◽  
Graduate Research ◽  
Government Laboratory ◽  
Mind Set ◽  
Tacit Belief

The purpose of research is to acquire knowledge. In pure fields such as philosophy or science, the pursuit of knowledge is ideally an open-minded affair engaged in for its own sake. In other activities such as applied research or industrial development, the inquiring mind seeks out new knowledge to support specific objectives. The open-ended nature of research endeavors and their lack of obvious solutions and promising avenues usually qualify them as difficult problems. This chapter explores a number of domain-independent issues and techniques for pursuing research in various disciplines. For the sake of concreteness, much of our discussion in this chapter focuses on the academic environment of graduate research. However, most of the topics and approaches pertain as well to research in other settings, whether a government laboratory or a corporate marketing office. The newcomer to the research enterprise tends to have a simple view of what research entails. He initially believes that following a few suggestions from the advisor will lead to demonstrable results, a series of advances that can be measured by the hour or week. He has a tacit belief that progress will ensue automatically over time, much like attending a hamburger stand, raking autumn leaves, or solving homework problems. How could he believe otherwise? He has little or no prior experience with difficult problems of the magnitude that now face him. Perhaps the most important thing he will learn in the first year or so is the environment of research. Addressing difficult problems requires a new mind-set, a willingness to explore new horizons, maintain an open mind, appreciate small insights, and even enjoy the steady stream of failures as well as successes. Learning to conduct research systematically will be the most important aspect of his education in the first year. If the research effort spans a planning horizon of about two years, the indoctrination will occur in conjunction with an orientation phase during the first half-year, a period for defining the problem and gathering relevant information.

scholarly journals Tomato Twisted Leaf Virus: A Novel Indigenous New World Monopartite Begomovirus Infecting Tomato in Venezuela

Viruses ◽  
2019 ◽  
Vol 11 (4) ◽  
pp. 327 ◽  
Author(s):  
Gustavo Romay ◽  
Francis Geraud-Pouey ◽  
Dorys Chirinos ◽  
Mathieu Mahillon ◽  
Annika Gillis ◽  
...  
Keyword(s):  
Crop Production ◽  
New World ◽  
Systemic Infection ◽  
Plant Viruses ◽  
Monopartite Begomoviruses ◽  
Bipartite Begomoviruses ◽  
Reading Frame ◽  
Reverse Transcription Pcr ◽  
Infectious Clones ◽  
Leaf Virus

Begomoviruses are one of the major groups of plant viruses with an important economic impact on crop production in tropical and subtropical regions. The global spread of its polyphagous vector, the whitefly Bemisia tabaci, has contributed to the emergence and diversification of species within this genus. In this study, we found a putative novel begomovirus infecting tomato plants in Venezuela without a cognate DNA-B component. This begomovirus was genetically characterized and compared with related species. Furthermore, its infectivity was demonstrated by agroinoculation of infectious clones in tomato (Solanum lycopersicum) and Nicotiana benthamiana plants. The name Tomato twisted leaf virus (ToTLV) is proposed. ToTLV showed the typical genome organization of the DNA-A component of New World bipartite begomoviruses. However, the single DNA component of ToTLV was able to develop systemic infection in tomato and N. benthamiana plants, suggesting a monopartite nature of its genome. Interestingly, an additional open reading frame ORF was observed in ToTLV encompassing the intergenic region and the coat protein gene, which is not present in other closely related begomoviruses. A putative transcript from this region was amplified by strand-specific reverse transcription-PCR. Along with recent studies, our results showed that the diversity of monopartite begomoviruses from the New World is greater than previously thought.

scholarly journals Genome-Based Taxonomic Rearrangement of the Order Geobacterales Including the Description of Geomonas azotofigens sp. nov. and Geomonas diazotrophica sp. nov.

2021 ◽  
Vol 12 ◽  
Author(s):  
Zhenxing Xu ◽  
Yoko Masuda ◽  
Xueding Wang ◽  
Natsumi Ushijima ◽  
Yutaka Shiratori ◽  
...  
Keyword(s):  
Taxonomic Status ◽  
Terrestrial Ecosystems ◽  
Single Copy ◽  
Amino Acid Identity ◽  
Taxonomic Structure ◽  
Phylogenomic Analysis ◽  
Genome Sequences ◽  
Average Amino Acid Identity ◽  
The Family ◽  
Genomic Similarity

Geobacterales is a recently proposed order comprising members who originally belonged to the well-known family Geobacteraceae, which is a key group in terrestrial ecosystems involved in biogeochemical cycles and has been widely investigated in bioelectrochemistry and bioenergy fields. Previous studies have illustrated the taxonomic structure of most members in this group based on genomic phylogeny; however, several members are still in a pendent or chaotic taxonomic status owing to the lack of genome sequences. To address this issue, we performed this taxonomic reassignment using currently available genome sequences, along with the description of two novel paddy soil-isolated strains, designated Red51T and Red69T, which are phylogenetically located within this order. Phylogenomic analysis based on 120 ubiquitous single-copy proteins robustly separated the species Geobacter luticola from other known genera and placed the genus Oryzomonas (fam. Geobacteraceae) into the family ‘Pseudopelobacteraceae’; thus, a novel genus Geomobilimonas is proposed, and the family ‘Pseudopelobacteraceae’ was emended. Moreover, genomic comparisons with similarity indexes, including average amino acid identity (AAI), percentage of conserved protein (POCP), and average nucleotide identity (ANI), showed proper thresholds as genera boundaries in this order with values of 70%, 65%, and 74% for AAI, POCP, and ANI, respectively. Based on this, the three species Geobacter argillaceus, Geobacter pelophilus, and Geobacter chapellei should be three novel genera, for which the names Geomobilibacter, Geoanaerobacter, and Pelotalea are proposed, respectively. In addition, the two novel isolated strains phylogenetically belonged to the genus Geomonas, family Geobacteraceae, and shared genomic similarity values higher than those of genera boundaries, but lower than those of species boundaries with each other and their neighbors. Taken together with phenotypic and chemotaxonomic characteristics similar to other Geomonas species, these two strains, Red51T and Red69T, represent two novel species in the genus Geomonas, for which the names Geomonas azotofigens sp. nov. and Geomonas diazotrophica sp. nov. are proposed, respectively.

A novel cytoskeletal associated protein: Genomic organization and protein pattern

1988 ◽  
Vol 53 (1) ◽  
pp. 198-201 ◽  
Author(s):  
Haralabos Zorbas ◽  
Ernst Pöschl ◽  
Antonia Pöschl ◽  
Peter K. Müller
Keyword(s):  
Genomic Organization ◽  
Genomic Library ◽  
Protein Pattern ◽  
Genomic Structure ◽  
Initial Results

c-DNA clones were constructed from chicken sternal m-RNA and screened for recognizing those m-RNA species the amount of which decreases during chondrocyte dedifferentiation. One such clone was used to screen a chicken genomic library and, furthermore, to deduce peptide sequences suitable for raising antibodies. Initial results on the genomic structure and on some biochemical and immunochemical properties are presented.

scholarly journals 651 Important Genes that Have Been Transferred or Are Available for Transfer

HortScience ◽  
1999 ◽  
Vol 34 (3) ◽  
pp. 560A-560
Author(s):  
D.M. Tricoli ◽  
K.J. Carney ◽  
L.J. Nea ◽  
J.M. Palys ◽  
J.F. Reynolds ◽  
...  
Keyword(s):  
Transgenic Plants ◽  
Shelf Life ◽  
Virus Resistance ◽  
Herbicide Tolerance ◽  
Plant Biotechnology ◽  
Food Product ◽  
Nematode Resistance ◽  
High Viscosity ◽  
Plant Viruses ◽  
Biological Traits

Many seed companies are using plant biotechnology as a valuable extension of conventional plant breeding with the goal of providing breeders with novel biological traits. The application of biotechnology allows scientists and breeders to make precise changes during the process of germplasm improvement. Many of the first improvements achieved using transgenic plants have involved the transfer of input traits. Some of these traits include, insect resistance, nematode resistance, disease resistance, and herbicide tolerance. For example, the insertion of a gene that produces the crystalline toxin from Bacillus thuringeinsis has led to the production of transgenic plants that are resistant to insects from the Order Lepidoptera. The transfer of coat protein genes from plant viruses has lead to the development of transgenic crops that are resistant to the virus from which the gene or genes were isolated. Various strategies have been developed that allow transgenic plants to tolerate applications of herbicides that allows for improved weed control. In addition to input traits, other strategies are now being used that are directed at improving output traits. These include such traits as enhanced shelf life, ripening control, altered oils, and superior processing characteristics. At Seminis Vegetable Seed Co., we are currently developing transgenic plants with enhanced input as well as output traits. We have an active program using pathogen derived genes to develop virus resistance cultivars in a range of crops including, tomato, cucurbits, and peppers. Using this approach, we have been able to develop plants with multiple virus resistance by transforming germplasm with constructs containing stacked genes. Seminis is currently marketing a hybrid squash variety with resistance to two major virus pathogens. Another major goal for Seminis is implementing biotechnology to improve various aspects of fruit quality including viscosity, color, softening, and shelf life. Through our collaboration with Zeneca we have developed a high viscosity tomato, which was produced by suppressing endogenous levels of polyglacturonase. This processed food product is currently on the market in the United Kingdom.

scholarly journals Production of recombinant antigens in plants for animal and human immunization - a review

1997 ◽  
Vol 20 (4) ◽  
pp. 703-711 ◽  
Author(s):  
Ekkehard Hansen
Keyword(s):  
Experimental Data ◽  
Transgenic Plants ◽  
Host Plants ◽  
New Technology ◽  
Cost Effective ◽  
Plant Viruses ◽  
Antigenic Peptides ◽  
Recombinant Antigens ◽  
Early Results ◽  
World Demand

Plants present a cost effective production system for high value proteins. There is an increasing world demand for cheap vaccines that can be readily administered to the population, especially in economically less developed regions. A promising concept is the production of vaccines in plants that could be grown locally. Expression of antigenic peptides in the palatable parts of plants can lead to the production of edible active vaccines. Two major strategies are: i) to express antigens in transgenic plants, and ii) to produce antigenic peptides on the surface of plant viruses that could be used to infect host plants. This review considers the experimental data and early results for both strategies, and discusses the potential and problems of this new technology

Taxonomy of the North Moroccan and Iberian species of the subgenus Amblypteraca (Coleoptera: Tenebrionidae: Pimeliinae: Pimelia)

Zootaxa ◽  
2021 ◽  
Vol 4963 (3) ◽  
pp. 457-482
Author(s):  
PALOMA MAS-PEINADO ◽  
JOSÉ L. RUIZ ◽  
OTTÓ MERKL ◽  
DAVID BUCKLEY ◽  
MARIO GARCÍA-PARÍS
Keyword(s):  
Ad Hoc ◽  
Taxonomic Status ◽  
Morphological Data ◽  
Taxonomic Structure ◽  
Narrow Strip ◽  
Geographic Ranges ◽  
The North ◽  
Moroccan Coast ◽  
Phylogenetic Hypotheses ◽  
Analytical Tools

The subgenus Amblypteraca Mas-Peinado, Buckley, Ruiz & García-París, 2018 of Pimelia Fabricius, 1775, is restricted to the southern Iberian Peninsula and western Maghreb (northern and western Morocco). The distribution of Amblypteraca throughout the African-European edges overlaps largely with the geographic range of the subgenus Amblyptera, which is sister to the clade grouping subgenera Amblypteraca and Ecphoroma Solier, 1836. Delimiting species boundaries in the speciose genus Pimelia is often challenging, and the taxonomic status of some groups within the aforementioned subgenera is still a matter of debate. Here, we aim to stabilize some of the available names in Amblypteraca, and to correct some previous misidentifications. For that purpose, we discuss the composition and taxonomic structure within Amblypteraca by (i) assessing the phylogenetic congruence between mitochondrial and nuclear markers, and (ii) examining external morphological traits in 568 Amblypteraca specimens under the light of the phylogenetic hypotheses proposed here. Based on our results, Amblypteraca consists of three species: P. rotundipennis Kraatz, 1865, P. fairmairii Kraatz, 1865 and P. chrysomeloides Pallas, 1781. Both molecular and morphological data revealed four lineages within P. chrysomeloides: P. chrysomeloides chrysomeloides, distributed on both sides of the Strait of Gibraltar; P. chrysomeloides fornicata Herbst, 1799 from Portugal (Troia region); P. chrysomeloides bathyglypta Antoine, 1949, restricted to a narrow strip between Larache and Arbaoua (northern atlantic Moroccan coast), and P. chrysomeloides subris Koch, 1941 from Kenitra-La Mamora forest (Morocco). We designate a neotype of Tenebrio chrysomeloides Pallas, 1781 and propose the synonymy of P. chrysomeloides (Pallas, 1781) = P. obesa Solier, 1836 syn. n. Pimelia tristis Haag-Rutenberg, 1875, previously misidentified and included in Amblypteraca, is now transferred back to Amblyptera. Further studies with ad hoc sampling designs and analytical tools would be in need to delimit the exact geographic ranges of these taxa, and to analyse the patterns of diversity within and among species and subspecies.

Gene for integrin-associated protein (IAP, CD47): Physical mapping, genomic structure, and expression studies in skeletal muscle

2002 ◽  
Vol 80 (2) ◽  
pp. 169-176 ◽  
Author(s):  
Jörg Schickel ◽  
Katharina Stahn ◽  
Klaus-Peter Zimmer ◽  
Ralf Sudbrak ◽  
Tim M Størm ◽  
...  
Keyword(s):  
Skeletal Muscle ◽  
Human Chromosome ◽  
Genomic Organization ◽  
Genomic Structure ◽  
Splice Form ◽  
Form Expression ◽  
Multiple Functions ◽  
Expression Studies ◽  
Tubular System ◽  
Neuronal Processes

Integrin-associated protein (IAP) is a widely expressed membrane protein with multiple functions in immunological and neuronal processes. Having physically mapped the IAP gene into a BAC/PAC contig covering approximately 1 Mb on human chromosome 3q13.1-q13.2, we determined the genomic organization of the gene, established its expression in skeletal muscle, and identified a novel splice variant. Our expression studies demonstrate expression of integrin-associated protein in the t-tubular system and the euchromatin of skeletal muscle cells where its function thus far is not known.Key words: integrin-associated protein, novel splice form, expression and subcellular localization in skeletal muscle, genomic organization.

scholarly journals Stability of recombinant plant viruses containing genes of unrelated plant viruses

2007 ◽  
Vol 88 (4) ◽  
pp. 1347-1355 ◽  
Author(s):  
Bong-Nam Chung ◽  
Tomas Canto ◽  
Peter Palukaitis
Keyword(s):  
Transgenic Plants ◽  
Transgenic Tobacco ◽  
Potato Virus ◽  
Tobacco Rattle Virus ◽  
Resistance Mechanism ◽  
Potato Virus X ◽  
Plant Viruses ◽  
Hybrid Plant ◽  
Expression Vectors ◽  
Post Inoculation

The stability of hybrid plant viruses that might arise by recombination in transgenic plants was examined using hybrid viruses derived from the viral expression vectors potato virus X (PVX) and tobacco rattle virus (TRV). The potato virus Y (PVY) NIb and HCPro open reading frames (ORFs) were introduced into PVX to generate PVX-NIb and PVX-HCPro, while the PVY NIb ORF was introduced into a vector derived from TRV RNA2 to generate TRV-NIb. All three viruses were unstable and most of the progeny viruses had lost the inserted sequences between 2 and 4 weeks post-inoculation. There was some variation in the rate of loss of part or all of the inserted sequence and the number of plants containing the deleted viruses, depending on the sequence, the host (Nicotiana tabacum vs Nicotiana benthamiana) or the vector, although none of these factors was associated consistently with the preferential loss of the inserted sequences. PVX-NIb was unable to accumulate in NIb-transgenic tobacco resistant to infection by PVY and also showed loss of the NIb insert from PVX-NIb in some NIb-transgenic tobacco plants susceptible to infection by PVY. These data indicate that such hybrid viruses, formed in resistant transgenic plants from a transgene and an unrelated virus, would be at a selective disadvantage, first by being targeted by the resistance mechanism and second by not being competitive with the parental virus.

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