scholarly journals Multilocus Sequence Analysis of Xanthomonads Causing Bacterial Spot of Tomato and Pepper Plants Reveals Strains Generated by Recombination among Species and Recent Global Spread of Xanthomonas gardneri

2014 ◽  
Vol 81 (4) ◽  
pp. 1520-1529 ◽  
Author(s):  
Sujan Timilsina ◽  
Mustafa O. Jibrin ◽  
Neha Potnis ◽  
Gerald V. Minsavage ◽  
Misrak Kebede ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Sequence Analysis ◽  
Housekeeping Genes ◽  
Global Distribution ◽  
Multilocus Sequence Analysis ◽  
Regional Differentiation ◽  
Bacterial Spot ◽  
Content Type ◽  
Global Spread ◽  
Pathogen Populations

ABSTRACTFourXanthomonasspecies are known to cause bacterial spot of tomato and pepper, but the global distribution and genetic diversity of these species are not well understood. A collection of bacterial spot-causing strains from the Americas, Africa, Southeast Asia, and New Zealand were characterized for genetic diversity and phylogenetic relationships using multilocus sequence analysis of six housekeeping genes. By examining strains from different continents, we found unexpected phylogeographic patterns, including the global distribution of a single multilocus haplotype ofX. gardneri, possible regional differentiation inX. vesicatoria, and high species diversity on tomato in Africa. In addition, we found evidence of multiple recombination events betweenX. euvesicatoriaandX. perforans.Our results indicate that there have been shifts in the species composition of bacterial spot pathogen populations due to the global spread of dominant genotypes and that recombination between species has generated genetic diversity in these populations.

scholarly journals Differentiation of Xylella fastidiosa Strains via Multilocus Sequence Analysis of Environmentally Mediated Genes (MLSA-E)

2011 ◽  
Vol 78 (5) ◽  
pp. 1385-1396 ◽  
Author(s):  
Jennifer K. Parker ◽  
Justin C. Havird ◽  
Leonardo De La Fuente
Keyword(s):  
Sequence Analysis ◽  
Genetic Variability ◽  
Xylella Fastidiosa ◽  
Genetic Relationships ◽  
Phylogenetic Analyses ◽  
Housekeeping Genes ◽  
The United States ◽  
Multilocus Sequence Analysis ◽  
Biological Traits ◽  
Content Type

ABSTRACTIsolates of the plant pathogenXylella fastidiosaare genetically very similar, but studies on their biological traits have indicated differences in virulence and infection symptomatology. Taxonomic analyses have identified several subspecies, and phylogenetic analyses of housekeeping genes have shown broad host-based genetic differences; however, results are still inconclusive for genetic differentiation of isolates within subspecies. This study employs multilocus sequence analysis of environmentally mediated genes (MLSA-E; genes influenced by environmental factors) to investigateX. fastidiosarelationships and differentiate isolates with low genetic variability. Potential environmentally mediated genes, including host colonization and survival genes related to infection establishment, were identifieda priori. The ratio of the rate of nonsynonymous substitutions to the rate of synonymous substitutions (dN/dS) was calculated to select genes that may be under increased positive selection compared to previously studied housekeeping genes. Nine genes were sequenced from 54X. fastidiosaisolates infecting different host plants across the United States. Results of maximum likelihood (ML) and Bayesian phylogenetic (BP) analyses are in agreement with knownX. fastidiosasubspecies clades but show novel within-subspecies differentiation, including geographic differentiation, and provide additional information regarding host-based isolate variation and specificity.dN/dSratios of environmentally mediated genes, though <1 due to high sequence similarity, are significantly greater than housekeeping genedN/dSratios and correlate with increased sequence variability. MLSA-E can more precisely resolve relationships between closely related bacterial strains with low genetic variability, such asX. fastidiosaisolates. Discovering the genetic relationships betweenX. fastidiosaisolates will provide new insights into the epidemiology of populations ofX. fastidiosa, allowing improved disease management in economically important crops.

scholarly journals Influence of Seasonality on the Genetic Diversity of Vibrio parahaemolyticus in New Hampshire Shellfish Waters as Determined by Multilocus Sequence Analysis

2012 ◽  
Vol 78 (10) ◽  
pp. 3778-3782 ◽  
Author(s):  
Crystal N. Ellis ◽  
Brian M. Schuster ◽  
Megan J. Striplin ◽  
Stephen H. Jones ◽  
Cheryl A. Whistler ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Sequence Analysis ◽  
Genetic Analysis ◽  
New Hampshire ◽  
Environmental Conditions ◽  
Vibrio Parahaemolyticus ◽  
Multilocus Sequence Analysis ◽  
Content Type ◽  
High Level

ABSTRACTRisk of gastric infection withVibrio parahaemolyticusincreases with favorable environmental conditions and population shifts that increase prevalence of infective strains. Genetic analysis of New Hampshire strains revealed a unique population with some isolates similar to outbreak-causing strains and high-level diversity that increased as waters warmed.

scholarly journals Occurrence of Bacterial Spot in Illinois Tomato Fields and Characteristics of the Causal Agents

HortScience ◽  
2021 ◽  
Vol 56 (1) ◽  
pp. 8-12
Author(s):  
Sabin Khanal ◽  
Sarah R. Hind ◽  
Mohammad Babadoost
Keyword(s):  
Sequence Analysis ◽  
Central Region ◽  
Housekeeping Genes ◽  
Northern Region ◽  
Southern Region ◽  
Multilocus Sequence Analysis ◽  
Bacterial Spot ◽  
Field Surveys ◽  
Endemic Population

Bacterial spot, caused by Xanthomonas spp., is one of the most important diseases of tomato in Illinois. Field surveys were conducted during 2017–19 to assess occurrence of bacterial spot in commercial tomato fields. Severity of foliage and fruit infection was recorded, and symptomatic samples were collected from three-to-five cultivars in three different farms in each of northern, central, and southern regions of Illinois. Severity of symptomatic foliage ranged from 0% to 91% (average 36.7%) and incidence of symptomatic fruit ranges from 0% to 30% (average 10.8%). During the surveys, 266 Xanthomonas isolates were collected and identified as Xanthomonas gardneri and X. perforans using Xanthomonas-specific hrp primers. Eighty-six percent of the isolates from the northern region were identified as X. gardneri, whereas 73% of the isolates from southern region were identified as X. perforans. Isolates from the central region were identified as X. perforans and X. gardneri 53% and 47% of the time, respectively. Multilocus sequence analysis using six housekeeping genes (fusA, gap-1, gltA, gyrB, lepA, and lacF) revealed the endemic population of X. gardneri and X. perforans. In addition to Xanthomonas, nine non-Xanthomonas bacterial genera were isolated from the samples, with most of the isolates classified as Microbacterium, Pantoea, and Pseudomonas.

Multilocus Sequence Analysis and Copper Ion Resistance Detection of 60 Xanthomonas arboricola pv. juglandis Isolates from China

Plant Disease ◽  
2021 ◽  
Author(s):  
Benzhong Fu ◽  
Jieqian Zhu ◽  
Conard Lee ◽  
Lihua Wang
Keyword(s):  
Sequence Analysis ◽  
Copper Ion ◽  
Housekeeping Genes ◽  
Threshold Value ◽  
Pcr Primers ◽  
Multilocus Sequence Analysis ◽  
Nucleotide Polymorphisms ◽  
Specific Pcr ◽  
Resistant Strains ◽  
Xanthomonas Arboricola

Walnut bacterial blight caused by Xanthomonas arboricola pv. juglandis (Xaj) has serious repercussions for walnut production around the world. Between 2015 and 2017, disease samples were collected from six counties (Danjiangkou, Baokang, Suizhou, Shennongjia, Zigui, and Xingshan) in Hubei province, China. Fifty-nine Xaj strains were identified by morphology and specific PCR primers from 206 isolates. The genetic diversity of 60 Xaj strains (59 from Hubei plus one from Beijing) was evaluated by Multilocus Sequence Analysis (MLST), and their resistance to copper ion (Cu2+) treatment was determined. A Neighbor Joining phylogenetic dendrogram was constructed based on four sequences of housekeeping genes (atpD-dnaK-glnA-gyrB). Two groups of strains were identified whose clustering was consistent with that of glnA. The minimal inhibitory concentration of copper ion on representative Xaj strain DW3F3 (the first genome sequenced Xaj from China) was 115 μg/ml. Setting the copper resistant threshold value to 125 μg/ml, 47 and 13 strains were considered sensitive and resistant to Cu2+, respectively. Furthermore, five strains showed Cu2+ resistance at 270 μg/ml. Compared to the copB from sensitive strains, the copB gene in resistant strains had a 15-bp insertion and eight scattered single nucleotide polymorphisms. Interestingly, the clustering based on MLSA was distinct between Xaj copper ion resistant and sensitive strains.

scholarly journals Multilocus Sequence Analysis of the Marine Bacterial Genus Tenacibaculum Suggests Parallel Evolution of Fish Pathogenicity and Endemic Colonization of Aquaculture Systems

2014 ◽  
Vol 80 (17) ◽  
pp. 5503-5514 ◽  
Author(s):  
Christophe Habib ◽  
Armel Houel ◽  
Aurélie Lunazzi ◽  
Jean-François Bernardet ◽  
Anne Berit Olsen ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
Parallel Evolution ◽  
Phylogenetic Reconstruction ◽  
Multilocus Sequence Analysis ◽  
Fish Pathogens ◽  
Long Distance ◽  
Marine Aquaculture ◽  
Content Type ◽  
The Family ◽  
Cohesive Group

ABSTRACTThe genusTenacibaculum, a member of the familyFlavobacteriaceae, is an abundant component of marine bacterial ecosystems that also hosts several fish pathogens, some of which are of serious concern for marine aquaculture. Here, we applied multilocus sequence analysis (MLSA) to 114 representatives of most known species in the genus and of the worldwide diversity of the major fish pathogenTenacibaculum maritimum. Recombination hampers precise phylogenetic reconstruction, but the data indicate intertwined environmental and pathogenic lineages, which suggests that pathogenicity evolved independently in several species. At lower phylogenetic levels recombination is also important, and the speciesT. maritimumconstitutes a cohesive group of isolates. Importantly, the data reveal no trace of long-distance dissemination that could be linked to international fish movements. Instead, the high number of distinct genotypes suggests an endemic distribution of strains. The MLSA scheme and the data described in this study will help in monitoringTenacibaculuminfections in marine aquaculture; we show, for instance, that isolates from tenacibaculosis outbreaks in Norwegian salmon farms are related toT. dicentrarchi, a recently described species.

scholarly journals Multilocus sequence analysis of Ensifer and related taxa

2007 ◽  
Vol 57 (3) ◽  
pp. 489-503 ◽  
Author(s):  
Miet Martens ◽  
Manuel Delaere ◽  
Renata Coopman ◽  
Paul De Vos ◽  
Monique Gillis ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
16S Rrna ◽  
Housekeeping Genes ◽  
16S Rrna Genes ◽  
New Combination ◽  
Rrna Genes ◽  
Multilocus Sequence Analysis ◽  
Bootstrap Support ◽  
Rrna Gene ◽  
Separate Species

Multilocus sequence analysis (MLSA) was performed on representatives of Ensifer (including species previously assigned to the genus Sinorhizobium) and related taxa. Neighbour-joining (NJ), maximum-parsimony (MP) and maximum-likelihood (ML) phylogenies of dnaK, gltA, glnA, recA, thrC and 16S rRNA genes were compared. The data confirm that the potential for discrimination of Ensifer species is greater using MLSA of housekeeping genes than 16S rRNA genes. In incongruence-length difference tests, the 16S rRNA gene was found to be significantly incongruent with the other genes, indicating that this gene should not be used as a single indicator of relatedness in this group. Significant congruence was detected for dnaK, glnA and thrC. Analyses of concatenated sequences of dnaK, glnA and thrC genes yielded very similar NJ, MP and ML trees, with high bootstrap support. In addition, analysis of a concatenation of all six genes essentially produced the same result, levelling out potentially conflicting phylogenetic signals. This new evidence supports the proposal to unite Ensifer and Sinorhizobium in a single genus. Support for an alternative solution preserving the two genera is less strong. In view of the opinions expressed by the Judicial Commission, the name of the genus should be Ensifer, as proposed by Young [Young, J. M. (2003). Int J Syst Evol Microbiol 53, 2107–2110]. Data obtained previously and these new data indicate that Ensifer adhaerens and ‘Sinorhizobium morelense’ are not heterotypic synonyms, but represent separate species. However, transfer to the genus Ensifer is not possible at present because the species name is the subject of a pending Request for an Opinion, which would affect whether a novel species in the genus Ensifer or a new combination based on a basonym would be created.

scholarly journals A New Borrelia Species Defined by Multilocus Sequence Analysis of Housekeeping Genes

2009 ◽  
Vol 75 (16) ◽  
pp. 5410-5416 ◽  
Author(s):  
Gabriele Margos ◽  
Stephanie A. Vollmer ◽  
Muriel Cornet ◽  
Martine Garnier ◽  
Volker Fingerle ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
Lyme Borreliosis ◽  
Phylogenetic Trees ◽  
Evolutionary History ◽  
Housekeeping Genes ◽  
Multilocus Sequence Analysis ◽  
Species Status ◽  
Borrelia Garinii ◽  
Analysis Scheme ◽  
History Of

ABSTRACT Analysis of Lyme borreliosis (LB) spirochetes, using a novel multilocus sequence analysis scheme, revealed that OspA serotype 4 strains (a rodent-associated ecotype) of Borrelia garinii were sufficiently genetically distinct from bird-associated B. garinii strains to deserve species status. We suggest that OspA serotype 4 strains be raised to species status and named Borrelia bavariensis sp. nov. The rooted phylogenetic trees provide novel insights into the evolutionary history of LB spirochetes.

scholarly journals Comprehensive Genome Scale Phylogenetic Study Provides New Insights on the Global Expansion of Chikungunya Virus

2016 ◽  
Vol 90 (23) ◽  
pp. 10600-10611 ◽  
Author(s):  
Rubing Chen ◽  
Vinita Puri ◽  
Nadia Fedorova ◽  
David Lin ◽  
Kumar L. Hari ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Indian Ocean ◽  
Chikungunya Virus ◽  
Pacific Islands ◽  
Indian Subcontinent ◽  
Global Distribution ◽  
Phylogenetic Study ◽  
Content Type ◽  
Factors Associated ◽  
Asian Lineage

ABSTRACT Since the India and Indian Ocean outbreaks of 2005 and 2006, the global distribution of chikungunya virus (CHIKV) and the locations of epidemics have dramatically shifted. First, the Indian Ocean lineage (IOL) caused sustained epidemics in India and has radiated to many other countries. Second, the Asian lineage has caused frequent outbreaks in the Pacific islands and in 2013 was introduced into the Caribbean, followed by rapid spread to nearly all of the neotropics. Further, CHIKV epidemics, as well as exported cases, have been reported in central Africa after a long period of perceived silence. To understand these changes and to anticipate the future of the virus, the exact distribution, genetic diversity, transmission routes, and future epidemic potential of CHIKV require further assessment. To do so, we conducted the most comprehensive phylogenetic analysis to date, examined CHIKV evolution and transmission, and explored distinct genetic factors associated with the emergence of the East/Central/South African (ECSA) lineage, the IOL, and the Asian lineage. Our results reveal contrasting evolutionary patterns among the lineages, with growing genetic diversities observed in each, and suggest that CHIKV will continue to be a major public health threat with the potential for further emergence and spread. IMPORTANCE Chikungunya fever is a reemerging infectious disease that is transmitted by Aedes mosquitoes and causes severe health and economic burdens in affected populations. Since the unprecedented Indian Ocean and Indian subcontinent outbreaks of 2005 and 2006, CHIKV has further expanded its geographic range, including to the Americas in 2013. Its evolution and transmission during and following these epidemics, as well as the recent evolution and spread of other lineages, require optimal assessment. Using newly obtained genome sequences, we provide a comprehensive update of the global distribution of CHIKV genetic diversity and analyze factors associated with recent outbreaks. These results provide a solid foundation for future evolutionary studies of CHIKV that can elucidate emergence mechanisms and also may help to predict future epidemics.

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