scholarly journals Analysis of DNA Polymorphism and Virulence in Philippine Strains of Xanthomonas oryzae pv. oryzicola

Plant Disease ◽  
1999 ◽  
Vol 83 (5) ◽  
pp. 434-440 ◽  
Author(s):  
A. K. Raymundo ◽  
A. M. Briones ◽  
E. Y. Ardales ◽  
M. T. Perez ◽  
L. C. Fernandez ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Rflp Analysis ◽  
The Philippines ◽  
Xanthomonas Oryzae ◽  
Bacterial Leaf Streak ◽  
Bootstrap Analysis ◽  
Transposase Gene ◽  
Group I ◽  
Dna Types ◽  
Promising Source

Molecular tools were used to analyze the genetic diversity and population structure of Xanthomonas oryzae pv. oryzicola, the bacterial leaf streak pathogen of rice in the Philippines. Representative pathogen strains were selected and used to assess resistance in rice germplasm. A partial genomic library of X. oryzae pv. oryzicola was constructed, and a 459-bp clone containing the repetitive DNA element R41 was selected as a probe for restriction fragment length polymorphism (RFLP) analysis and sequenced. R41 shared 44% sequence homology with the putative transposase gene of IS1112, an insertion element cloned from X. oryzae pv. oryzae. Using R41 as a probe for RFLP analysis, 26 band profiles were discerned in a collection of 123 strains of X. oryzae pv. oryzicola. Analysis of PstI digestion patterns of DNA from the same collection resolved 36 haplotypes. Several clusters of strains were detected after grouping of data based on either pR41 as a probe or Pst1 digestion patterns. However, based on bootstrap analysis, the clusters were not robust. Genetic diversity was high for the entire collection as well as within spatially and temporally defined subsets of strains. Even a set of strains collected from a single site at a single time was highly diverse. Strains representing the different DNA types were inoculated to a set of diverserice cultivars. Consistent rice varietal groupings were obtained from disease reaction data, but there was no correlation between pathogen isolate cluster and host reaction across inoculation trials. Isozyme group I of rice, representing tropical japonica and javanica germplasm, is a promising source of resistance to bacterial leaf streak.

scholarly journals First Report of Bacterial Leaf Streak Caused by Xanthomonas oryzae pv. oryzicola on Rice in Burkina Faso

Plant Disease ◽  
2011 ◽  
Vol 95 (1) ◽  
pp. 72-72 ◽  
Author(s):  
I. Wonni ◽  
L. Ouedraogo ◽  
V. Verdier
Keyword(s):  
Burkina Faso ◽  
Multiplex Pcr ◽  
The Philippines ◽  
Xanthomonas Oryzae ◽  
Distilled Water ◽  
Sterile Water ◽  
Bacterial Leaf Streak ◽  
First Report ◽  
Wild Rice Species ◽  
Strain Collection

Bacterial leaf streak (BLS) caused by Xanthomonas oryzae pv. oryzicola is prevalent in Asia where it can decrease yield by as much as 30%. In Africa, BLS has been reported in Madagascar, Nigeria, Senegal, and recently in Mali (1). The pathogen is seed transmitted and rice seeds can be a source of primary inoculum (3). In October 2009, leaf streak symptoms were observed on 3-month-old field rice grown in three regions of Burkina Faso (Haut-Bassin, Cascades, and East Center). Disease was found on cultivated Oryza sativa (varieties TS2, FKR19, and FKR56N), wild rice species (O. longistaminata and O. barthii), and weeds. Symptoms consisted of water-soaked lesions that developed into translucent, yellow streaks with visible exudates at the leaf surface. Yellow-pigmented Xanthomonas-like colonies were isolated on PSA semiselective medium (peptone 10 g, sucrose 10 g, bacto agar 16 g, distilled water 1,000 ml, actidione 50 mg liter–1, cephalexin 40 mg liter–1, and kasugamycin 20 mg liter–1). A multiplex PCR developed for the identification of Xanthomonas oryzae pathovars (2) was used to check the identity of Xanthomonas-like isolates. X. oryzae pv. oryzicola strains BLS256 from the Philippines and CFBP 7331 from Mali were used as positive controls. Three expected DNA fragments (331, 691, and 945 bp) corresponding to X. oryzae pv. oryzicola were obtained from all isolates using the multiplex PCR. No fragment was observed for negative controls (distilled water as the template). Five X. oryzae pv. oryzicola isolates were further analyzed by sequence analysis using portions of the gyrB housekeeping gene together with reference strains. Two sequence types were identified among Burkinabe isolates differing by only one nucleotide. When compared with the nucleotide database with BLAST, three isolates (BAI6, BAI15, and BAI19) were 100% identical to the type culture strain X. oryzae pv. oryzicola BLS256 (gyrB sequence was obtained from GenBank AAQN01000001.1) while the other two (BAI5 and BAI20) demonstrated 99% sequence similarity. The nucleotide sequence of isolate BAI5 was submitted to GenBank (HQ112342). Pathogenicity tests were performed on greenhouse-grown 3-week-old rice plants cv. Nipponbare. Cultures were grown overnight in PSA medium and adjusted in sterile water to 1 × 108 CFU/ml and inoculated into rice leaves with the blunt end of a 1-ml syringe. Four infiltrations were done per isolate per leaf and two leaves were inoculated per plant. Control plants were inoculated with sterile water. After 15 days of incubation in the greenhouse at 27 ± 1°C with a 12-h photoperiod, inoculated leaves exhibited water-soaked lesions with yellow exudates that were identical to symptoms seen in the field. Control plants remained symptomless. Colonies with morphology typical of Xanthomonas were recovered from the symptomatic leaves and typed using multiplex PCR to fulfill Koch's postulates. Three isolates have been deposited in the Collection Française de Bactéries Phytopathogènes (CFBP) and identified as X. oryzae pv. oryzicola strains CFBP7341–43. To our knowledge, this is the first report of X. oryzae pv. oryzicola in Burkina Faso. Further surveys and strain collection will be necessary to evaluate the geographic distribution and prevalence of BLS in Burkina Faso and neighboring countries. References: (1) C. Gonzalez et al. Mol. Plant-Microbe Interact. 20:534, 2007. (2) J. Lang et al. Plant Dis. 94:311, 2010. (3) G. Xie and T. Mew. Plant Dis. 82:1007, 1998.

Xanthomonas oryzae. [Descriptions of Fungi and Bacteria].

1970 ◽  
Author(s):  
J. F. Bradbury
Keyword(s):  
Geographical Distribution ◽  
Vascular System ◽  
Natural Infection ◽  
The Philippines ◽  
Cyperus Rotundus ◽  
Xanthomonas Oryzae ◽  
Zizania Latifolia ◽  
Tropical Regions ◽  
Zizania Aquatica ◽  
Weed Hosts

Abstract A description is provided for Xanthomonas oryzae. Information is included on the disease caused by the organism, its transmission, geographical distribution, and hosts. HOSTS: On Oryza sativa. Natural infection of Leersia oryzaides, Leersia oryzaides var. japonica and Zizania latifolia[Zizania aquatica] is known (Mizukami & Wakimoto, 1959). Natural infection of Cyperus rotundus and C. difformis was reported in India (48, 460), but inoculation of these hosts in the Philippines failed (48, 1689). By inoculation many wild species of Oryza (45, 1789), Leptochloa filiformis (48, 1689), L. chinensis, L. panacea and Zizania aquatica (48, 1683) have all been found susceptible. DISEASE: Bacterial blight of rice and kresek disease of rice. Blight most commonly appears on leaves of young plants, after planting out, as water-soaked stripes at the margins. These enlarge and coalesce to give the characteristic yellowish lesions with wavy edges that occur mainly along the margins of the upper parts of the leaves. These lesions may later expand to cover much of the leaf, which turns whitish or greyish and dies. Leaf sheaths of the more susceptible varieties may be affected. Kresek, which occurs in tropical regions, is a strong systemic infection in which leaves or whole young plants wither and die. In older plants the leaves become pale yellow. GEOGRAPHICAL DISTRIBUTION: Limited to Asia (CMI Map 304, ed. 2, 1964). Occurrences not shown on this map include Korea, Taiwan and Indonesia (Mizukami & Wakimoto, 1969). TRANSMISSION: Spread locally by wind and rain and also by flood and irrigation waters; gains entry to the field in infected planting material, to the nursery in seed, and to both nursery and field from volunteer rice plants and weed hosts usually via the irrigation water. Overwintering may occur on volunteers, on or in the rhizospheres of weed hosts, in stored infected straw and in seed, but it is unlikely in soil and plant debris exposed to the weather, at least under Japanese conditions (Mizukami & Wakimoto, 1969). Infection is through hydathodes and wounds. Penetration through stomata results in a build-up of bacteria in the intercellular spaces, but it is not until they have been exuded on to the leaf surface and re-admitted through the hydathodes and thence into the vascular system, that symptoms of the disease appear (46, 2720).

scholarly journals Molecular Characterization of Pathogenicity Locus (PaLoc) and tcdC Genetic Diversity Among tcdA+B+ Clostridioides Difficile Clinical Isolates in Tehran, Iran

2020 ◽  
Author(s):  
Mansoor Kodori ◽  
Zohreh Ghalavand ◽  
Abbas Yadegar ◽  
Gita Eslami ◽  
Masoumeh Azimirad ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Molecular Characterization ◽  
Disease Severity ◽  
Genetic Variants ◽  
Rflp Analysis ◽  
Clostridioides Difficile ◽  
Pcr Rflp ◽  
The Common ◽  
Healthcare Associated

Abstract Background: Clostridioides difficile is the main cause of healthcare-associated diarrhea worldwide. It is proposed that certain C. difficile toxinotypes with distinct pathogenicity locus (PaLoc) variants are associated with disease severity and outcomes. Additionally, few studies have described the common C. difficile toxinotypes, and also little is known about the tcdC variants in Iranian isolates. We characterized the toxinotypes and the tcdC genotypes from a collection of Iranian clinical C. difficile tcdA+B+ isolates with known ribotypes (RTs).Methods: Fifty C. difficile isolates with known RTs and carrying the tcdA and tcdB toxin genes were analyzed. Toxinotyping was carried out based on a PCR-RFLP analysis of a 19.6 kb region encompassing the PaLoc. Genetic diversity of the tcdC gene was determined by the sequencing of the gene.Results: Of the 50 C. difficile isolates investigated, five distinct toxinotypes were recognized. Toxinotypes 0 (33/50, 66%) and V (11/50, 22%) were the most frequently found. C. difficile isolates of the toxinotype 0 mostly belonged to RT 001 (12/33, 36.4%), whereas toxinotype V consisted of RT 126 (9/11, 81.8%). The tcdC sequencing showed six variants (35/50, 70%); tcdC-sc3 (24%), tcdC-A (22%), tcdC-sc9 (18%), tcdC-B (2%), tcdC-sc14 (2%), and tcdC-sc15 (2%). The remaining isolates were wild-types (15/50, 30%) in the tcdC gene.Conclusions: The present study demonstrates that the majority of clinical tcdA+B+ isolates of C. difficile frequently harbor tcdC genetic variants. We also found that the RT 001/ toxinotype 0 and the RT 126/ toxinotype V are the most common types among Iranian isolates. Further studies are needed to investigate the putative association of various tcdC genotypes with CDI severity and its recurrence.

scholarly journals Genetic diversity of Pongamia pinnata in Bali, Indonesia using Inter Simple Sequence Repeat markers

2019 ◽  
Vol 20 (8) ◽  
Author(s):  
Ni Luh Arpiwi ◽  
I Gusti Ayu Sugi Wahyuni ◽  
I Ketut Muksin
Keyword(s):  
Genetic Diversity ◽  
Genetic Distance ◽  
Simple Sequence Repeat ◽  
Inter Simple Sequence Repeat ◽  
Pongamia Pinnata ◽  
Sequence Repeat ◽  
Binary Matrix ◽  
Simple Sequence Repeat Markers ◽  
Group I ◽  
Simple Sequence

Abstract. Arpiwi NL, Wahyuni IGAS, Muksin IK. 2019. Genetic diversity of Pongamia pinnata in Bali, Indonesia using Inter Simple Sequence Repeat markers. Biodiversitas 20: 2134-2142. Pongamia pinnata (L.) Pierre is a member of family Leguminosae that produces seed oil for biodiesel feedstock. The aim of the present study was to determine genetic diversity of pongamia trees that grow in Bali using Inter Simple Sequence Repeat (ISSR) markers. This study is important to support the breeding program for the improvement of the biodiesel producing species. Leaf samples were taken from 26 pongamia trees grown on northern and southern coastal areas of Bali. Genomic DNA was isolated from fresh leaves sample and was amplified by Polymerase Chain Reaction (PCR) using 9 ISSR primers. The banding patterns of DNA after PCR were scored and tabulated into a binary matrix. Genetic distance was generated by pairwise distance using composite maximum likelihood. A dendrogram was constructed using Unweighted Pair Group Method Arithmetic (UPGMA) method. The binary matrix was further analyzed for Nonmetric Multidimensional Scaling (NMDS) with Primer E V.6 software. DNA concentrations ranged from 98.59-100.55 ng/μL with sufficient quality for PCR. The number of alleles for 9 primers was 43, the number of the polymorphic band was 35, and the number of monomorphic bands was 8. Percentage of polymorphism ranged from 50 to 100%. Cluster analysis of 26 DNA of pongamia trees showed that the trees were grouped into two, namely group I and II. Group I consisted of two trees only, namely Uma Anyar 1 and Penarukan 1. Group II consisted of 24 pongamia trees which were divided into 3 subgroups, namely IIA, IIB, and IIC with close genetic distance. Analysis of NMDS supported cluster analysis that 23 out of 26 pongamia trees had close genetic distance, and possibly they come from a similar source. Genetic diversity of pongamia in Bali needs to be widen possibly by the introduction of new planting materials from across Indonesia or seed procurement from different sources.

scholarly journals Confirmation of Bacterial Leaf Streak of Rice Caused by Xanthomonas oryzae pv. oryzicola in Vietnam

Plant Disease ◽  
2015 ◽  
Vol 99 (12) ◽  
pp. 1853-1853 ◽  
Author(s):  
T. T. Tran ◽  
N. V. Nga ◽  
P. T. Ngan ◽  
N. T. Hong ◽  
B. Szurek ◽  
...  
Keyword(s):  
Xanthomonas Oryzae ◽  
Bacterial Leaf Streak

scholarly journals Discovery of Novel Dihydrolipoamide S-Succinyltransferase Inhibitors Based on Fragment Virtual Screening

2021 ◽  
Vol 22 (23) ◽  
pp. 12953
Author(s):  
Chengqian Wei ◽  
Junjie Huang ◽  
Yu Wang ◽  
Yifang Chen ◽  
Xin Luo ◽  
...  
Keyword(s):  
Virtual Screening ◽  
Antibacterial Agents ◽  
High Efficiency ◽  
Leaf Blight ◽  
Xanthomonas Oryzae ◽  
Bacterial Leaf Blight ◽  
Extracellular Polysaccharides ◽  
Bacterial Leaf Streak ◽  
Bacterial Diseases ◽  
Sulfone Derivatives

A series of new oxadiazole sulfone derivatives containing an amide moiety was synthesized based on fragment virtual screening to screen high-efficiency antibacterial agents for rice bacterial diseases. All target compounds showed greater bactericidal activity than commercial bactericides. 3-(4-fluorophenyl)-N-((5-(methylsulfonyl)-1,3,4-oxadiazol-2-yl)methyl)acrylamide (10) showed excellent antibacterial activity against Xanthomonas oryzae pv. oryzae and Xanthomonas oryzae pv. oryzicola, with EC50 values of 0.36 and 0.53 mg/L, respectively, which were superior to thiodiazole copper (113.38 and 131.54 mg/L) and bismerthiazol (83.07 and 105.90 mg/L). The protective activity of compound 10 against rice bacterial leaf blight and rice bacterial leaf streak was 43.2% and 53.6%, respectively, which was superior to that of JHXJZ (34.1% and 26.4%) and thiodiazole copper (33.0% and 30.2%). The curative activity of compound 10 against rice bacterial leaf blight and rice bacterial leaf streak was 44.5% and 51.7%, respectively, which was superior to that of JHXJZ (32.6% and 24.4%) and thiodiazole copper (27.1% and 28.6%). Moreover, compound 10 might inhibit the growth of Xanthomonas oryzae pv. oryzae and Xanthomonas oryzae pv. oryzicola by affecting the extracellular polysaccharides, destroying cell membranes, and inhibiting the enzyme activity of dihydrolipoamide S-succinyltransferase.

scholarly journals Genetic Diversity of Xanthomonas campestris pv. vitians, the Causal Agent of Bacterial Leafspot of Lettuce

2003 ◽  
Vol 93 (5) ◽  
pp. 596-603 ◽  
Author(s):  
Jeri D. Barak ◽  
Robert L. Gilbertson
Keyword(s):  
Genetic Diversity ◽  
Repetitive Dna ◽  
Dna Sequences ◽  
Plasmid Dna ◽  
Xanthomonas Campestris ◽  
Rflp Analysis ◽  
Dna Probe ◽  
Internal Transcribed Spacer Region ◽  
Geographical Regions

Bacterial leafspot of lettuce (BLS), caused by Xanthomonas campes-tris pv. vitians, has become more prevalent in many lettuce-growing areas of the world over the past decade. To gain insight into the nature of these outbreaks, the genetic variation in X. campestris pv. vitians strains from different geographical locations was examined. All strains were first tested for pathogenicity on lettuce plants, and then genetic diversity was assessed using (i) gas-chromatographic analysis of bacterial fatty acids, (ii) polymerase chain reaction analysis of repetitive DNA sequences (rep-PCR), (iii) DNA sequence analysis of the internal transcribed spacer region 1 (ITS1) of the ribosomal RNA, (iv) restriction fragment length polymorphism (RFLP) analysis of total genomic DNA with a repetitive DNA probe, and (v) detection and partial characterization of plasmid DNA. Fatty acid analysis identified all pathogenic strains as X. campestris, but did not consistently identify all the strains as X. campestris pv. vitians. The rep-PCR fingerprints and ITS1 sequences of all pathogenic X. campestris pv. vitians strains examined were identical, and distinct from those of the other X. campestris pathovars. Thus, these characteristics did not reveal genetic diversity among X. campestris pv. vitians strains, but did allow for differentiation of X. campestris pathovars. Genetic diversity among X. campestris pv. vitians strains was revealed by RFLP analysis with a repetitive DNA probe and by characterization of plasmid DNA. This diversity was greatest among strains from different geographical regions, although diversity among strains from the same location also was detected. The results of this study suggest that these X. campestris pv. vitians strains are not clonal, but comprise a relatively homogeneous group.

Resolving the Tetrastigma loheri s. l. Species Complex (Vitaceae) in the Philippines: No Evidence for Recognizing More than One Species

2021 ◽  
Author(s):  
Jasper John A. Obico ◽  
Julie F. Barcelona ◽  
Vincent Bonhomme ◽  
Marie Hale ◽  
Pieter B. Pelser
Keyword(s):  
Genetic Diversity ◽  
Species Complex ◽  
Species Recognition ◽  
Principal Component ◽  
The Philippines ◽  
Geometric Morphometric ◽  
Putative Species ◽  
Principal Coordinates ◽  
Multiple Species ◽  
Vegetative Characters

Tetrastigma loheri (Vitaceae) is a vine species native to Borneo and the Philippines. Because it is a commonly encountered forest species in the Philippines, T. loheri is potentially suitable for studying patterns of genetic diversity and connectivity among fragmented forestecosystems in various parts of this country. However, previous research suggests that T. loheri is part of a species complex in the Philippines (i.e. the T. loheri s. l. complex) that potentially also contains Philippine plants identified as T. diepenhorstii, T. philippinense, T. stenophyllum, andT. trifoliolatum. This uncertainty about its taxonomic delimitation can make it challenging to draw conclusions that are relevant to conservation from genetic studies using this species. Here, we tested the hypothesis that T. loheri s. l. is composed of more than one species in the Philippines.For this, we used generalized mixed Yule coalescent (GMYC) and Poisson tree process (PTP) species delimitation models to identify clades within DNA sequence phylogenies of T. loheri s. l. that might constitute species within this complex. Although these methods identified several putative species, these are statistically poorly supported and subsequent random forest analyses using a geometric morphometric leafshape dataset and several other vegetative characters did not result in the identification of characters that can be used to discriminate these putative species morphologically. Furthermore, the results of principal component and principal coordinates analyses of these data suggest the absence of morphological discontinuities within the species complex. Under a unified species concept that uses phylogenetic and morphological distinction as operational criteria for species recognition, we therefore conclude that the currently available data do not support recognizing multiple species in the T. loheri s. l. complex. This implies that T. loheri is best considered as a single, morphologically variable specieswhen used for studying patterns of genetic diversity and connectivity in the Philippines.

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