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Comparative Genomic Analysis of Hyperthermophilic Archaeal Fuselloviridae Viruses

Comparative Genomic Analysis of Hyperthermophilic Archaeal Fuselloviridae Viruses

SSVs and their Sulfolobus hosts are emerging as a model system for examining archaea and life at high temperatures. We are interested in the evolution of SSVs, the function of SSV-encoded gene products, and viral adaptations required for replication in high-temperature environments. Here we present the genomes of two additional SSV-like viruses, one from Kamchatka, Russia (SSV K1), and the other from Yel- lowstone National Park, United States (SSV RH). These ge- nomes in combination with the previously determined SSV1 and SSV2 genomes provide us with four geographically distinct isolates that we have used in a comparative genomic analysis.
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Comparative genomic analysis of six Glossina genomes, vectors of African trypanosomes

Comparative genomic analysis of six Glossina genomes, vectors of African trypanosomes

Conclusions The comparative genomic analysis of these six Glossina species highlights the important aspects of Glossina evo- lution and provides further insights into their unique biology. Additional documentation of other comparative analyses is included in Additional file 1. These include additional information on Glossina-specific gene enrich- ments/expansions/contractions, Glossina salivary protein genes, genes encoding neuropeptides and their receptors (Additional file 1: Table S11 and S12), cuticular protein genes (Additional file 1: Table S13, Additional file 11), Glossina transcription factor genes and their putative binding sites (Additional file 2: Figure S12, Additional file 12), and peritrophic matrix protein genes (Add- itional file 1: Table S14). The results derived from the analysis of these genomes are applicable to many aspects of tsetse biology including host seeking, digestion, im- munity, metabolism, endocrine function, reproduction, and evolution. This expanded knowledge has important practical relevance. Indeed, tsetse control strategies utilize trapping as a key aspect of population manage- ment. These traps use both olfactory and visual stimuli to attract tsetse. The findings of a reduced contingent of olfactory-associated genes and the variability of color sensing Rhodopsin genes provide research avenues into improvements of trap efficacy. A deeper understanding of the important chemosensory and visual stimuli associ- ated with the different species could facilitate the refine- ment of trap designs for specific species. The findings associated with Glossina digestive biology, including the enrichment of proteolysis-associated genes and identifi- cation of Glossina-specific expansions of immune-associ- ated proteins, provide new insights and avenues of investigation into vector competence and vector/parasite relationships. Analysis of the female and male reproduction-associated genes reveals the differential evolutionary pressures on females and males. The
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Comparative genomic analysis of six Glossina genomes, vectors of African trypanosomes

Comparative genomic analysis of six Glossina genomes, vectors of African trypanosomes

Conclusions The comparative genomic analysis of these six Glossina species highlights the important aspects of Glossina evo- lution and provides further insights into their unique biology. Additional documentation of other comparative analyses is included in Additional file 1. These include additional information on Glossina-specific gene enrich- ments/expansions/contractions, Glossina salivary protein genes, genes encoding neuropeptides and their receptors (Additional file 1: Table S11 and S12), cuticular protein genes (Additional file 1: Table S13, Additional file 11), Glossina transcription factor genes and their putative binding sites (Additional file 2: Figure S12, Additional file 12), and peritrophic matrix protein genes (Add- itional file 1: Table S14). The results derived from the analysis of these genomes are applicable to many aspects of tsetse biology including host seeking, digestion, im- munity, metabolism, endocrine function, reproduction, and evolution. This expanded knowledge has important practical relevance. Indeed, tsetse control strategies utilize trapping as a key aspect of population manage- ment. These traps use both olfactory and visual stimuli to attract tsetse. The findings of a reduced contingent of olfactory-associated genes and the variability of color sensing Rhodopsin genes provide research avenues into improvements of trap efficacy. A deeper understanding of the important chemosensory and visual stimuli associ- ated with the different species could facilitate the refine- ment of trap designs for specific species. The findings associated with Glossina digestive biology, including the enrichment of proteolysis-associated genes and identifi- cation of Glossina-specific expansions of immune-associ- ated proteins, provide new insights and avenues of investigation into vector competence and vector/parasite relationships. Analysis of the female and male reproduction-associated genes reveals the differential evolutionary pressures on females and males. The
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Genome sequencing, annotation and comparative genomic analysis of Shigella dysenteriae strain SD1D

Genome sequencing, annotation and comparative genomic analysis of Shigella dysenteriae strain SD1D

reference to epidemics. The current gold standard for the detection of Shigella species in fecal specimens involves isolation, growth and identification of Shigella in the cul- tures. Isolates of Shigella can also be identified using sero- logical tests [6]. Understanding the antibiotic resistance patterns of Shigellae and molecular characterization of plasmids and other genetic elements are also epidemiolog- ically useful. All the four species of the genus Shigella have been whole genome sequenced: Shigella boydii (02 iso- lates) strain BS512, Shigella dysenteriae (01 isolate) strain M131649, Shigella flexneri 2a (04 isolates) strain 2457T and Shigella sonnei (02 isolates) strain 53G. For the first time we have performed whole genome sequencing, as- sembly and annotation of strain Shigella dysenteriae SD1D, which was isolated from the stool sample of healthy individual. In order to understand the correlation between Shigella dysenteriae strain SD1D and Shigella spp., it is im- perative to explore the genome of the strain SD1D and perform a comparative genomic analysis with Shigella spp.
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Comparative genomic analysis of bacteriophages specific to the channel catfish pathogen Edwardsiella ictaluri

Comparative genomic analysis of bacteriophages specific to the channel catfish pathogen Edwardsiella ictaluri

34.1% identical at the nucleotide level. A comparative genomic analysis between the genome of phage eiAU and that of phage SSL-2009a revealed that genome regions encoding many putative structural and replica- tion proteins are shared by both phages (Figure 2). The predicted gene products with sequence similarity between the eiAU and SSL-2009a phage genomes include the putative minor tail proteins/tail tape mea- sure, major tail proteins, major capsid proteins, head morphogenesis, phage terminase small subunit, and the phage terminase large subunit. Interestingly, other struc- tural proteins including the host specificity proteins, the tail assembly proteins, and particularly the tail fiber/
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Comparative genomic analysis of multidrug-resistant <em>Streptococcus pneumoniae</em> isolates

Comparative genomic analysis of multidrug-resistant <em>Streptococcus pneumoniae</em> isolates

In all, further investigation of the function of some of the genes identified in this study is essential. In conclusion, by undertaking WGRS and comparative genomic analysis of 25 pneumococcal isolates, we have shown that although pneumococcal isolates were similar on genetic background, strains were diverse at the genomic level. These strains exhibited distinct variations in their indel and SNP compositions, which are potentially correlated with drug resistance. Here, we have simply reported the genomic variation present in the isolates. Further in-depth investiga- tions of these variations and their associations with antibiotic resistance mechanisms are required.
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Comparative genomic analysis of the ‘pseudofungus’ Hyphochytrium catenoides

Comparative genomic analysis of the ‘pseudofungus’ Hyphochytrium catenoides

8 School of Life Sciences, University of Nottingham, Nottingham NG7 2UH, UK GL, 0000-0002-4607-2064; AS-P, 0000-0002-9896-9746; JES, 0000-0002-7591-0020; BW, 0000-0002-4620-9091; TAR, 0000-0002-9692-0973 Eukaryotic microbes have three primary mechanisms for obtaining nutrients and energy: phagotrophy, photosynthesis and osmotrophy. Traits associated with the latter two functions arose independently multiple times in the eukar- yotes. The Fungi successfully coupled osmotrophy with filamentous growth, and similar traits are also manifested in the Pseudofungi (oomycetes and hyphochytriomycetes). Both the Fungi and the Pseudofungi encompass a diversity of plant and animal parasites. Genome-sequencing efforts have focused on host-associated microbes (mutualistic symbionts or parasites), providing limited comparisons with free-living relatives. Here we report the first draft genome sequence of a hyphochytriomycete ‘pseudofungus’; Hypho- chytrium catenoides. Using phylogenomic approaches, we identify genes of recent viral ancestry, with related viral derived genes also present on the gen- omes of oomycetes, suggesting a complex history of viral coevolution and integration across the Pseudofungi. H. catenoides has a complex life cycle involving diverse filamentous structures and a flagellated zoospore with a single anterior tinselate flagellum. We use genome comparisons, drug sensi- tivity analysis and high-throughput culture arrays to investigate the ancestry of oomycete/pseudofungal characteristics, demonstrating that many of the genetic features associated with parasitic traits evolved specifically within the oomycete radiation. Comparative genomics also identified differences in the repertoire of genes associated with filamentous growth between the Fungi and the Pseudofungi, including differences in vesicle trafficking sys- tems, cell-wall synthesis pathways and motor protein repertoire, demonstrating that unique cellular systems underpinned the convergent evolution of filamentous osmotrophic growth in these two eukaryotic groups.
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Comparative genomic analysis of the Tribolium immune system

Comparative genomic analysis of the Tribolium immune system

To date, components of the innate immune system are hardly known in T. castaneum and neither is it clear how they differ from homologous molecules in the honeybee, mosquito or fruitfly [6,7,18]. This lack of knowledge does not seem to rec- oncile with the critical phylogenetic position of this coleop- teran species, which should inform us a lot about genetic variations in the evolution of holometabolous insects. Infor- mation regarding defense responses in T. castaneum, a mem- ber of the largest and most diverse order of eukaryotes, is highly desirable for the biological control of crop pests and disease vectors. Consequently, we have used its newly availa- ble genome assembly to annotate immunity-related genes and analyze their phylogenetic relationships with homolo- gous sequences from other insects. In this comparative over- view of the Tribolium defense system, we describe plausible immune pathway models and present information regarding the molecular evolution of innate immunity in holometabo- lous species.
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Complete Genome Sequence and Comparative Genomic Analysis of

Complete Genome Sequence and Comparative Genomic Analysis of

Fig. 1. Circular representation of the M. massiliense JCM 15300 genome and comparative analysis among the complete genomes of Mycobacterium species. A. BLAST atlas of M. massiliense JCM 15300. The coding region of strain JCM 15300 was aligned against those of 14 other Mycobacterium genomes using BLASTP. The results are displayed as colored circles with increasing color intensity signifying increased similarity. It was estimated that the number of conserved proteins was 1,516 among all 14 Mycobacterium genomes. B. Box plot of identity percentage of conserved proteins between M. massiliense JCM 15300 and 14 other Mycobacterium spp. The top of each box in the box plot indicates the 75th percentile, the bottom of each box indicates the 25th percentile and the center bar represents the median. C. Neighbor-joining phylogenetic tree based on 16S rRNA gene sequencing of Mycobacterium with 1,000-fold bootstrapping. Scale bar indicates number of substitutions per site. The number at each branch node represents the bootstrapping value. Nocardia abscessus JCM 6043 (GenBank: AF430018) and Gordonia aichiensis DSM43978T (X80633) were used as outgroups.
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Comparative genomic analysis of C4 photosynthetic pathway evolution in grasses

Comparative genomic analysis of C4 photosynthetic pathway evolution in grasses

Compared to their rice ortholog, sorghum and maize PPDK-RP genes have accumulated sig- nificantly more amino acid substitutions (Table 1; Table S4 in Additional data file 1), providing s[r]

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Delineation of Steroid Degrading Microorganisms through Comparative Genomic Analysis

Delineation of Steroid Degrading Microorganisms through Comparative Genomic Analysis

E.C. and J.H. contributed equally to the manuscript. ABSTRACT Steroids are ubiquitous in natural environments and are a significant growth substrate for microorganisms. Micro- bial steroid metabolism is also important for some pathogens and for biotechnical applications. This study delineated the distri- bution of aerobic steroid catabolism pathways among over 8,000 microorganisms whose genomes are available in the NCBI Ref- Seq database. Combined analysis of bacterial, archaeal, and fungal genomes with both hidden Markov models and reciprocal BLAST identified 265 putative steroid degraders within only Actinobacteria and Proteobacteria, which mainly originated from soil, eukaryotic host, and aquatic environments. These bacteria include members of 17 genera not previously known to contain steroid degraders. A pathway for cholesterol degradation was conserved in many actinobacterial genera, particularly in members of the Corynebacterineae, and a pathway for cholate degradation was conserved in members of the genus Rhodococcus. A path- way for testosterone and, sometimes, cholate degradation had a patchy distribution among Proteobacteria. The steroid degrada- tion genes tended to occur within large gene clusters. Growth experiments confirmed bioinformatic predictions of steroid me- tabolism capacity in nine bacterial strains. The results indicate there was a single ancestral 9,10-seco-steroid degradation pathway. Gene duplication, likely in a progenitor of Rhodococcus, later gave rise to a cholate degradation pathway. Proteobacte- ria and additional Actinobacteria subsequently obtained a cholate degradation pathway via horizontal gene transfer, in some cases facilitated by plasmids. Catabolism of steroids appears to be an important component of the ecological niches of broad groups of Actinobacteria and individual species of Proteobacteria.
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Comparative genomic analysis of primary tumors and metastases in breast cancer

Comparative genomic analysis of primary tumors and metastases in breast cancer

and timings of metastases, even if the concordance does not seem different according to these parameters, but the number of pairs precluded any statistical analysis; iii) the delivery of different systemic treatments before the metastatic progression; iv) the relatively small number of genes analyzed by NGS, even if more comprehensive sequencing (whole exome, whole genome) did not identify any additional metastasis-specific actionable alterations in small recent series of breast [22] and colon [28] cancers, when compared to targeted NGS; v) the relatively small number of drugs available in the two tested clinical trials of personalized medicine, when compared to the much higher number of therapeutic targets tested. Whether the concordance rate in the therapeutic decision would be as high as 96% with drugs targeting all screened genes remains unknown, even if we showed strong concordance of recurrent alterations between primaries and metastases.
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Comparative genomic analysis of the multispecies probiotic-marketed product VSL#3

Comparative genomic analysis of the multispecies probiotic-marketed product VSL#3

* willem.devos@wur.nl Abstract Several probiotic-marketed formulations available for the consumers contain live lactic acid bacteria and/or bifidobacteria. The multispecies product commercialized as VSL#3 has been used for treating various gastro-intestinal disorders. However, like many other prod- ucts, the bacterial strains present in VSL#3 have only been characterized to a limited extent and their efficacy as well as their predicted mode of action remain unclear, preventing further applications or comparative studies. In this work, the genomes of all eight bacterial strains present in VSL#3 were sequenced and characterized, to advance insights into the possible mode of action of this product and also to serve as a basis for future work and trials. Phylo- genetic and genomic data analysis allowed us to identify the 7 species present in the VSL#3 product as specified by the manufacturer. The 8 strains present belong to the species Strep- tococcus thermophilus, Lactobacillus acidophilus, Lactobacillus paracasei, Lactobacillus plantarum, Lactobacillus helveticus, Bifidobacterium breve and B. animalis subsp. lactis (two distinct strains). Comparative genomics revealed that the draft genomes of the S. ther- mophilus and L. helveticus strains were predicted to encode most of the defence systems such as restriction modification and CRISPR-Cas systems. Genes associated with a variety of potential probiotic functions were also identified. Thus, in the three Bifidobacterium spp., gene clusters were predicted to encode tight adherence pili, known to promote bacteria-host interaction and intestinal barrier integrity, and to impact host cell development. Various rep- ertoires of putative signalling proteins were predicted to be encoded by the genomes of the Lactobacillus spp., i.e. surface layer proteins, LPXTG-containing proteins, or sortase- dependent pili that may interact with the intestinal mucosa and dendritic cells. Taken alto- gether, the individual genomic characterization of the strains present in the VSL#3 product confirmed the product specifications, determined its coding capacity as well as identified potential probiotic functions.
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Massive comparative genomic analysis reveals convergent evolution of specialized bacteria

Massive comparative genomic analysis reveals convergent evolution of specialized bacteria

According to your suggestion, we have performed the con- trol analysis to verify that the 100 lost COGs are specific to the reductive evolution of obligate intracellular bacte- ria. For that we have separated free-living bacteria into two groups: free-living small genomes and free-living large genomes using the cut-off of 2.92 Mb which is the mean genome size of facultative host-associated bacteria. In order to make the comparison between phylogenetically close relatives, we have treated the only phyla where there were small and large genomes. Genome sizes are given in additional file 1. We got 8 phyla Alpha-, Beta- and Gamm- aproteobacteria, Clostridia, Lactobacillales, Bacillales, Actino- bacteria, and Cyanobacteria, which represent a total of 168 free-living to include in the analysis. In each phylogenetic group, we identified COGs that are lost by 75% of the small free-living and conserved in more than 25% of the large free-living. First, we looked for COGs that are lost in common, i.e. by small free-living from more than one phylum. Second, in order to see if the 100 lost COGs are specific to the obligate intracellular reductive evolution, we studied the losses of small free-living bacteria. Thus, we compared their loss distribution for a COG in the set of the 100 COGs to the loss distribution for a COG in all the other COGs (among COGs lost at least once in small free-living), using a Chi-squared test for independence.
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Comparative genomic analysis of fungal genomes reveals intron rich ancestors

Comparative genomic analysis of fungal genomes reveals intron rich ancestors

Click here for file Acknowledgements We wish to thank BA Friedman, MW Hahn, TY James, V Maselli, MK Uyenoyama, and M Yandell for helpful discussion of this work. SWR thanks Walter Gilbert, Daniel Hartl, and David Penny for financial and intellectual support through the course of the project. We also thank HD Nguyen for kindly providing the C code for their method, M Csűrös for making Java implementation of his approach available on his website and L Carmel for assistance getting EREM to run. Computational analysis and genome anno- tation pipelines were performed on the Duke Shared Cluster Resource in the Center for Computational Science, Engineering, and Medicine. Website hosting for [50] is provided by the Duke Institute for Genome Science and Policy. JES was supported by an NSF graduate research fellowship and FSD was supported by NIH grant NS042263-03.
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Comparative genomic analysis reveals bilateral breast cancers are genetically independent

Comparative genomic analysis reveals bilateral breast cancers are genetically independent

In summary, with the help of whole-exome sequencing and CGH techniques, we systematically revealed the independent genomes of BBC in Han Chinese women, both synchronous and metachronous. Even the two synchronous tumors that occurred within as short as a month also have very diverse mutation profiles thus representing two independent tumors. This is a revelation at the genomic level that provides new insight into the development of bilateral breast cancer, although we cannot completely rule out the possibility of that they have the same clonal or sub-clonal origin because of our limited sample size. These findings appear to have a practical impact on the therapeutic regimen for BBC, as the clinical management of localized breast cancer is critically different from that of metastatic disease. It is essential to consider BBC as two diseases because similar systemic management for the two may not be applicable. Finally, this proof-of-principle study should be further tested by additional large and comprehensive research to provide important new insights into the biological mechanism of this uncommon disease.
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Comparative genomic analysis of Ralstonia solanacearum reveals candidate genes for host specificity

Comparative genomic analysis of Ralstonia solanacearum reveals candidate genes for host specificity

Due to the large pan-genome, each strain appeared to exhibit highly diverse genetic content even within the Moko, NPB and brown rot groups. This variability can be partially explained by the estimation of gene gain and loss rates along lineages. Indeed, each phylogenetic node of the species complex appears to have undergone hun- dreds of gain and loss events, thus creating mosaic ge- nomes (Additional file 2). This gain and loss explains why some homolog families are shared by distant line- ages but not by closer ones. Nonetheless, it is important to consider that the new genomes are in draft form and are divided into contigs. Thus, these genomes contain fragmented CDSs that can artificially increase the num- ber of predicted gene families and introduce some bias into subsequent analysis.
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OrthoList 2: A New Comparative Genomic Analysis of Human and Caenorhabditis elegans Genes

OrthoList 2: A New Comparative Genomic Analysis of Human and Caenorhabditis elegans Genes

Evaluating the utility of reliability scores in meta- analysis approaches Two different approaches have been used to infer reliability of predictions in meta-analyses. One is to use the number of methods that support an orthology prediction as a “simple score” for the reliability of the prediction. The other is to use different “weighting” approaches to emphasize predictions of some methods over others. However, our results here raise doubts as to whether either of these approaches is an appro- priate scoring methodology, because the level of support is not only dependent on which programs are used, but also on when these programs were sampled. Furthermore, our work, and that of Pryszcz et al. demonstrates that increasing the number of orthology-prediction methods does not have a major impact on the performance of a meta-analysis. The study that generated the MetaPhOrs database (Pryszcz et al. 2011) noted a significant increase in recall (fewer false negatives) when results from two orthology-prediction pro- grams were combined, compared to when individual pro- grams were sampled. However, there was little difference in recall, or precision, metrics when results from a third pro- gram were added to the combinations of two. Our results here support this observation, as addition of two more pro- grams (OMA and OrthoInspector) to the four already used for OL1 did not greatly increase recall, leading to addition of only 100 worm genes to OrthoList. Given the lack of corre- lation between having more programs in the meta-analysis, and increased recall or precision, we caution researchers against discarding hits with lower simple scores, for example uniques, as it would lead to a higher false negative rate when performing large-scale studies using meta-analysis-derived databases.
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Comparative genomic analysis and phenazine production of Pseudomonas chlororaphis, a plant growth-promoting rhizobacterium

Comparative genomic analysis and phenazine production of Pseudomonas chlororaphis, a plant growth-promoting rhizobacterium

Our analysis showed that P. chlororaphis strains are highly similar in genomic level. Additionally, we analyzed genes related to plant growth promotion. The genomic information indicated that the production of antifungal metabolites differed but all of four strains have one phenazine biosynthesis gene cluster. But the phenazine derivative found in HT66 is PCN whereas the other three strains produce 2-OH-PHZ and PCA. How- ever, only HT66 contains putative genes encoding orfamide A. Also, all of four P. chlororaphis strains contain the complete fit locus, suggesting that P. chlororaphis strains possess potent insecticidal activity. The diver- sity of antibiotics may allow P. chlororaphis to inhibit various pathogens, such as fungi, bacteria and some kinds of insects. Besides, the production of phenazines in HT66 is obviously higher than other strains, and some genes related to the regulation of phenazine biosynthesis have been detected in the four genomes. The analysis of genes contributing to the regulation and biosynthesis of antibiotics may lay the foundation for transforming P. chlororaphis to produce high levels of antibiotics. Finally, key virulence or virulence-related factors were absent from the P. chlororaphis strains, indicating that P. chlororaphis is safe and suitable to be applied in agriculture.
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Comparative genomic analysis and characteristics of NCCP15740, the major type of enterotoxigenic Escherichia coli in Korea

Comparative genomic analysis and characteristics of NCCP15740, the major type of enterotoxigenic Escherichia coli in Korea

According to the whole-genome phylogeny, NCCP15740 belonged to one of the two groups of strains that were isolated in 2011, but belonged to the group that included the majority of O6 strains in the MLST-based phylogeny (Fig. 2). There are many genomic changes that determine the branch of a strain in a phylogenetic tree, includ- ing SNPs, insertions, deletions, prophages, and other insertion sequence elements. However, MLST genes are housekeeping genes and are more conserved than other genomic loci. Therefore, whole-genome-based phylogeny is more sensitive than MLST-based phylogeny, although it is more difficult to group strains with whole-genome- based phylogeny. Accordingly, it is necessary to select whole-genome- or MLST-based phylogeny according to the needs of the study design and aim. An MLST-base phylogeny is suitable for clustering strains according to
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