scholarly journals Genomic sequence data of bacterial isolates from pistachio trees and other woody plants in California are inconsistent with a role of Rhodococcus as the causative agent of Pistachio Bushy Top Syndrome

2021 ◽  
Author(s):  
Brendan Riely ◽  
Mohamed Taieb Nouri ◽  
Kashif Riaz ◽  
Muhammad Rizwan Tufail ◽  
Yunpeng Gai ◽  
...  
Keyword(s):  
Native Species ◽  
Genomic Sequence ◽  
Sequence Data ◽  
Core Gene ◽  
Point Sources ◽  
Whole Genome Sequence ◽  
Rhodococcus Species ◽  
Genome Analyses ◽  
Pistachio Trees

Pistachio Bushy Top Syndrome (PBTS) is a serious problem for pistachio growers in the western U.S. but the cause of this disorder remains controversial. Recently, it was proposed that the Rhodococcus species, R. fascians and R. corynebacterioides caused PBTS outbreaks in 2011 and 2015. To investigate the association of Rhodococcus spp with PBTS in California’s pistachio growing region, Rhodococcus-like isolates were collected from diverse hosts and environments, including pistachio nurseries and orchards. Whole genome sequence analysis of 231 isolates revealed their evolutionary relationships and identified six Rhodococcus species. Combined with data on geography and host of origin, the data reveal that Rhodococcus generally, and R. fascians specifically, is ubiquitous in nature, frequently occurring in both symptomatic and asymptomatic pistachio trees and on other woody and native species. Core gene and SNP-based phylogenies, and pan-genome analyses differentiate R. fascians into distinct genotypes. Although we found examples of common genotypes shared between nurseries and orchards, the observed patterns are most consistent with an environmental source of strains and do not support a scenario where individual nurseries are point sources of Rhodococcus. Moreover, none of the collected strains harbored known virulence genes, calling into question the role of these common, environmental bacteria in causing PBTS.

scholarly journals Molecular Assay Validation Using Genomic Sequence Databases

2016 ◽  
Vol 54 (12) ◽  
pp. 2854-2856 ◽  
Author(s):  
John P. Dekker
Keyword(s):  
Clinical Microbiology ◽  
Genomic Sequence ◽  
Sequence Data ◽  
Whole Genome Sequence ◽  
Clinical Microbiology Laboratory ◽  
Microbiology Laboratory ◽  
Molecular Assay ◽  
Pcr Assay ◽  
Content Type ◽  
Sequence Databases

Whole-genome sequence databases offer newin silicoapproaches for designing and validating PCR assays in the clinical microbiology laboratory. An article in this issue of theJournal of Clinical Microbiology(M. J. Jansen van Rensburg, C. Swift, A. J. Cody, C. Jenkins, and M. C. J. Maiden, J Clin Microbiol, 54:2882–2890, 2016,http://dx.doi.org/10.1128/JCM.01522-16) demonstrates the use of publicly available genomic sequence data to evaluate a PCR assay for distinguishingCampylobacterspecies.

scholarly journals Nephila clavata L. Koch, the Joro Spider of East Asia, newly recorded from North America (Araneae: Nephilidae)

2014 ◽  
Author(s):  
E. Richard Hoebeke ◽  
Wesley Huffmaster ◽  
Byron J Freeman
Keyword(s):  
North America ◽  
East Asia ◽  
Native Species ◽  
Genomic Sequence ◽  
Sequence Data ◽  
Coi Gene ◽  
Background Information ◽  
Invasion History ◽  
Nephila Clavipes ◽  
Species Identity

Nephila clavata L. Koch, known as the Joro spider and native to East Asia (Japan, China, Korea, and Taiwan), is newly reported from North America. Specimens from several locations in northeast Georgia were collected from around residential properties in Barrow, Jackson, and Madison counties in late October and early November 2014. These are the first confirmed records of the species in the New World. Our collections, along with confirmed images provided by private citizens, suggest the Joro spider is established in northeast Georgia. Genomic sequence data for the COI gene obtained from two specimens conforms to published sequences for N. clavata, providing additional confirmation of species identity. Known collection records are listed and mapped using geocoding. Our observations are summarized along with published background information on biology in Asia and we hypothesize on the invasion history and mode of introduction into North America. Recognition features are given and photographic images of the male and female are provided to aid in their differentiation from the one native species of the genus (Nephila clavipes) in North America.

scholarly journals SNP analysis implicates role of cytosine methylation in introducing consequential mutations inVibrio choleraegenomes

2016 ◽  
Author(s):  
Mohak Sharda ◽  
Aswin Sai Narain Seshasayee ◽  
Supriya Khedkar
Keyword(s):  
Vibrio Cholerae ◽  
Cytosine Methylation ◽  
Sequence Data ◽  
Genotypic Diversity ◽  
Whole Genome Sequence ◽  
Snp Analysis ◽  
Coding Region ◽  
Positive Role ◽  
Mutational Effect

AbstractEpigenetic modifications play a key role in gene regulation and in recognition of self DNA in bacteria. In-spite of their positive role in cell survival, modifications like cytosine methylation incur a mutational cost. Cytosine methylation, specifically 5-methylcytosine, is prone to hydrolytic deamination which leads to C → T and G → A transitions. Here, we first study the abundance of mutagenic cytosine methylation target motifs and show that bacteria likeVibrio choleraemight use motif avoidance as a strategy to minimize the mutational effect of deamination of methylated cytosine. Second by performing SNP analysis on whole genome sequence data fromVibrio choleraepatient isolates we show a) high abundance of cytosine methylation-dependent mutations in the cytosine methylation target motif RCCGGY, b) 95% of these C → T and G → A transitions in the coding region lead to non-synonymous substitutions and c) many of these transitions are associated with membrane proteins and are implicated in virulence. Thus, our SNP analysis ofV. choleraegenomes implicates the role of cytosine methylation in generating genotypic diversity with adaptive potential.

scholarly journals Nephila clavata L. Koch, the Joro Spider of East Asia, newly recorded from North America (Araneae: Nephilidae)

2014 ◽  
Author(s):  
E. Richard Hoebeke ◽  
Wesley Huffmaster ◽  
Byron J Freeman
Keyword(s):  
North America ◽  
East Asia ◽  
Native Species ◽  
Genomic Sequence ◽  
Sequence Data ◽  
Coi Gene ◽  
Background Information ◽  
Invasion History ◽  
Nephila Clavipes ◽  
Species Identity

Nephila clavata L. Koch, known as the Joro spider and native to East Asia (Japan, China, Korea, and Taiwan), is newly reported from North America. Specimens from several locations in northeast Georgia were collected from around residential properties in Barrow, Jackson, and Madison counties in late October and early November 2014. These are the first confirmed records of the species in the New World. Our collections, along with confirmed images provided by private citizens, suggest the Joro spider is established in northeast Georgia. Genomic sequence data for the COI gene obtained from two specimens conforms to published sequences for N. clavata, providing additional confirmation of species identity. Known collection records are listed and mapped using geocoding. Our observations are summarized along with published background information on biology in Asia and we hypothesize on the invasion history and mode of introduction into North America. Recognition features are given and photographic images of the male and female are provided to aid in their differentiation from the one native species of the genus (Nephila clavipes) in North America.

scholarly journals Complex introgression history of the erato-sara clade of Heliconius butterflies

2021 ◽  
Author(s):  
Yuttapong Thawornwattana ◽  
Fernando A. Seixas ◽  
Ziheng Yang ◽  
James Mallet
Keyword(s):  
Gene Flow ◽  
Genomic Sequence ◽  
Sequence Data ◽  
Whole Genome Sequence ◽  
Hybrid Origin ◽  
Ancestral Population ◽  
Ancestral Gene ◽  
Species Phylogeny ◽  
Full Likelihood ◽  
History Of

AbstractIntrogression plays a key role in adaptive evolution and species diversification in many groups of species including Heliconius butterflies. However, frequent hybridization and subsequent gene flow between species makes estimation of the species phylogeny challenging. Here, we infer species phylogeny and introgression events from whole-genome sequence data of six members of the erato-sara clade of Heliconius using a multispecies coalescent model with introgression (MSci) and an isolation-with-migration (IM) model. These approaches probabilistically capture the genealogical heterogeneity across the genome due to introgression and incomplete lineage sorting in a full likelihood framework. We detect robust signals of introgression across the genome, and estimate the direction, timing and magnitude of each introgression event. The results clarify several processes of speciation and introgression in the erato-sara group. In particular, we confirm ancestral gene flow between the sara clade and an ancestral population of H. telesiphe, a hybrid origin of H. hecalesia, and gene flow between the sister species H. erato and H. himera. The ability to confidently infer the presence, timing and magnitude of introgression events using genomic sequence data is helpful for understanding speciation in the presence of gene flow and will be useful for understanding the adaptive consequences of introgressed regions of the genome. Our analysis serves to highlight the power of full likelihood methods under the MSci model to the history of species divergence and cross-species introgression from genome-scale data.

scholarly journals Nephila clavata L. Koch, the Joro Spider of East Asia, newly recorded from North America (Araneae: Nephilidae)

2014 ◽  
Author(s):  
E. Richard Hoebeke ◽  
Wesley Huffmaster ◽  
Byron J Freeman
Keyword(s):  
North America ◽  
East Asia ◽  
Native Species ◽  
Genomic Sequence ◽  
Sequence Data ◽  
Coi Gene ◽  
Background Information ◽  
Invasion History ◽  
Nephila Clavipes ◽  
Species Identity

Nephila clavata L. Koch, known as the Joro spider and native to East Asia (Japan, China, Korea, and Taiwan), is newly reported from North America. Specimens from several locations in northeast Georgia were collected from around residential properties in Barrow, Jackson, and Madison counties in late October and early November 2014. These are the first confirmed records of the species in the New World. Our collections, along with confirmed images provided by private citizens, suggest the Joro spider is established in northeast Georgia. Genomic sequence data for the COI gene obtained from two specimens conforms to published sequences for N. clavata, providing additional confirmation of species identity. Known collection records are listed and mapped using geocoding. Our observations are summarized along with published background information on biology in Asia and we hypothesize on the invasion history and mode of introduction into North America. Recognition features are given and photographic images of the male and female are provided to aid in their differentiation from the one native species of the genus (Nephila clavipes) in North America.

scholarly journals Nephila clavata L. Koch, the Joro Spider of East Asia, newly recorded from North America (Araneae: Nephilidae)

2014 ◽  
Author(s):  
E. Richard Hoebeke ◽  
Wesley Huffmaster ◽  
Byron J Freeman
Keyword(s):  
North America ◽  
East Asia ◽  
Native Species ◽  
Genomic Sequence ◽  
Sequence Data ◽  
Coi Gene ◽  
Background Information ◽  
Invasion History ◽  
Nephila Clavipes ◽  
Species Identity

Nephila clavata L. Koch, known as the Joro spider and native to East Asia (Japan, China, Korea, and Taiwan), is newly reported from North America. Specimens from several locations in northeast Georgia were collected from around residential properties in Barrow, Jackson, and Madison counties in late October and early November 2014. These are the first confirmed records of the species in the New World. Our collections, along with confirmed images provided by private citizens, suggest the Joro spider is established in northeast Georgia. Genomic sequence data for the COI gene obtained from two specimens conforms to published sequences for N. clavata, providing additional confirmation of species identity. Known collection records are listed and mapped using geocoding. Our observations are summarized along with published background information on biology in Asia and we hypothesize on the invasion history and mode of introduction into North America. Recognition features are given and photographic images of the male and female are provided to aid in their differentiation from the one native species of the genus (Nephila clavipes) in North America.

scholarly journals BacWGSTdb 2.0: a one-stop repository for bacterial whole-genome sequence typing and source tracking

2020 ◽  
Vol 49 (D1) ◽  
pp. D644-D650 ◽  
Author(s):  
Ye Feng ◽  
Shengmei Zou ◽  
Hangfei Chen ◽  
Yunsong Yu ◽  
Zhi Ruan
Keyword(s):  
Genome Sequence ◽  
Genomic Sequence ◽  
Sequence Data ◽  
Bacterial Genome ◽  
Whole Genome Sequence ◽  
Source Tracking ◽  
Resistant Bacteria ◽  
Computational Techniques ◽  
Whole Genome ◽  
One Stop

Abstract An increasing prevalence of hospital acquired infections and foodborne illnesses caused by pathogenic and multidrug-resistant bacteria has stimulated a pressing need for benchtop computational techniques to rapidly and accurately classify bacteria from genomic sequence data, and based on that, to trace the source of infection. BacWGSTdb (http://bacdb.org/BacWGSTdb) is a free publicly accessible database we have developed for bacterial whole-genome sequence typing and source tracking. This database incorporates extensive resources for bacterial genome sequencing data and the corresponding metadata, combined with specialized bioinformatics tools that enable the systematic characterization of the bacterial isolates recovered from infections. Here, we present BacWGSTdb 2.0, which encompasses several major updates, including (i) the integration of the core genome multi-locus sequence typing (cgMLST) approach, which is highly scalable and appropriate for typing isolates belonging to different lineages; (ii) the addition of a multiple genome analysis module that can process dozens of user uploaded sequences in a batch mode; (iii) a new source tracking module for comparing user uploaded plasmid sequences to those deposited in the public databases; (iv) the number of species encompassed in BacWGSTdb 2.0 has increased from 9 to 20, which represents bacterial pathogens of medical importance; (v) a newly designed, user-friendly interface and a set of visualization tools for providing a convenient platform for users are also included. Overall, the updated BacWGSTdb 2.0 bears great utility in continuing to provide users, including epidemiologists, clinicians and bench scientists, with a one-stop solution to bacterial genome sequence analysis.

scholarly journals rMAP: the Rapid Microbial Analysis Pipeline for ESKAPE bacterial group whole-genome sequence data

2021 ◽  
Vol 7 (6) ◽  
Author(s):  
Ivan Sserwadda ◽  
Gerald Mboowa
Keyword(s):  
Low Income ◽  
Type Species ◽  
Genomic Sequence ◽  
Sequence Data ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Analysis Pipeline ◽  
Content Type ◽  
Link Type ◽  
Microbial Analysis

The recent re-emergence of multidrug-resistant pathogens has exacerbated their threat to worldwide public health. The evolution of the genomics era has led to the generation of huge volumes of sequencing data at an unprecedented rate due to the ever-reducing costs of whole-genome sequencing (WGS). We have developed the Rapid Microbial Analysis Pipeline (rMAP), a user-friendly pipeline capable of profiling the resistomes of ESKAPE pathogens ( Enterococcus faecium , Staphylococcus aureus , Klebsiella pneumoniae , Acinetobacter baumannii , Pseudomonas aeruginosa and Enterobacter species) using WGS data generated from Illumina’s sequencing platforms. rMAP is designed for individuals with little bioinformatics expertise, and automates the steps required for WGS analysis directly from the raw genomic sequence data, including adapter and low-quality sequence read trimming, de novo genome assembly, genome annotation, single-nucleotide polymorphism (SNP) variant calling, phylogenetic inference by maximum likelihood, antimicrobial resistance (AMR) profiling, plasmid profiling, virulence factor determination, multi-locus sequence typing (MLST), pangenome analysis and insertion sequence characterization (IS). Once the analysis is finished, rMAP generates an interactive web-like html report. rMAP installation is very simple, it can be run using very simple commands. It represents a rapid and easy way to perform comprehensive bacterial WGS analysis using a personal laptop in low-income settings where high-performance computing infrastructure is limited.

scholarly journals Nephila clavata L. Koch, the Joro Spider of East Asia, newly recorded from North America (Araneae: Nephilidae)

2014 ◽  
Author(s):  
E. Richard Hoebeke ◽  
Wesley Huffmaster ◽  
Byron J Freeman
Keyword(s):  
North America ◽  
East Asia ◽  
Native Species ◽  
Genomic Sequence ◽  
Sequence Data ◽  
Coi Gene ◽  
Background Information ◽  
Invasion History ◽  
Nephila Clavipes ◽  
Species Identity

Nephila clavata L. Koch, known as the Joro spider and native to East Asia (Japan, China, Korea, and Taiwan), is newly reported from North America. Specimens from several locations in northeast Georgia were collected from around residential properties in Barrow, Jackson, and Madison counties in late October and early November 2014. These are the first confirmed records of the species in the New World. Our collections, along with confirmed images provided by private citizens, suggest the Joro spider is established in northeast Georgia. Genomic sequence data for the COI gene obtained from two specimens conforms to published sequences for N. clavata, providing additional confirmation of species identity. Known collection records are listed and mapped using geocoding. Our observations are summarized along with published background information on biology in Asia and we hypothesize on the invasion history and mode of introduction into North America. Recognition features are given and photographic images of the male and female are provided to aid in their differentiation from the one native species of the genus (Nephila clavipes) in North America.

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