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Jishuang Chen - One of the best experts on this subject based on the ideXlab platform.

  • RAPID COMMUNICATION Seed-borne viral dsRNA elements in three cultivated Raphanus and Brassica plants suggest three cryptoviruses
    2020
    Co-Authors: Liqiang Li, Qiong Zhang, Runying Fu, Chao Li, Jishuang Chen
    Abstract:

    Since the 1970s, several dsRNA viruses, including Radish yellow edge virus, Raphanus sativus virus 1, Raphanus sativus virus 2, and Raphanus sativus virus 3, have been identified and reported as infecting radish. In the present study, in conjunction with a survey of seed-borne viruses in cultivated Brassica and Raphanus using the dsRNA diagnostic method, we discovered 3 novel cryptoviruses that infect Brassica and Raphanus: Raphanus sativus partitivirus 1, which infects radish (Raphanus sativus); Sinapis alba cryptic virus 1, which infects Sinapis alba; and Brassica rapa cryptic virus 1 (BrCV1), which infects Brassica rapa. The genomic organization of these crypto- viruses was analyzed and characterized. BrCV1 might represent the first plant partitivirus found in Gammapartitivirus. Additionally, the evolutionary relationships among all of the partitiviruses reported in Raphanus and Brassica were analyzed.

  • Seed-borne viral dsRNA elements in three cultivated Raphanus and Brassica plants suggest three cryptoviruses.
    Canadian Journal of Microbiology, 2016
    Co-Authors: Liqiang Li, Qiong Zhang, Runying Fu, Chao Li, Jishuang Chen
    Abstract:

    Since the 1970s, several dsRNA viruses, including Radish yellow edge virus, Raphanus sativus virus 1, Raphanus sativus virus 2, and Raphanus sativus virus 3, have been identified and reported as infecting radish. In the present study, in conjunction with a survey of seed-borne viruses in cultivated Brassica and Raphanus using the dsRNA diagnostic method, we discovered 3 novel cryptoviruses that infect Brassica and Raphanus: Raphanus sativus partitivirus 1, which infects radish (Raphanus sativus); Sinapis alba cryptic virus 1, which infects Sinapis alba; and Brassica rapa cryptic virus 1 (BrCV1), which infects Brassica rapa. The genomic organization of these cryptoviruses was analyzed and characterized. BrCV1 might represent the first plant partitivirus found in Gammapartitivirus. Additionally, the evolutionary relationships among all of the partitiviruses reported in Raphanus and Brassica were analyzed.

  • molecular evolution of turnip mosaic virus evidence of host adaptation genetic recombination and geographical spread
    Journal of General Virology, 2002
    Co-Authors: Kazusato Ohshima, Yuka Yamaguchi, Ryo Hirota, Tamaki Hamamoto, Kenta Tomimura, Teruo Sano, Fumio Azuhata, John A Walsh, J D Fletcher, Jishuang Chen
    Abstract:

    Turnip mosaic virus (TuMV), a species of the genus Potyvirus, occurs worldwide. Seventy-six isolates of TuMV were collected from around the world, mostly from Brassica and Raphanus crops, but also from several non-brassica species. Host tests grouped the isolates into one or other of two pathotypes; Brassica (B) and Brassica-Raphanus (BR). The nucleotide sequences of the first protein (P1) and coat protein (CP) genes of the isolates were determined. One-tenth of the isolates were found to have anomalous and variable phylogenetic relationships as a result of re- combination. The 5«-terminal 300 nt of the P1 gene of many isolates was also variable and phylogenetically anomalous, whereas the 380 nt 3« terminus of the CP gene was mostly conserved. Trees calculated from the remaining informative parts of the two genes of the non-recombinant sequences by neighbour-joining, maximum-likelihood and maximum-parsimony methods were closely similar, and so these parts of the sequences were concatenated and trees calculated from the resulting 1150 nt. The isolates fell into four consistent groups; only the relationships of these groups with one another and with the outgroup differed. The 'basal-B' cluster of eight B-pathotype isolates was most variable, was not monophyletic, and came from both brassicas and non-brassicas from southwest and central Eurasia. Closest to it, and forming a monophyletic subgroup of it in most trees, and similarly variable, was the 'basal-BR' group of eight BR pathotype Eurasian isolates. The third and least variable group, the 'Asian-BR' group, was of 22 BR-pathotype isolates, all from brassicas, mostly Raphanus, and all from east Asia mostly Japan. The fourth group of 36 isolates, the 'world-B' group, was from all continents, most were isolated from brassicas and most were of the B-pathotype. The simplest of several possible interpretations of the trees is that TuMV originated, like its brassica hosts, in Europe and spread to the other parts of the world, and that the BR pathotype has recently evolved in east Asia.

Kazusato Ohshima - One of the best experts on this subject based on the ideXlab platform.

  • Mutations in Turnip mosaic virus genomes that have adapted to Raphanus sativus
    Journal of General Virology, 2005
    Co-Authors: Adrian J. Gibbs, Yasuhiro Tomitaka, Flora Sánchez, Fernando Ponz, Kazusato Ohshima
    Abstract:

    The genetic basis for virulence in potyviruses is largely unknown. Earlier studies showed that there are two host types of Turnip mosaic virus (TuMV); the Brassica/Raphanus (BR)-host type infects both Brassica and Raphanus systemically, whereas the Brassica (B)-host type infects Brassica fully and systemically, but not Raphanus. The genetic basis of this difference has been explored by using the progeny of an infectious clone, p35Tunos; this clone is derived from the UK1 isolate, which is of the B-host type, but rarely infects Raphanus systemically and then only asymptomatically. Two inocula from one such infection were adapted to Raphanus by passaging, during which the infectivity and concentration of the virions of successive infections increased. The variant genomes in the samples, 16 in total, were sequenced fully. Four of the 39 nucleotide substitutions that were detected among the Raphanus sativus-adapted variant genomes were probably crucial for adaptation, as they were found in several variants with independent passage histories. These four were found in the protein 1 (P1), protein 3 (P3), cylindrical inclusion protein (CI) and genome-liked viral protein (VPg) genes. One of four ‘parallel evolution’ substitutions, 3430G→A, resulted in a 1100Met→Ile amino acid change in the C terminus of P3. It seems likely that this site is important in the initial stages of adaptation to R. sativus. Other independent substitutions were mostly found in the P3, CI and VPg genes.

  • molecular evolution of turnip mosaic virus evidence of host adaptation genetic recombination and geographical spread
    Journal of General Virology, 2002
    Co-Authors: Kazusato Ohshima, Yuka Yamaguchi, Ryo Hirota, Tamaki Hamamoto, Kenta Tomimura, Teruo Sano, Fumio Azuhata, John A Walsh, J D Fletcher, Jishuang Chen
    Abstract:

    Turnip mosaic virus (TuMV), a species of the genus Potyvirus, occurs worldwide. Seventy-six isolates of TuMV were collected from around the world, mostly from Brassica and Raphanus crops, but also from several non-brassica species. Host tests grouped the isolates into one or other of two pathotypes; Brassica (B) and Brassica-Raphanus (BR). The nucleotide sequences of the first protein (P1) and coat protein (CP) genes of the isolates were determined. One-tenth of the isolates were found to have anomalous and variable phylogenetic relationships as a result of re- combination. The 5«-terminal 300 nt of the P1 gene of many isolates was also variable and phylogenetically anomalous, whereas the 380 nt 3« terminus of the CP gene was mostly conserved. Trees calculated from the remaining informative parts of the two genes of the non-recombinant sequences by neighbour-joining, maximum-likelihood and maximum-parsimony methods were closely similar, and so these parts of the sequences were concatenated and trees calculated from the resulting 1150 nt. The isolates fell into four consistent groups; only the relationships of these groups with one another and with the outgroup differed. The 'basal-B' cluster of eight B-pathotype isolates was most variable, was not monophyletic, and came from both brassicas and non-brassicas from southwest and central Eurasia. Closest to it, and forming a monophyletic subgroup of it in most trees, and similarly variable, was the 'basal-BR' group of eight BR pathotype Eurasian isolates. The third and least variable group, the 'Asian-BR' group, was of 22 BR-pathotype isolates, all from brassicas, mostly Raphanus, and all from east Asia mostly Japan. The fourth group of 36 isolates, the 'world-B' group, was from all continents, most were isolated from brassicas and most were of the B-pathotype. The simplest of several possible interpretations of the trees is that TuMV originated, like its brassica hosts, in Europe and spread to the other parts of the world, and that the BR pathotype has recently evolved in east Asia.

Willem F Broekaert - One of the best experts on this subject based on the ideXlab platform.

  • determination of the three dimensional solution structure of Raphanus sativus antifungal protein 1 by 1h nmr
    Journal of Molecular Biology, 1998
    Co-Authors: Franky Fant, Wim F Vranken, Willem F Broekaert, Frans Borremans
    Abstract:

    Abstract Raphanus sativus Antifungal Protein 1 (Rs-AFP1) is a 51 amino acid residue plant defensin isolated from radish ( Raphanus sativus L.) seeds. The three-dimensional structure in aqueous solution has been determined from two-dimensional 1 H NMR data recorded at 500 MHz using the DIANA/REDAC calculation protocols. Experimental constraints consisted of 787 interproton distances extracted from NOE cross-peaks, 89 torsional constraints from 106 vicinal interproton coupling constants and 32 stereospecific assignments of prochiral protons. Further refinement by simulated annealing resulted in a set of 20 structures having pairwise root-mean-square differences of 1.35(±0.35) A over the backbone heavy atoms and 2.11(±0.46) A over all heavy atoms. The molecule adopts a compact globular fold comprising an α-helix from Asn18 till Leu28 and a triple-stranded β-sheet (β1=Lys2-Arg6, β2=His33-Tyr38 and β3=His43-Pro50). The central strand of this β-sheet is connected by two disulfide bridges (Cys21–Cys45 and Cys25–Cys47) to the α-helix. The connection between β-strand 2 and 3 is formed by a type VIa β-turn. Even the loop (Pro7 to Asn17) between β-strand 1 and the α-helix is relatively well defined. The structure of Raphanus sativus Antifungal Protein 1 features all the characteristics of the “cysteine stabilized αβ motif”. A comparison of the complete structure and of the regions important for interaction with the fungal receptor according to a mutational study, is made with the structure of γ-thionin, a plant defensin that has no antifungal activity. It is concluded that this interaction is both electrostatic and specific, and some possible scenarios for the mode of action are given.

  • in vitro antifungal activity of a radish Raphanus sativus l seed protein homologous to nonspecific lipid transfer proteins
    Plant Physiology, 1992
    Co-Authors: Franky R G Terras, Bruno P A Cammue, Inge J W M Goderis, Fred Van Leuven, Jozef Vanderleyden, Willem F Broekaert
    Abstract:

    A basic 9-kD protein was purified from seeds of radish (Raphanus sativus L.). The 43 amino-terminal amino acids show extensive sequence identity with nonspecific lipid transfer proteins from other plant species. The radish seed nonspecific lipid transfer protein-like protein inhibits the growth of several fungi in vitro.

Norman C Ellstrand - One of the best experts on this subject based on the ideXlab platform.

  • long term persistence of crop alleles in weedy populations of wild radish Raphanus raphanistrum
    New Phytologist, 2010
    Co-Authors: Allison A Snow, Theresa M Culley, Lesley G Campbell, Patricia M Sweeney, S G Hegde, Norman C Ellstrand
    Abstract:

    Summary • Hybridization allows transgenes and other crop alleles to spread to wild ⁄ weedy populations of related taxa. Researchers have debated whether such alleles will persist because low hybrid fitness and linkage to domestication traits could severely impede introgression. • To examine variation in the fates of three unlinked crop alleles, we monitored four experimental, self-seeding, hybrid populations of Raphanus raphanistrum · Raphanus sativus (radish) in Michigan, USA, over a decade. We also compared the fecundity of advanced-generation hybrid plants with wild plants in a common garden experiment. • Initially, F1 hybrids had reduced fitness, but the populations quickly evolved wild-type pollen fertility. In Year 10, the fecundity of plants from the experimental populations was similar to that of wild genotypes. Crop-specific alleles at the three loci persisted for 10 yr in all populations, and their frequencies varied among loci, populations and years. • This research provides a unique case study of substantial variation in the rates and patterns of crop allele introgression after a single hybridization event. Our findings demonstrate that certain crop alleles can introgress easily while others remain rare, supporting the assumption that neutral or beneficial transgenes that are not linked to maladaptive traits can persist in the wild.

Bruno P A Cammue - One of the best experts on this subject based on the ideXlab platform.