Genome analysis of Spiroplasma citri strains from different host plants and its leafhopper vectors

Abstract Background Spiroplasma citri comprises a complex of bacteria that cause diseases in citrus, horseradish, carrot, sesame, and also infect a wide array of ornamental and weed species. S. citri is transmitted in a persistent propagative manner by the beet leafhopper, Neoaliturus tenellus in North America and Circulifer haematoceps in the Mediterranean region. Leafhopper transmission and the pathogen’s wide host range serve as drivers of genetic diversity. This diversity was examined by comparing the genome sequences of seven S. citri strains from the United States (BR12, CC2, C5, C189, LB319, BLH-13, and BLH-MB) collected from different hosts and times with other publicly available spiroplasmas.Results Phylogenetic analysis using 16S rRNA sequences from 39 spiroplasmas obtained from NCBI database showed that S. citri strains, along with S. kunkelii and S. phoeniceum, two other plant pathogenic spiroplasmas, formed a monophyletic group. To refine genetic relationships among S. citri strains, phylogenetic analyses with 863 core orthologous sequences were performed. Strains that clustered together were: CC-12 and C5; C189 and R8-A2; BR12, BLH-MB, BLH13 and LB 319. Strain GII3-3 remained in a separate branch. Sequence rearrangements were observed among S. citri strains, predominantly in the center of the chromosome. One to nine plasmids were identified in the seven S. citri strains analyzed in this study. Plasmids were most abundant in strains isolated from the beet leafhopper, followed by strains from carrot, Chinese cabbage, horseradish and citrus, respectively. All these S. citri strains contained one plasmid with high similarity to plasmid pSci6 from S. citri strain GII3-3X which is known to confer insect transmissibility. Additionally, 17 to 25 prophage-like elements were identified in these genomes, which may promote rearrangements and contribute to repetitive regions. Conclusions The genome of seven S. citri strains were found to contain a single circularized chromosome, ranging from 1.58 Mbp to 1.74 Mbp and 1,597-2,232 protein-coding genes. These strains possessed a plasmid similar to pSci6 from the GII3-3X strain associated with leafhopper transmission. Prophage sequences found in the S. citri genomes may contribute to the extension of its host range. These findings increase our understanding of S. citri genetic diversity.

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Genome analysis of Spiroplasma citri strains from different host plants and its leafhopper vectors

BMC Genomics ◽

10.1186/s12864-021-07637-8 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Rachel Rattner ◽

Shree Prasad Thapa ◽

Tyler Dang ◽

Fatima Osman ◽

Vijayanandraj Selvaraj ◽

...

Keyword(s):

Genetic Diversity ◽

Host Range ◽

Genetic Relationships ◽

Phylogenetic Analyses ◽

The United States ◽

Weed Species ◽

Protein Coding ◽

Spiroplasma Citri ◽

Beet Leafhopper ◽

Separate Branch

Abstract Background Spiroplasma citri comprises a bacterial complex that cause diseases in citrus, horseradish, carrot, sesame, and also infects a wide array of ornamental and weed species. S. citri is transmitted in a persistent propagative manner by the beet leafhopper, Neoaliturus tenellus in North America and Circulifer haematoceps in the Mediterranean region. Leafhopper transmission and the pathogen’s wide host range serve as drivers of genetic diversity. This diversity was examined in silico by comparing the genome sequences of seven S. citri strains from the United States (BR12, CC-2, C5, C189, LB 319, BLH-13, and BLH-MB) collected from different hosts and times with other publicly available spiroplasmas. Results Phylogenetic analysis using 16S rRNA sequences from 39 spiroplasmas obtained from NCBI database showed that S. citri strains, along with S. kunkelii and S. phoeniceum, two other plant pathogenic spiroplasmas, formed a monophyletic group. To refine genetic relationships among S. citri strains, phylogenetic analyses with 863 core orthologous sequences were performed. Strains that clustered together were: CC-2 and C5; C189 and R8-A2; BR12, BLH-MB, BLH-13 and LB 319. Strain GII3–3X remained in a separate branch. Sequence rearrangements were observed among S. citri strains, predominantly in the center of the chromosome. One to nine plasmids were identified in the seven S. citri strains analyzed in this study. Plasmids were most abundant in strains isolated from the beet leafhopper, followed by strains from carrot, Chinese cabbage, horseradish, and citrus, respectively. All these S. citri strains contained one plasmid with high similarity to plasmid pSci6 from S. citri strain GII3–3X which is known to confer insect transmissibility. Additionally, 17 to 25 prophage-like elements were identified in these genomes, which may promote rearrangements and contribute to repetitive regions. Conclusions The genome of seven S. citri strains were found to contain a single circularized chromosome, ranging from 1.58 Mbp to 1.74 Mbp and 1597–2232 protein-coding genes. These strains possessed a plasmid similar to pSci6 from the GII3–3X strain associated with leafhopper transmission. Prophage sequences found in the S. citri genomes may contribute to the extension of its host range. These findings increase our understanding of S. citri genetic diversity.

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Genome Analysis of Spiroplasma Citri Strains From Different Host Plants and Its Leafhopper Vectors

10.21203/rs.3.rs-71511/v1 ◽

2020 ◽

Author(s):

Rachel Rattner ◽

Shree Prasad Thapa ◽

Tyler Dang ◽

Fatima Osman ◽

Vijayanandraj Selvaraj ◽

...

Keyword(s):

Genetic Diversity ◽

Host Range ◽

Genetic Relationships ◽

Phylogenetic Analyses ◽

The United States ◽

Weed Species ◽

Protein Coding ◽

Spiroplasma Citri ◽

Beet Leafhopper ◽

Separate Branch

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Genetic Diversity of Wild Oat (Avena fatua)Populations from China and the United States

Weed Science ◽

10.1614/ws-06-108.1 ◽

2007 ◽

Vol 55 (2) ◽

pp. 95-101 ◽

Cited By ~ 21

Author(s):

Runzhi Li ◽

Shiwen Wang ◽

Liusheng Duan ◽

Zhaohu Li ◽

Michael J. Christoffers ◽

...

Keyword(s):

United States ◽

Genetic Diversity ◽

Gene Diversity ◽

Genetic Relationships ◽

The United States ◽

Mantel Test ◽

Wild Oat ◽

Chinese Populations ◽

Nei's Distance ◽

The Impact

Weed genetic diversity is important for understanding the ability of weeds to adapt to different environments and the impact of herbicide selection on weed populations. Genetic diversity within and among six wild oat populations in China varying in herbicide selection pressure and one population in North Dakota were surveyed using 64 polymorphic alleles resulting from 25 microsatellite loci. Mean Nei's gene diversity (h) for six wild oat populations from China was between 0.17 and 0.21, and total diversity (HT) was 0.23. A greater proportion of this diversity, however, was within (Hs= 0.19) rather than among (Gst= 0.15) populations. For the wild oat population from the United States,h= 0.24 andHT= 0.24 were comparable to the values for the six populations from China. Cluster analysis divided the seven populations into two groups, where one group was the United States population and the other group included the six Chinese populations. The genetic relationships among six populations from China were weakly correlated with their geographic distribution (r= 0.22) using the Mantel test. Minimal difference in gene diversity and small genetic distance (Nei's distance 0.07 or less) among six populations from China are consistent with wide dispersal of wild oat in the 1980s. Our results indicate that the wild oat populations in China are genetically diverse at a level similar to North America, and the genetic diversity of wild oat in the broad spatial scale is not substantially changed by environment, agronomic practices, or herbicide usage.

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(1) Genetic Diversity of Cowpea [Vigna unguiculata (L.) Walp.] Breeding Lines from Different Countries Determined by AFLP Markers

HortScience ◽

10.21273/hortsci.40.4.998a ◽

2005 ◽

Vol 40 (4) ◽

pp. 998A-998 ◽

Cited By ~ 1

Author(s):

Jinggui Fang ◽

Panchanoor S. Devanand ◽

Chih Cheng T. Chao ◽

Philip A. Roberts ◽

Jeff D. Ehlers

Keyword(s):

Genetic Diversity ◽

South America ◽

Near Infrared ◽

Genetic Relationships ◽

The United States ◽

Aflp Markers ◽

Sub Saharan Africa ◽

Breeding Programs ◽

Breeding Lines

Cowpea (2n=2x=22) is a high protein, short-cycle, and essential legume food crop of the tropics, especially in the low input agricultural areas of sub-Saharan Africa, Asia, and South America. Lack of genetic diversity within breeding programs can limit long-term gains from selection. The cowpea gene pool is thought to be narrow and the genetic diversity within breeding programs could be even less diverse. Genetic relationships among 87 cowpea accessions, including 60 advanced breeding lines from six breeding programs in Africa and the United States, and 27 accessions from Africa, Asia, and South America were examined using amplified fragment length polymorphism (AFLP) markers with six near-infrared fluorescence labeled EcoR I + 3/Mse I + 3 primer sets. A total of 382 bands were scored among the accessions with 207 polymorphic bands (54.2%). Overall, the 87 cowpea accessions have narrow genetic basis and they shared minimum 86% genetic similarities. The data also show that the advanced breeding lines of different programs have higher genetic affinities with lines from the same program but not with lines from other programs. The results suggest that there is a need to incorporate additional germplasm of different genetic background into these breeding lines and to ensure the long-term genetic gains of the programs.

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Molecular Genetic Diversity Among 12 Clones of Lagerstroemia fauriei Revealed by AFLP and RAPD Markers

HortScience ◽

10.21273/hortsci.38.2.256 ◽

2003 ◽

Vol 38 (2) ◽

pp. 256-259 ◽

Cited By ~ 12

Author(s):

Margaret R. Pooler

Keyword(s):

Genetic Diversity ◽

Genetic Relationships ◽

Molecular Genetic ◽

Genetic Material ◽

The United States ◽

Aflp Markers ◽

Economic Significance ◽

Molecular Genetic Diversity ◽

In The Wild ◽

The U.S

Many popular crapemyrtle (Lagerstroemia L.) cultivars grown in the United States are interspecific hybrids between L. indica L. and L. fauriei Koehne. The 22 hybrid cultivars released from the U.S. National Arboretum contain primarily genetic material from L. fauriei PI 237884. Examining the genetic diversity ofL. fauriei specimens in the U.S. is valuable because of the historical and economic significance of the species, the increasing interest it is receiving as a source of new cultivars, and its threatened status in the wild. Our objectives were to examine molecular genetic diversity among L. fauriei accessions using Randomly Amplified Polymorphic DNA (RAPD) and Amplified Fragment Length Polymorphisms (AFLP) markers. Our results indicate: 1) RAPD and AFLP markers are generally consistent in the genetic relationships that they suggest; 2) the L. fauriei germplasm we examined falls into at least three distinct clusters; and 3) the genetic base of cultivated Lagerstroemia could be broadened significantly by incorporating some of this more diverse L. fauriei germplasm into breeding programs.

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First Report of Puccinia coronata var. coronata sensu stricto Infecting Alder Buckthorn in the United States

Plant Health Progress ◽

10.1094/php-01-17-0003-br ◽

2017 ◽

Vol 18 (2) ◽

pp. 84-86

Author(s):

Shawn C. Kenaley ◽

Geoffrey Ecker ◽

Gary C. Bergstrom

Keyword(s):

United States ◽

North America ◽

Host Range ◽

Geographic Distribution ◽

Phylogenetic Analyses ◽

Rust Fungus ◽

The United States ◽

Sensu Stricto ◽

Puccinia Coronata ◽

First Report

Field symptoms, host distribution, pathogen morphology, and phylogenetic analyses clearly demonstrated that the rust fungus infecting alder buckthorn in Connecticut is Puccinia coronata var. coronata sensu stricto. To our knowledge, this is the first report and confirmation of P. coronata var. coronata s.s. in the United States. Additional collections from purported aecial and telial hosts of P. coronata var. coronata s.s. are necessary to determine its host range, geographic distribution, and incidence within the United States and elsewhere in North America.

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Allelic Diversity and Population Structure in Oenococcus oeni as Determined from Sequence Analysis of Housekeeping Genes

Applied and Environmental Microbiology ◽

10.1128/aem.70.12.7210-7219.2004 ◽

2004 ◽

Vol 70 (12) ◽

pp. 7210-7219 ◽

Cited By ~ 75

Author(s):

Blanca de las Rivas ◽

Ángela Marcobal ◽

Rosario Muñoz

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Genetic Relationships ◽

Allelic Diversity ◽

Rflp Analysis ◽

The United States ◽

Oenococcus Oeni ◽

23S Rrna ◽

Rrna Gene ◽

Single Strain

ABSTRACT Oenococcus oeni is the organism of choice for promoting malolactic fermentation in wine. The population biology of O. oeni is poorly understood and remains unclear. For a better understanding of the mode of genetic variation within this species, we investigated by using multilocus sequence typing (MLST) with the gyrB, pgm, ddl, recP, and mleA genes the genetic diversity and genetic relationships among 18 O. oeni strains isolated in various years from wines of the United States, France, Germany, Spain, and Italy. These strains have also been characterized by ribotyping and restriction fragment length polymorphism (RFLP) analysis of the PCR-amplified 16S-23S rRNA gene intergenic spacer region (ISR). Ribotyping grouped the strains into two groups; however, the RFLP analysis of the ISRs showed no differences in the strains analyzed. In contrast, MLST in oenococci had a good discriminatory ability, and we have found a higher genetic diversity than indicated by ribotyping analysis. All sequence types were represented by a single strain, and all the strains could be distinguished from each other because they had unique combinations of alleles. Strains assumed to be identical showed the same sequence type. Phylogenetic analyses indicated a panmictic population structure in O. oeni. Sequences were analyzed for evidence of recombination by split decomposition analysis and analysis of clustered polymorphisms. All results indicated that recombination plays a major role in creating the genetic heterogeneity of O. oeni. A low standardized index of association value indicated that the O. oeni genes analyzed are close to linkage equilibrium. This study constitutes the first step in the development of an MLST method for O. oeni and the first example of the application of MLST to a nonpathogenic food production bacteria.

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Case Report: First Report and Phylogenetic Analysis of Porcine Astroviruses in Chile

Frontiers in Veterinary Science ◽

10.3389/fvets.2021.764837 ◽

2021 ◽

Vol 8 ◽

Author(s):

Carlos Flores ◽

Naomi Ariyama ◽

Benjamín Bennett ◽

Juan Mena ◽

Claudio Verdugo ◽

...

Keyword(s):

Genetic Diversity ◽

Phylogenetic Analyses ◽

The United States ◽

Swine Industry ◽

High Genetic Diversity ◽

Monophyletic Cluster ◽

Genetic Lineages ◽

Young Pigs ◽

Human Astroviruses ◽

Porcine Astrovirus

Porcine Astrovirus (PoAstV) causes mild diarrhea in young pigs and is considered an emerging virus in the swine industry worldwide. PoAstV has high genetic diversity and has been classified into five genetic lineages, PoAstV1–5. In Chile, only human astroviruses have been reported. This study aimed to determine the presence and genetic diversity of PoAstV circulating in intensive pig farms in Chile. Seventeen Chilean intensive swine farms from Valparaíso, Metropolitana, O'Higgins, Ñuble and Araucanía regions were sampled. A selection of oral fluid and fecal material samples from 1–80 days-old pigs were collected and analyzed using next-generation sequencing. The circulation of PoAstV was confirmed in all studied farms. We obtained complete or partial sequences of PoAstV-2 (n = 3), PoAstV-4 (n = 2), and PoAstV-5 (n = 7). In 15 out of 17 farms, we detected more than one lineage co-circulating. Phylogenetic analyses grouped the seven PoAstV-5 strains in a monophyletic cluster, closely related to the United States PoAstV-5 strains. The three PoAstV-2 were located into two separate sub-clusters. PoAstV-4 sequences are also grouped in two different clusters, all related to Japanese strains. Thus, our results indicate that PoAstV circulates in Chile with high frequency and diversity. However, the lack of reference sequences impairs local evolution patterns establishment and regional comparisons. This is the first contribution of PoAstV genomes in Latin America; more studies are needed to understand the diversity and impact of PoAstV on swine health.

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

Applied and Environmental Microbiology ◽

10.1128/aem.06679-11 ◽

2011 ◽

Vol 78 (5) ◽

pp. 1385-1396 ◽

Cited By ~ 22

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.

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Insights into the Host Range, Genetic Diversity, and Geographical Distribution of Jingmenviruses

mSphere ◽

10.1128/msphere.00645-19 ◽

2019 ◽

Vol 4 (6) ◽

Cited By ~ 11

Author(s):

Sarah Temmam ◽

Thomas Bigot ◽

Delphine Chrétien ◽

Mathilde Gondard ◽

Philippe Pérot ◽

...

Keyword(s):

Genetic Diversity ◽

Host Range ◽

Geographical Distribution ◽

Phylogenetic Analyses ◽

Lao Pdr ◽

Health Concern ◽

Serological Screening ◽

Content Type ◽

Amblyomma Testudinarium ◽

Cattle Infections

ABSTRACT Jingmenvirus is a recently identified group of segmented RNA viruses phylogenetically linked with unsegmented Flaviviridae viruses. Primarily identified in various tick genera originating in China, Jingmenvirus geographical distribution has rapidly expanded to cover Africa, South America, Caribbean, and Europe. The identification of Jingmen-related viruses in various mammals, including febrile humans, opens the possibility that Jingmenviruses may be novel tick-borne arboviruses. In this study, we aimed at increasing knowledge of the host range, genetic diversity, and geographical distribution of Jingmenviruses by reporting for the first time the identification of Jingmenviruses associated with Rhipicephalus microplus ticks originating in the French Antilles (Guadeloupe and Martinique islands), with Amblyomma testudinarium ticks in Lao PDR, and with Ixodes ricinus ticks in metropolitan France, and from urine of Pteropus lylei bats in Cambodia. Analyses of the relationships between the different Jingmenvirus genomes resulted in the identification of three main phylogenic subclades, each of them containing both tick-borne and mammal-borne strains, reinforcing the idea that Jingmenviruses may be considered as tick-borne arboviruses. Finally, we estimated the prevalence of Jingmenvirus-like infection using luciferase immunoprecipitation assay screening (LIPS) of asymptomatic humans and cattle highly exposed to tick bites. Among 70 French human, 153 Laotian human, and 200 Caribbean cattle sera tested, only one French human serum was found (slightly) positive, suggesting that the prevalence of Jingmenvirus human and cattle infections in these areas is probably low. IMPORTANCE Several arboviruses emerging as new pathogens for humans and domestic animals have recently raised public health concern and increased interest in the study of their host range and in detection of spillover events. Recently, a new group of segmented Flaviviridae-related viruses, the Jingmenviruses, has been identified worldwide in many invertebrate and vertebrate hosts, pointing out the issue of whether they belong to the arbovirus group. The study presented here combined whole-genome sequencing of three tick-borne Jingmenviruses and one bat-borne Jingmenvirus with comprehensive phylogenetic analyses and high-throughput serological screening of human and cattle populations exposed to these viruses to contribute to the knowledge of Jingmenvirus host range, geographical distribution, and mammalian exposure.

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