scholarly journals Phylogenomic analyses and distribution of terpene synthases amongStreptomyces

2019 ◽  
Vol 15 ◽  
pp. 1181-1193 ◽  
Author(s):  
Lara Martín-Sánchez ◽  
Kumar Saurabh Singh ◽  
Mariana Avalos ◽  
Gilles P van Wezel ◽  
Jeroen S Dickschat ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Terpene Synthase ◽  
Phylogenomic Analysis ◽  
Whole Genome ◽  
Phylogenetic Groups ◽  
Terpene Synthases ◽  
Whole Genomes ◽  
Phylogenomic Analyses

Terpene synthases are widely distributed among microorganisms and have been mainly studied in members of the genusStreptomyces. However, little is known about the distribution and evolution of the genes for terpene synthases. Here, we performed whole-genome based phylogenetic analysis ofStreptomycesspecies, and compared the distribution of terpene synthase genes among them. Overall, our study revealed that ten major types of terpene synthases are present within the genusStreptomyces, namely those for geosmin, 2-methylisoborneol,epi-isozizaene, 7-epi-α-eudesmol,epi-cubenol, caryolan-1-ol, cyclooctat-9-en-7-ol, isoafricanol, pentalenene and α-amorphene. TheStreptomycesspecies divide in three phylogenetic groups based on their whole genomes for which the distribution of the ten terpene synthases was analysed. Geosmin synthases were the most widely distributed and were found to be evolutionary positively selected. Other terpene synthases were found to be specific for one of the three clades or a subclade within the genusStreptomyces. A phylogenetic analysis of the most widely distributed classes ofStreptomycesterpene synthases in comparison to the phylogenomic analysis of this genus is discussed.

scholarly journals Genomics in Bacterial Taxonomy: Impact on the Genus Pseudomonas

Genes ◽  
2020 ◽  
Vol 11 (2) ◽  
pp. 139 ◽  
Author(s):  
Jorge Lalucat ◽  
Magdalena Mulet ◽  
Margarita Gomila ◽  
Elena García-Valdés
Keyword(s):  
New Technologies ◽  
Genome Comparison ◽  
Whole Genome ◽  
Bacterial Taxonomy ◽  
Phylogenetic Groups ◽  
Genomic Species ◽  
Subspecies Level ◽  
Taxonomic Approach ◽  
Phylogenomic Analyses ◽  
Genome Analyses

The introduction of genomics is profoundly changing current bacterial taxonomy. Phylogenomics provides accurate methods for delineating species and allows us to infer the phylogeny of higher taxonomic ranks as well as those at the subspecies level. We present as a model the currently accepted taxonomy of the genus Pseudomonas and how it can be modified when new taxonomic methodologies are applied. A phylogeny of the species in the genus deduced from analyses of gene sequences or by whole genome comparison with different algorithms allows three main conclusions: (i) several named species are synonymous and have to be reorganized in a single genomic species; (ii) many strains assigned to known species have to be proposed as new genomic species within the genus; and (iii) the main phylogenetic groups defined by 4-, 100- and 120-gene multilocus sequence analyses are concordant with the groupings in the whole genome analyses. Moreover, the boundaries of the genus Pseudomonas are also discussed based on phylogenomic analyses in relation to other genera in the family Pseudomonadaceae. The new technologies will result in a substantial increase in the number of species and probably split the current genus into several genera or subgenera, although these classifications have to be supported by a polyphasic taxonomic approach.

scholarly journals Whole-genome-based phylogenomic analysis of the Belgian 2016–2017 influenza A(H3N2) outbreak season allows improved surveillance

2021 ◽  
Vol 7 (9) ◽  
Author(s):  
Laura A. E. Van Poelvoorde ◽  
Bert Bogaerts ◽  
Qiang Fu ◽  
Sigrid C. J. De Keersmaecker ◽  
Isabelle Thomas ◽  
...  
Keyword(s):  
Influenza A ◽  
Viral Infections ◽  
Illumina Miseq ◽  
World Health ◽  
Influenza Surveillance ◽  
Phylogenomic Analysis ◽  
Whole Genome ◽  
Phylogenetic Groups ◽  
Mortality And Morbidity ◽  
Real Time Analysis

Seasonal influenza epidemics are associated with high mortality and morbidity in the human population. Influenza surveillance is critical for providing information to national influenza programmes and for making vaccine composition predictions. Vaccination prevents viral infections, but rapid influenza evolution results in emerging mutants that differ antigenically from vaccine strains. Current influenza surveillance relies on Sanger sequencing of the haemagglutinin (HA) gene. Its classification according to World Health Organization (WHO) and European Centre for Disease Prevention and Control (ECDC) guidelines is based on combining certain genotypic amino acid mutations and phylogenetic analysis. Next-generation sequencing technologies enable a shift to whole-genome sequencing (WGS) for influenza surveillance, but this requires laboratory workflow adaptations and advanced bioinformatics workflows. In this study, 253 influenza A(H3N2) positive clinical specimens from the 2016–2017 Belgian season underwent WGS using the Illumina MiSeq system. HA-based classification according to WHO/ECDC guidelines did not allow classification of all samples. A new approach, considering the whole genome, was investigated based on using powerful phylogenomic tools including beast and Nextstrain, which substantially improved phylogenetic classification. Moreover, Bayesian inference via beast facilitated reassortment detection by both manual inspection and computational methods, detecting intra-subtype reassortants at an estimated rate of 15 %. Real-time analysis (i.e. as an outbreak is ongoing) via Nextstrain allowed positioning of the Belgian isolates into the globally circulating context. Finally, integration of patient data with phylogenetic groups and reassortment status allowed detection of several associations that would have been missed when solely considering HA, such as hospitalized patients being more likely to be infected with A(H3N2) reassortants, and the possibility to link several phylogenetic groups to disease severity indicators could be relevant for epidemiological monitoring. Our study demonstrates that WGS offers multiple advantages for influenza monitoring in (inter)national influenza surveillance, and proposes an improved methodology. This allows leveraging all information contained in influenza genomes, and allows for more accurate genetic characterization and reassortment detection.

scholarly journals Electron microscopic observation of infected CCB and whole genome analysis of Koi herpesvirus isolate GY01

2020 ◽  
Author(s):  
Hongan Duan ◽  
Ye Xu ◽  
Yi Zhou ◽  
Fengzhi Wang ◽  
Chao Ding ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Phylogenetic Analysis ◽  
Genome Analysis ◽  
Multiple Alignment ◽  
Whole Genome ◽  
Electron Microscopic ◽  
Whole Genome Analysis ◽  
Koi Herpesvirus ◽  
Whole Genomes ◽  
Microscopy Examination

AbstractBackgroundCyprinid herpesvirus- 3 (CyHV-3), commonly known as Koi herpesvirus (KHV) can induce infectious and acute viremia in common/koi carp (Cyprinus carpio). In an earlier study in this laboratory a KHV isolate GY1506 (KHV GY01 in GeneBank) was isolated from diseased common carp, replicated on CCB cells and identified by PCR targeted on and phylogenetic analysis of thymidine kinase (TK) gene. Electron microscopy examination of GY01 infected CCB cell line and whole genome analysis was studied for further characteristics and epidemiological features of this strain.ResultsElectron microscopy examination of CCB infected with KHV GY01 strain revealed destruct of infected cells including incomplete nuclear membranes, deformed nucleus, marginalized nuclear chromosome, and the virus of different development stages and morphologies in the cytoplasm and nucleus, which resembles the herpesvirus. MEGA X and phyML were used for multiple alignment and phylogenetic analysis of whole genomes of GY01 and other 21 KHV strains available in GeneBank. analysis showed that GY01 was more close to E and KHV-I and was predicted it originated from the same ancestor as the E and KHV-I. Pairwise alignment of strain GY01 and strain E by Geneious software and YASS online version revealed that two strains had high identity(99.1%) at the nucleotide sequence level although variations and disagreement existed. The number and structure arrangement of open reading frames (orfs) or protein-encoding genes of GY01 is very similar to KHV E, and also to KHV-U but different from KHV-I. The characteristics and function of each orf need further study in the future.ConclusionsPathogenic changes of infected CCB cells and morphologies of KHV GY01 resembles the herpesvirus. Pairwise, multiple alignment and phylogenetic analysis of whole genomes of GY01 and other 21 KHV strains available in GeneBank demonstrated that the GY01 is closely related to strain KHV E and KHV-I and suggested it originated from the same ancestor as the E and KHV-I.

Phylogenetic Analysis of T-Box Genes Demonstrates the Importance of Amphioxus for Understanding Evolution of the Vertebrate Genome

Genetics ◽  
2000 ◽  
Vol 156 (3) ◽  
pp. 1249-1257
Author(s):  
Ilya Ruvinsky ◽  
Lee M Silver ◽  
Jeremy J Gibson-Brown
Keyword(s):  
Phylogenetic Analysis ◽  
Whole Genome Duplication ◽  
Genome Duplication ◽  
Gene Families ◽  
Vertebrate Evolution ◽  
Whole Genome ◽  
Vertebrate Genome ◽  
T Box ◽  
Genetic Complexity ◽  
History Of

Abstract The duplication of preexisting genes has played a major role in evolution. To understand the evolution of genetic complexity it is important to reconstruct the phylogenetic history of the genome. A widely held view suggests that the vertebrate genome evolved via two successive rounds of whole-genome duplication. To test this model we have isolated seven new T-box genes from the primitive chordate amphioxus. We find that each amphioxus gene generally corresponds to two or three vertebrate counterparts. A phylogenetic analysis of these genes supports the idea that a single whole-genome duplication took place early in vertebrate evolution, but cannot exclude the possibility that a second duplication later took place. The origin of additional paralogs evident in this and other gene families could be the result of subsequent, smaller-scale chromosomal duplications. Our findings highlight the importance of amphioxus as a key organism for understanding evolution of the vertebrate genome.

Whole Genome Sequencing and Phylogenetic Analysis of the Rabies Virus Strain Moscow 3253 Adapted to a Vero Cell Line

2020 ◽  
Vol 35 (4) ◽  
pp. 237-242
Author(s):  
Ya. M. Krasnov ◽  
Zh. V. Alkhova ◽  
S. V. Generalov ◽  
I. V. Tuchkov ◽  
E. A. Naryshkina ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Vero Cell ◽  
Whole Genome Sequencing ◽  
Cell Line ◽  
Rabies Virus ◽  
Genome Sequencing ◽  
Virus Strain ◽  
Whole Genome ◽  
Vero Cell Line ◽  
Rabies Virus Strain

Identification of multiple species and subpopulations among Australian clinical Sporothrix isolates using whole genome sequencing

2018 ◽  
Vol 57 (7) ◽  
pp. 905-908 ◽  
Author(s):  
David New ◽  
Alicia G Beukers ◽  
Sarah E Kidd ◽  
Adam J Merritt ◽  
Kerry Weeks ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Sporothrix Schenckii ◽  
Sensu Stricto ◽  
Northern Territory ◽  
Whole Genome ◽  
Phylogenetic Resolution ◽  
Genetic Clustering ◽  
Multiple Species

AbstractWhole genome sequencing (WGS) was used to demonstrate the wide genetic variability within Sporothrix schenckii sensu lato and establish that there are two main species of Sporothrix within Australian clinical isolates—S. schenckii sensu stricto and Sporothrix globosa. We also demonstrated southwest Western Australia contained genetically similar S. schenckii ss strains that are distinct from strains isolated in the eastern and northern states of Australia. Some genetic clustering by region was also noted for northern NSW, Queensland, and Northern Territory. Phylogenetic analysis of WGS data provided greater phylogenetic resolution compared to analysis of the calmodulin gene alone.

scholarly journals Genetic Diversity and Phylogenetic Analysis of Citrus tristeza virus Isolates from Turkey

2019 ◽  
Vol 2019 ◽  
pp. 1-11 ◽  
Author(s):  
Gözde Erkiş-Güngör ◽  
Bayram Çevik
Keyword(s):  
Phylogenetic Analysis ◽  
Citrus Tristeza Virus ◽  
Molecular Characteristics ◽  
Cloning And Sequencing ◽  
Phylogenetic Groups ◽  
The 1960S ◽  
Tristeza Virus ◽  
Virus Isolates ◽  
Stem Pitting ◽  
Citrus Tristeza

The presence of Citrus tristeza virus (CTV) in Turkey has been known since the 1960s and the virus was detected in all citrus growing regions of the country. Even though serological and biological characteristics of CTV have been studied since the 1980s, molecular characteristics of CTV isolates have not been studied to date in Turkey. In this study, molecular characteristics of 15 CTV isolates collected from different citrus growing regions of Turkey were determined by amplification, cloning, and sequencing of their major coat protein (CP) genes. The sequence analysis showed that the CP genes were highly conserved among Turkish isolates. However, isolates from different regions showed more genetic variation than isolates from the same region. Turkish isolates were clustered into three phylogenetic groups showing no association with geographical origins, host, or symptoms induced in indicator plants. Phylogenetic analysis of Turkish isolates with isolates from different citrus growing regions of the world including well-characterized type isolates of previously established strain specific groups revealed that some Turkish isolates were closely related to severe quick decline or stem pitting isolates. The results demonstrated that although CTV isolates from Turkey are considered biologically mild, majority of them contain severe components potentially causing quick decline or stem pitting.

scholarly journals Whole genome-based phylogenetic analysis of Rickettsiae

2009 ◽  
Vol 15 ◽  
pp. 336-337 ◽  
Author(s):  
V. Merhej ◽  
K. El Karkouri ◽  
D. Raoult
Keyword(s):  
Phylogenetic Analysis ◽  
Whole Genome

scholarly journals GeneContent: software for whole-genome phylogenetic analysis

2004 ◽  
Vol 21 (8) ◽  
pp. 1713-1714 ◽  
Author(s):  
X. Gu ◽  
W. Huang ◽  
D. Xu ◽  
H. Zhang
Keyword(s):  
Phylogenetic Analysis ◽  
Whole Genome

scholarly journals Putative Integrative Mobile Elements That Exploit the Xer Recombination Machinery Carrying blaIMI-Type Carbapenemase Genes in Enterobacter cloacae Complex Isolates in Singapore

2017 ◽  
Vol 62 (1) ◽  
Author(s):  
Tse H. Koh ◽  
Nurdyana Binte Abdul Rahman ◽  
Jeanette W. P. Teo ◽  
My-Van La ◽  
Balamurugan Periaswamy ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Multilocus Sequence Typing ◽  
Enterobacter Cloacae ◽  
Mobile Elements ◽  
Whole Genome ◽  
Content Type ◽  
Flanking Regions ◽  
Enterobacter Cloacae Complex

ABSTRACT Whole-genome sequencing was performed on 16 isolates of the carbapenemase-producing Enterobacter cloacae complex to determine the flanking regions of bla IMI-type genes. Phylogenetic analysis of multilocus sequence typing (MLST) targets separated the isolates into 4 clusters. The bla IMI-type genes were all found on Xer-dependent integrative mobile elements (IMEX). The IMEX elements of 5 isolates were similar to those described in Canada, while the remainder were novel. Five isolates had IMEX elements lacking a resolvase and recombinase.

Sign in / Sign up

Export Citation Format

Share Document