scholarly journals Prokaryotic Phylogenies Inferred from Whole-Genome Sequence and Annotation Data

2013 ◽  
Vol 2013 ◽  
pp. 1-15 ◽  
Author(s):  
Wei Du ◽  
Zhongbo Cao ◽  
Yan Wang ◽  
Ying Sun ◽  
Enrico Blanzieri ◽  
...  
Keyword(s):  
Phylogenetic Trees ◽  
Sequence Similarity ◽  
Genomic Structure ◽  
Evolutionary Relationship ◽  
Orthologous Gene ◽  
Gene Clusters ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Orthologous Genes ◽  
Single Chromosome

Phylogenetic trees are used to represent the evolutionary relationship among various groups of species. In this paper, a novel method for inferring prokaryotic phylogenies using multiple genomic information is proposed. The method is called CGCPhy and based on the distance matrix of orthologous gene clusters between whole-genome pairs. CGCPhy comprises four main steps. First, orthologous genes are determined by sequence similarity, genomic function, and genomic structure information. Second, genes involving potential HGT events are eliminated, since such genes are considered to be the highly conserved genes across different species and the genes located on fragments with abnormal genome barcode. Third, we calculate the distance of the orthologous gene clusters between each genome pair in terms of the number of orthologous genes in conserved clusters. Finally, the neighbor-joining method is employed to construct phylogenetic trees across different species. CGCPhy has been examined on different datasets from 617 complete single-chromosome prokaryotic genomes and achieved applicative accuracies on different species sets in agreement with Bergey's taxonomy in quartet topologies. Simulation results show that CGCPhy achieves high average accuracy and has a low standard deviation on different datasets, so it has an applicative potential for phylogenetic analysis.

scholarly journals Characterization of methicillin-resistant Staphylococcus aureus through genomics approach

3 Biotech ◽  
2020 ◽  
Vol 10 (9) ◽  
Author(s):  
Romen Singh Naorem ◽  
Peter Urban ◽  
Gunajit Goswami ◽  
Csaba Fekete
Keyword(s):  
Phylogenetic Trees ◽  
Antibiotic Resistance Genes ◽  
Improve Patient Care ◽  
Gene Clusters ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Specific Sequence ◽  
Methicillin Resistant ◽  
Mrsa Strains ◽  
Species Specific

Abstract In the present study, a total of 35 S. aureus isolates collected from two different geographical locations viz., Germany and Hungary were tested for their methicillin-resistant phenotype which revealed a high incidence of methicillin-resistant S. aureus. The quantitative test for biofilm production revealed that 73.3% of isolates were biofilm producers. The isolates were further characterized using a set of biochemical and genotypic methods such as amplification and analysis of S. aureus species-specific sequence and mecA gene. The 33 mecA positive isolates were then characterized by the amplification of SCCmec and pvl toxin genes. Further, based on the biofilm-forming phenotype, 15 isolates were selected and characterized through PCR–RFLP of coa gene, polymorphism of spa gene and amplification of biofilm-associated genes. The dendrogram prepared from the results of both biochemical and genotypic analyses of the 15 isolates showed that except for the isolates SA G5 and SA H29, the rest of the isolates grouped themselves according to their locations. Thus, the two isolates were selected for further characterization through whole-genome sequencing. Comparative genome analysis revealed that SA G5 and SA H29 have 97.20% ANI values with 2344 gene clusters (core-genome) of which 16 genes were related to antibiotic resistance genes and 57 genes encode virulence factors. The highest numbers of singleton genes were found in SA H29 that encodes proteins for virulence, resistance, mobile elements, and lanthionine biosynthesis. The high-resolution phylogenetic trees generated based on shared proteins and SNPs revealed a clear difference between the two strains and can be useful in distinguishing closely related genomes. The present study demonstrated that the whole-genome sequence analysis technique is required to get a better insight into the MRSA strains which would be helpful in improving diagnostic investigations in real-time to improve patient care.

scholarly journals Characterization of the Aerobic Anoxygenic Phototrophic Bacterium Sphingomonas sp. AAP5

2021 ◽  
Vol 9 (4) ◽  
pp. 768
Author(s):  
Karel Kopejtka ◽  
Yonghui Zeng ◽  
David Kaftan ◽  
Vadim Selyanin ◽  
Zdenko Gardian ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
Orthologous Gene ◽  
Gene Clusters ◽  
Rrna Gene ◽  
Unidentified Phospholipid ◽  
Respiratory Quinone ◽  
Polar Lipid Profile ◽  
Close Phylogenetic Relationship

An aerobic, yellow-pigmented, bacteriochlorophyll a-producing strain, designated AAP5 (=DSM 111157=CCUG 74776), was isolated from the alpine lake Gossenköllesee located in the Tyrolean Alps, Austria. Here, we report its description and polyphasic characterization. Phylogenetic analysis of the 16S rRNA gene showed that strain AAP5 belongs to the bacterial genus Sphingomonas and has the highest pairwise 16S rRNA gene sequence similarity with Sphingomonas glacialis (98.3%), Sphingomonas psychrolutea (96.8%), and Sphingomonas melonis (96.5%). Its genomic DNA G + C content is 65.9%. Further, in silico DNA-DNA hybridization and calculation of the average nucleotide identity speaks for the close phylogenetic relationship of AAP5 and Sphingomonas glacialis. The high percentage (76.2%) of shared orthologous gene clusters between strain AAP5 and Sphingomonas paucimobilis NCTC 11030T, the type species of the genus, supports the classification of the two strains into the same genus. Strain AAP5 was found to contain C18:1ω7c (64.6%) as a predominant fatty acid (>10%) and the polar lipid profile contained phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, sphingoglycolipid, six unidentified glycolipids, one unidentified phospholipid, and two unidentified lipids. The main respiratory quinone was ubiquinone-10. Strain AAP5 is a facultative photoheterotroph containing type-2 photosynthetic reaction centers and, in addition, contains a xathorhodopsin gene. No CO2-fixation pathways were found.

scholarly journals Whole-Genome Sequencing Reveals a New Genospecies ofMethylobacteriumsp. GXS13, Isolated fromVitis viniferaL. Xylem Sap

2016 ◽  
Vol 4 (1) ◽  
Author(s):  
Wan Xin Lai ◽  
Han Ming Gan ◽  
André O. Hudson ◽  
Michael A. Savka
Keyword(s):  
Xylem Sap ◽  
Gene Clusters ◽  
Homoserine Lactone ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Acyl Homoserine Lactone ◽  
Biosynthetic Gene ◽  
Biosynthetic Gene Clusters ◽  
Cell Wall Modification ◽  
Cytokinin Synthesis

The whole-genome sequence of a new genospecies ofMethylobacteriumsp., named GXS13 and isolated from grapevine xylem sap, is reported and demonstrates potential for methylotrophy, cytokinin synthesis, and cell wall modification. In addition, biosynthetic gene clusters were identified for cupriachelin, carotenoid, and acyl-homoserine lactone using the antiSMASH server.

scholarly journals Evolutionary Dynamics of rDNA Clusters in Chromosomes of Five Clam Species Belonging to the Family Veneridae (Mollusca, Bivalvia)

2014 ◽  
Vol 2014 ◽  
pp. 1-9 ◽  
Author(s):  
Concepción Pérez-García ◽  
Ninoska S. Hurtado ◽  
Paloma Morán ◽  
Juan J. Pasantes
Keyword(s):  
Phylogenetic Trees ◽  
Evolutionary Dynamics ◽  
5S Rdna ◽  
Gene Clusters ◽  
Ruditapes Philippinarum ◽  
Ruditapes Decussatus ◽  
Rdna Cluster ◽  
Single Chromosome ◽  
Molecular Phylogenetic ◽  
Chromosomal Changes

The chromosomal changes accompanying bivalve evolution are an area about which few reports have been published. To improve our understanding on chromosome evolution in Veneridae, ribosomal RNA gene clusters were mapped by fluorescentin situhybridization (FISH) to chromosomes of five species of venerid clams (Venerupis corrugata,Ruditapes philippinarum,Ruditapes decussatus,Dosinia exoleta, andVenus verrucosa). The results were anchored to the most comprehensive molecular phylogenetic tree currently available for Veneridae. While a single major rDNA cluster was found in each of the five species, the number of 5S rDNA clusters showed high interspecies variation. Major rDNA was either subterminal to the short arms or intercalary to the long arms of metacentric or submetacentric chromosomes, whereas minor rDNA signals showed higher variability. Major and minor rDNAs map to different chromosome pairs in all species, but inR. decussatusone of the minor rDNA gene clusters and the major rDNA cluster were located in the same position on a single chromosome pair. This interspersion of both sequences was confirmed by fiber FISH. Telomeric signals appeared at both ends of every chromosome in all species. FISH mapping data are discussed in relation to the molecular phylogenetic trees currently available for Veneridae.

scholarly journals Draft Whole Genome Sequence Analyses on Pseudomonas syringae pv. actinidiae Hypersensitive Response Negative Strains Detected from Kiwifruit Bleeding Sap Samples

2018 ◽  
Vol 108 (5) ◽  
pp. 552-560 ◽  
Author(s):  
Enrico Biondi ◽  
Alan Zamorano ◽  
Ernesto Vega ◽  
Stefano Ardizzi ◽  
Davide Sitta ◽  
...  
Keyword(s):  
Pseudomonas Syringae ◽  
Genome Sequence ◽  
Hypersensitive Response ◽  
Time Window ◽  
Gene Clusters ◽  
Whole Genome Sequence ◽  
Optimal Time ◽  
Whole Genome ◽  
Isolation And Identification ◽  
The Difference

Kiwifruit bleeding sap samples, collected in Italian and Chilean orchards from symptomatic and asymptomatic plants, were evaluated for the presence of Pseudomonas syringae pv. actinidiae, the causal agent of bacterial canker. The saps were sampled during the spring in both hemispheres, before the bud sprouting, during the optimal time window for the collection of an adequate volume of sample for the early detection of the pathogen, preliminarily by molecular assays, and then through its direct isolation and identification. The results of molecular analyses showed more effectiveness in the P. syringae pv. actinidiae detection when compared with those of microbiological analyses through the pathogen isolation on the nutritive and semiselective media selected. The bleeding sap analyses allowed the isolation and identification of two hypersensitive response (HR) negative and hypovirulent P. syringae pv. actinidiae strains from different regions in Italy. Moreover, multilocus sequence analysis (MLSA) and whole genome sequence (WGS) were carried out on selected Italian and Chilean P. syringae pv. actinidiae virulent strains to verify the presence of genetic variability compared with the HR negative strains and to compare the variability of selected gene clusters between strains isolated in both countries. All the strains showed the lack of argK and coronatine gene clusters as reported for the biovar 3 P. syringae pv. actinidiae strains. Despite the biologic differences obtained in the tobacco bioassays and in pathogenicity assays, the MLSA and WGS analyses did not show significant differences between the WGS of the HR negative and HR positive strains; the difference, on the other hand, between PAC_ICE sequences of Italian and Chilean P. syringae pv. actinidiae strains was confirmed. The inability of the hypovirulent strains IPV-BO 8893 and IPV-BO 9286 to provoke HR in tobacco and the low virulence shown in this host could not be associated with mutations or recombinations in T3SS island.

scholarly journals Whole genome sequence of Peribacillus sp. MUM 13 derived from mangrove forest in Malaysia

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Hooi-Leng Ser ◽  
Jodi Woan-Fei Law ◽  
Wen-Si Tan ◽  
Wai-Fong Yin ◽  
Kok-Gan Chan ◽  
...  
Keyword(s):  
Genome Analysis ◽  
Mangrove Forest ◽  
Screening Program ◽  
Gene Clusters ◽  
Bioinformatic Analysis ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Chemical Structures ◽  
Pathogenic Microbes ◽  
Unique Chemical

Acting like mini-factories, microorganisms are a valuable source of naturalbioactive compounds of unique chemical structures. Peribacillus sp. MUM 13 was recoveredfrom the mangrove forest in Malaysia during a screening program for bioactive microbes.Whole genome analysis revealed that the genome size of MUM 13 as 4,649,225 bp (with G+ C content of 40.8 %). Bioinformatic analysis predicted the presence of lassopeptidebiosynthetic gene clusters within the genome of MUM 13, which indicates the bioactivepotential of the strain and calls for further experiments to explore the strain characteristics,particularly in combatting against pathogenic microbes.

scholarly journals Rapid statistical methods for inferring intra- and inter-hospital transmission of nosocomial pathogens from whole genome sequence data

2018 ◽  
Author(s):  
Marianne Aspbury ◽  
James Sciberras ◽  
Jukka Corander ◽  
Sion C. Bayliss ◽  
Tjibbe Donker ◽  
...  
Keyword(s):  
Statistical Methods ◽  
Genome Sequence ◽  
Phylogenetic Trees ◽  
Sequence Data ◽  
Bacterial Pathogens ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Transmission Networks ◽  
Genome Sequence Data ◽  
Hospital Transmission

AbstractWhole genome sequence (WGS) data for bacterial pathogens can provide evidence as to the source of nosocomial infection, and more specifically the ability to distinguish between intra- and inter-hospital transmission. This is currently achieved either through using SNP thresholds, which can lack statistical robustness, or by constructing phylogenetic trees, which can be computationally expensive and difficult to interpret. Here we compare two alternative statistical approaches using 1022 genomes of methicillin resistantStaphylococcus aureus(MRSA) clone ST22. In 71% of cases both methods predict the same hospital origin, which is also supported by the ML tree. Robust assignments are divided approximately equally between intra-hospital transmission and inter-hospital transmission. Our approaches are rapid and produce intuitive output that could inform on immediate infection control priorities, as well as providing long-term data on inter-hospital transmission networks. We discuss the strengths and weakness of our methods, and the generalisability of this approach.One Sentence SummaryWe present rapid statistical methods for distinguishing intra- versus inter-hospital transmission of bacterial pathogens using whole genome sequence data; these methods do not require the use of SNP thresholds or the generation and interpretation of phylogenetic trees.

scholarly journals Genome-based analyses reveal the presence of 12 heterotypic synonyms in the genus Streptomyces and emended descriptions of Streptomyces bottropensis, Streptomyces celluloflavus, Streptomyces fulvissimus, Streptomyces glaucescens, Streptomyces murinus, and Streptomyces variegatus

2020 ◽  
Vol 70 (6) ◽  
pp. 3924-3929 ◽  
Author(s):  
Munusamy Madhaiyan ◽  
Venkatakrishnan Sivaraj Saravanan ◽  
Wah-Seng See-Too
Keyword(s):  
Type Species ◽  
Sequence Similarity ◽  
Orthologous Gene ◽  
Gene Clusters ◽  
Amino Acid Identity ◽  
Rrna Gene ◽  
Genus Streptomyces ◽  
Content Type ◽  
Link Type ◽  
Streptomyces Glaucescens

Phylogenetic analysis based on 16S rRNA gene sequences of the genus Streptomyces showed the presence of six distinguishable clusters, with 100 % sequence similarity values among strains in each cluster; thus they shared almost the same evolutionary distance. This result corroborated well with the outcome of core gene (orthologous gene clusters) based genome phylogeny analysis of 190 genomes including the Streptomyces species in those six clusters. These preeminent results led to an investigation of genome-based indices such as digital DNA–DNA hybridization (dDDH), average nucleotide identity (ANI) and average amino acid identity (AAI) for the strains in those six clusters. Certain strains recorded genomic indices well above the threshold values (70 %, 95–96 % and >95 % for dDDH, ANI and AAI, respectively) determined for species affiliation, suggesting only one type strain belongs to described species and the other(s) may need to be reduced in taxa to a later heterotypic synonym. To conclude, the results of comprehensive analyses based on phylogenetic and genomic indices suggest that the following six reclassifications are proposed: Streptomyces flavovariabilis as a later heterotypic synonym of Streptomyces variegatus ; Streptomyces griseofuscus as a later heterotypic synonym of Streptomyces murinus ; Streptomyces kasugaensis as a later heterotypic synonym of Streptomyces celluloflavus ; Streptomyces luridiscabiei as a later heterotypic synonym of Streptomyces fulvissimus ; Streptomyces pharetrae as a later heterotypic synonym of Streptomyces glaucescens ; and Streptomyces stelliscabiei as a later heterotypic synonym of Streptomyces bottropensis .

scholarly journals Analysis of Draft Genome Resources of Thirty-Three Canadian Strains of Pseudomonas syringae pv. tomato isolated between 1992 and 2008 Reveals achromobactin virulence cluster that is absent in the reference strain DC3000

2021 ◽  
Author(s):  
James Tambong ◽  
Renlin Xu ◽  
Diane Cuppels ◽  
Julie T Chapados ◽  
suzanne Gerdis ◽  
...  
Keyword(s):  
Pseudomonas Syringae ◽  
Draft Genome ◽  
Genome Mining ◽  
Gene Clusters ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Genome Sequences ◽  
Protein Coding ◽  
Genome Data ◽  
Bacterial Speck Disease

Pseudomonas syringae pv. tomato is the causal agent of bacterial speck disease of field and greenhouse tomato plants. Only one Canadian whole genome sequence of this economically important pathogen is publicly available in NCBI GenBank. Here, we report 33 whole genome sequences of Canadian strains of P. syringae pv. tomato isolated in Ontario, Canada, between 1992 and 2008. The genome sequences exhibited average nucleotide identity values of 98.64-98.72 % with P. syringae pv. tomato ICMP 2844PT and DC3000, validating the taxonomic standing of these Canadian strains. The genome sizes ranged from 6.20-6.39 Mbp with G+C content of 58.6% and comprised 5,889-6,166 protein-coding sequences (CDSs). The strains had pan- and core-genomes of 6808 and 4,993 gene clusters, respectively. Genome mining of the strains for virulence factors identified typical adherence genes, proteins related to antiphagocytosis, secretion system apparatuses and effectors. Also, partial or complete achromobactin biosynthetic cluster and iron transport genes were identified in all the Canadian strains but absent in P. syringae pv. tomato DC3000 or ICMP 2844 (pathotype). These new whole genome data of Canadian strains of P. syringae pv. tomato could be useful resources in understanding the evolution of this pathogen.

scholarly journals Whole genome sequence of Streptomyces humi strain MUSC 119T isolated from intertidal soil

2019 ◽  
Vol 2 (1) ◽  
Author(s):  
Hooi-Leng Ser ◽  
Wen-Si Tan ◽  
Wai-Fong Yin ◽  
Kok-Gan Chan ◽  
Nurul Syakima Ab Mutalib ◽  
...  
Keyword(s):  
Gene Clusters ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Biosynthetic Gene Clusters ◽  
Streptomyces Species ◽  
Genus Streptomyces ◽  
The Past ◽  
Mangrove Soil ◽  
Natural Product Research ◽  
Biochemical Assays

Over the past few decades, microorganisms have made major contribution in natural product research, particularly those from the genus Streptomyces. Streptomyces humi MUSC 119T was previously isolated as novel streptomycete from mangrove soil in Malaysia. During the screening programme for bioactive strains, this strain was discovered to possess antioxidant activity – scavenging and reducing accumulation of free radicals in biochemical assays. Consequently, whole genome sequencing was performed to evaluate genomic potential of the strain. Based on our analysis, the genome size of MUSC 119T is described to be 10.01 Mbps with G + C content of 71.80%. Based on antiSMASH analysis, the strain possess great genomic potential, having nine biosynthetic gene clusters displaying high similarities to known gene clusters. These findings indicates that mangrove Streptomyces species like MUSC 119T may potentially play an important role in drug development process, while the availability of its whole genome sequences allows further manipulation to isolate and identify compound of interest.

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