scholarly journals Genomic analysis of coxsackieviruses A1, A19, A22, enteroviruses 113 and 104: viruses representing two clades with distinct tropism within enterovirus C

2013 ◽  
Vol 94 (9) ◽  
pp. 1995-2004 ◽  
Author(s):  
Rafal Tokarz ◽  
Saddef Haq ◽  
Stephen Sameroff ◽  
Stephen R. C. Howie ◽  
W. Ian Lipkin
Keyword(s):  
Phylogenetic Analysis ◽  
Sequence Analysis ◽  
Genomic Analysis ◽  
The Other ◽  
High Rate ◽  
Structural Genes ◽  
Genome Sequences ◽  
Capsid Region ◽  
High Degree ◽  
Degree Of Similarity

Coxsackieviruses (CV) A1, CV-A19 and CV-A22 have historically comprised a distinct phylogenetic clade within Enterovirus (EV) C. Several novel serotypes that are genetically similar to these three viruses have been recently discovered and characterized. Here, we report the coding sequence analysis of two genotypes of a previously uncharacterized serotype EV-C113 from Bangladesh and demonstrate that it is most similar to CV-A22 and EV-C116 within the capsid region. We sequenced novel genotypes of CV-A1, CV-A19 and CV-A22 from Bangladesh and observed a high rate of recombination within this group. We also report genomic analysis of the rarely reported EV-C104 circulating in the Gambia in 2009. All available EV-C104 sequences displayed a high degree of similarity within the structural genes but formed two clusters within the non-structural genes. One cluster included the recently reported EV-C117, suggesting an ancestral recombination between these two serotypes. Phylogenetic analysis of all available complete genome sequences indicated the existence of two subgroups within this distinct Enterovirus C clade: one has been exclusively recovered from gastrointestinal samples, while the other cluster has been implicated in respiratory disease.

scholarly journals Assessment of intraspecific genetic variation between three morphotypes of Cissus quadrangularis using CCMP markers

2015 ◽  
Vol 24 (2) ◽  
pp. 205-212
Author(s):  
Ritesh Kaur ◽  
CP Malik
Keyword(s):  
Genetic Variation ◽  
Sequence Analysis ◽  
Chloroplast Genome ◽  
Intraspecific Variation ◽  
Microsatellite Primers ◽  
Genome Sequences ◽  
Chloroplast Microsatellite ◽  
Cissus Quadrangularis ◽  
High Degree ◽  
Degree Of Similarity

The objective of the current study was to assess and establish intraspecific variation between three morphotypes of Cissus quadrangularis using ten Consensus Chloroplast Microsatellite Primers. Significant level of genetic variation was detected between the three morphotypes. Sequence analysis of the CCMP PCR fragment showed the high degree of similarity to the chloroplast genome sequences of other Vitaceae members indicating that these regions are highly conserved.Plant Tissue Cult. & Biotech. 24(2): 205-212, 2014 (December)

scholarly journals Complete Genome Sequences of Two Salmonella Viruses, VSe11 and VSe102 (Family Myoviridae, Subfamily Ounavirinae), with a Very High Degree of Similarity

2018 ◽  
Vol 6 (21) ◽  
Author(s):  
Nikolay V. Volozhantsev ◽  
Egor A. Denisenko ◽  
Angelina A. Kislichkina ◽  
Vera P. Myakinina ◽  
Valentina M. Krasilnikova ◽  
...  
Keyword(s):  
Broad Spectrum ◽  
Complete Genome ◽  
Genome Sequences ◽  
Coding Sequences ◽  
Content Type ◽  
Double Stranded Dna ◽  
Poultry Farms ◽  
High Degree ◽  
Degree Of Similarity ◽  
Very High

ABSTRACT Two lytic double-stranded DNA bacteriophages, VSe11 and VSe102, infecting broad-spectrum Salmonella enterica were isolated from the sewage of two different poultry farms. The phage genomes comprise 86,360 bp and 86,365 bp, respectively, with a G+C content of 39.0%, and both contain 129 putative coding sequences.

scholarly journals Natural Merodiploidy of the lux-rib Operon of Photobacterium leiognathi from Coastal Waters of Honshu, Japan

2007 ◽  
Vol 189 (17) ◽  
pp. 6148-6158 ◽  
Author(s):  
Jennifer C. Ast ◽  
Henryk Urbanczyk ◽  
Paul V. Dunlap
Keyword(s):  
Phylogenetic Analysis ◽  
Sequence Analysis ◽  
Coastal Waters ◽  
Efflux Pump ◽  
Bacterial Species ◽  
Genomic Analysis ◽  
Multidrug Efflux Pump ◽  
Photobacterium Leiognathi ◽  
Content Organization ◽  
Luminous Bacteria

ABSTRACT Sequence analysis of the bacterial luminescence (lux) genes has proven effective in helping resolve evolutionary relationships among luminous bacteria. Phylogenetic analysis using lux genes, however, is based on the assumptions that the lux genes are present as single copies on the bacterial chromosome and are vertically inherited. We report here that certain strains of Photobacterium leiognathi carry multiple phylogenetically distinct copies of the entire operon that codes for luminescence and riboflavin synthesis genes, luxCDABEG-ribEBHA. Merodiploid lux-rib strains of P. leiognathi were detected during sequence analysis of luxA. To define the gene content, organization, and sequence of each lux-rib operon, we constructed a fosmid library of genomic DNA from a representative merodiploid strain, lnuch.13.1. Sequence analysis of fosmid clones and genomic analysis of lnuch.13.1 defined two complete, physically separate, and apparently functional operons, designated lux-rib 1 and lux-rib 2. P. leiognathi strains lelon.2.1 and lnuch.21.1 were also found to carry lux-rib 1 and lux-rib 2, whereas ATCC 25521T apparently carries only lux-rib 1. In lnuch.13.1, lelon.2.1, lnuch.21.1, and ATCC 25521T, lux-rib 1 is flanked upstream by lumQ and putA and downstream by a gene for a hypothetical multidrug efflux pump. In contrast, transposase genes flank lux-rib 2 of lnuch.13.1, and the chromosomal location of lux-rib 2 apparently differs in lnuch.13.1, lelon.2.1, and lnuch.21.1. Phylogenetic analysis demonstrated that lux-rib 1 and lux-rib 2 are more closely related to each other than either one is to the lux and rib genes of other bacterial species, which rules out interspecies lateral gene transfer as the origin of lux-rib 2 in P. leiognathi; lux-rib 2 apparently arose within a previously unsampled or extinct P. leiognathi lineage. Analysis of 170 additional strains of P. leiognathi, for a total of 174 strains examined from coastal waters of Japan, Taiwan, the Philippine Islands, and Thailand, identified 106 strains that carry only a single lux-rib operon and 68 that carry multiple lux-rib operons. Strains bearing a single lux-rib operon were obtained throughout the geographic sampling range, whereas lux-rib merodiploid strains were found only in coastal waters of central Honshu. This is the first report of merodiploidy of lux or rib genes in a luminous bacterium and the first indication that a natural merodiploid state in bacteria can correlate with geography.

scholarly journals Sequencing, Cloning, and High-Level Expression of the pfp Gene, Encoding a PPi-Dependent Phosphofructokinase from the Extremely Thermophilic EubacteriumDictyoglomus thermophilum

2000 ◽  
Vol 182 (16) ◽  
pp. 4661-4666 ◽  
Author(s):  
Yan-Huai R. Ding ◽  
Ron S. Ronimus ◽  
Hugh W. Morgan
Keyword(s):  
Phylogenetic Analysis ◽  
Cloning And Expression ◽  
High Level Expression ◽  
Gene Encoding ◽  
Thermoproteus Tenax ◽  
High Level ◽  
High Degree ◽  
Dictyoglomus Thermophilum ◽  
Degree Of Similarity

ABSTRACT The sequencing, cloning, and expression of the pfp gene from Dictyoglomus thermophilum, which consists of 1,041 bp and encodes a pyrophosphate-dependent phosphofructokinase, are described. A phylogenetic analysis indicates that the enzyme is closely related to the pyrophosphate-dependent enzyme from Thermoproteus tenax. The recombinant and native enzymes share a high degree of similarity for most properties examined.

scholarly journals Sequence analysis of a rice BAC covering the syntenous barley Rpg1 region

Genome ◽  
1999 ◽  
Vol 42 (6) ◽  
pp. 1071-1076 ◽  
Author(s):  
F Han ◽  
A Kilian ◽  
J P Chen ◽  
D Kudrna ◽  
B Steffenson ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
Rust Resistance ◽  
Artificial Chromosome ◽  
Stem Rust Resistance ◽  
Chromosome 4 ◽  
Stem Rust Resistance Gene ◽  
Gene Encoding ◽  
Rice Sequence ◽  
High Degree ◽  
Degree Of Similarity

In the course of map-based cloning of the barley stem rust resistance gene Rpg1, we identified a rice bacterial artificial chromosome (BAC) containing the Rpg1 flanking markers. Based on the excellent gene order colinearity between barley and rice in this region, we expected that this rice BAC would contain the barley Rpg1 homologue. In order to identify the putative rice homologue, we sequenced ca. 35 kb of the rice BAC at random and then an additional 33 kb of contiguous sequence between the two most closely spaced Rpg1 flanking markers. Sequence analysis revealed a total of 15 putative genes, 5 within the 33-kb contiguous region. A rice Rpg1 homologue was not identified, although a gene encoding a hypothetical polypeptide with similarity to a membrane protein could not be eliminated as a candidate. Surprisingly, four of the genes identified in the 33-kb contiguous rice sequence showed a high degree of similarity with genes on Arabidopsis chromosome 4. The genome regions harboring these genes showed some relatedness, but many rearrangements were also evident. These data suggest that some genes have remained linked even over the long evolutionary separation of Arabidopsis and rice, as has also been reported for mammals and invertebrates.Key words: genes, genome, rice, synteny, sequence.

scholarly journals Complete Genome Sequences of Four Coxsackievirus A16 Strains Isolated from Four Children with Severe Hand, Foot, and Mouth Disease

2017 ◽  
Vol 5 (31) ◽  
Author(s):  
Shao-Jian Xu ◽  
Hong Yang ◽  
Xiang-Jie Yao ◽  
Hai-Long Zhang ◽  
Yan Ren ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Complete Genome ◽  
Foot And Mouth Disease ◽  
Mouth Disease ◽  
The Other ◽  
Vp1 Gene ◽  
Coxsackievirus A16 ◽  
Genome Sequences ◽  
Foot And Mouth

ABSTRACT Here, we report the complete genome sequences of four coxsackievirus A16 strains isolated from four children with severe hand, foot, and mouth disease. Three of them were assigned to subgenotype B1b based on phylogenetic analysis of the VP1 gene, and the other one belonged to subgenotype B1a.

scholarly journals Evolution of an Eleusine-Specific Subgroup of Pyricularia oryzae Through a Gain of an Avirulence Gene

2020 ◽  
Vol 33 (2) ◽  
pp. 153-165
Author(s):  
Soichiro Asuke ◽  
Masaki Tanaka ◽  
Gang-Su Hyon ◽  
Yoshihiro Inoue ◽  
Trinh Thi Phuong Vy ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Finger Millet ◽  
Phylogenetic Analyses ◽  
Pyricularia Oryzae ◽  
The Other ◽  
Avirulence Gene ◽  
Whole Genome ◽  
Genome Sequences ◽  
Specific Subgroup ◽  
Dna Fragment

Eleusine isolates (members of the Eleusine pathotype) of Pyricularia oryzae are divided into two subgroups, EC-I and EC-II, differentiated by molecular markers. A multilocus phylogenetic analysis revealed that these subgroups are very close to Eragrostis isolates. EC-II and Eragrostis isolates were exclusively virulent on finger millet and weeping lovegrass, respectively, while EC-I isolates were virulent on both. The avirulence of EC-II on weeping lovegrass was conditioned by an avirulence gene, PWL1. All EC-II isolates shared a peculiar structure (P structure) that was considered to be produced by an insertion (or translocation) of a DNA fragment carrying PWL1. On the other hand, all EC-I and Eragrostis isolates were noncarriers of PWL1 and shared a gene structure that should have predated the insertion of the PWL1-containing fragment. These results, together with phylogenetic analyses using whole-genome sequences, suggest that the Eleusine-specific subgroup (EC-II) evolved through a loss of pathogenicity on weeping lovegrass caused by a gain of PWL1.

scholarly journals Evolutionary and genomic analysis of four SARS-CoV-2 isolates circulating in March 2020 in Sri Lanka; Additional evidence on multiple introduction and further transmission

2021 ◽  
Vol 149 ◽  
Author(s):  
Dilan Amila Satharasinghe ◽  
Parakatawella Mudiyanselage Shalini Daupadi Kumari Parakatawella ◽  
Jayasekara Mudiyanselage Krishanthi Jayarukshi Kumari Premarathne ◽  
L. J. P. Anura P. Jayasooriya ◽  
Gamika A. Prathapasinghe ◽  
...  
Keyword(s):  
Sri Lanka ◽  
Disease Transmission ◽  
Genomic Analysis ◽  
Virus Evolution ◽  
Control Measures ◽  
The Other ◽  
Whole Genome ◽  
Genome Sequences ◽  
Main Cluster ◽  
Multiple Introduction

Abstract The molecular epidemiology of the virus and mapping helps understand the epidemics' evolution and apply quick control measures. This study provides genomic evidence of multiple severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) introductions into Sri Lanka and virus evolution during circulation. Whole-genome sequences of four SARS-CoV-2 strains obtained from coronavirus disease 2019 (COVID-19) positive patients reported in Sri Lanka during March 2020 were compared with sequences from Europe, Asia, Africa, Australia and North America. The phylogenetic analysis revealed that the sequence of the sample of the first local patient collected on 10 March, who contacted tourists from Italy, was clustered with SARS-CoV-2 strains collected from Italy, Germany, France and Mexico. Subsequently, the sequence of the isolate obtained on 19 March also clustered in the same group with the samples collected in March and April from Belgium, France, India and South Africa. The other two strains of SARS-CoV-2 were segregated from the main cluster, and the sample collected from 16 March clustered with England and the sample collected on 30 March showed the highest genetic divergence to the isolate of Wuhan, China. Here we report the first molecular epidemiological study conducted on circulating SARS-CoV-2 in Sri Lanka. The finding provides the robustness of molecular epidemiological tools and their application in tracing possible exposure in disease transmission during the pandemic.

scholarly journals Complete Genome Sequences of Two Porcine Deltacoronavirus Strains from Henan Province, China

2019 ◽  
Vol 8 (10) ◽  
Author(s):  
Qingqing Liang ◽  
Bingxiao Li ◽  
Honglei Zhang ◽  
Hui Hu
Keyword(s):  
Sequence Analysis ◽  
Complete Genome ◽  
Genomic Sequence ◽  
Henan Province ◽  
Full Length ◽  
The Other ◽  
Genome Sequences ◽  
Fecal Samples ◽  
Genomic Sequence Analysis

In 2016 and 2018, two porcine deltacoronavirus (PDCoV) strains, CH-01 and HNZK-02, were identified from fecal samples of piglets with diarrhea in Henan Province, China. The full-length genomic sequence analysis indicated that these two strains had high nucleotide identities with the other Chinese PDCoV epidemic strains.

scholarly journals Identifying Overlapping Phylogenetic and Geographic Roots of HIV – 1 Evolution through Computational Analyses

2013 ◽  
Vol 7 ◽  
pp. 23-29
Author(s):  
Pankaj Kumar Singh ◽  
Rahul Banik ◽  
Hirak Jyoti Chakraborty ◽  
Sasti Gopal Das ◽  
Sayak Ganguli ◽  
...  
Keyword(s):  
Deficiency Syndrome ◽  
High Rate ◽  
Genome Sequences ◽  
Human Immuno Deficiency Virus ◽  
The Difference ◽  
Phylogenetic Lineages ◽  
Computational Analyses ◽  
High Degree ◽  
Parameter Values ◽  
Hiv 1

HIV-1 or Human Immuno Deficiency Virus-1 is the main causative agent of Acquired Immuno Deficiency Syndrome (AIDS). Human host infected with HIV - 1 extensively harbours many viral variants but very little is known about the difference in pattern[17] of evolution of phylogenetic lineages of HIV-1 non recombinant, normal inter subtype recombinant and main two specific recombinant forms of HIV-1 i.e., Circulating Recombinant Forms (CRFs) and Unique Recombinant Forms (URFs). This study is mainly concerned with study of the difference in evolutionary lineages of non-recombinant and recombinant sequences of HIV-1 genome sequences and identification of geographically rich areas which has reported high degree of HIV-1 occurrence and variety. Total 1550 HIV-1 genome sequences were obtained from HIV Los Alamos Database. The sequences were aligned using MAFFT (Multiple Alignment using Fast Fourier Transform) web server tool. Alignment was carried out using 10 different set of alignment parameter values. After alignment the aligned file was used for constructing N-J phylogenetic tree using Clustal X2 tool. Phylogenetic analysis was performed keeping in mind the category to which the sequence belongs. Upon analysis it was observed that the clade containing the probable ancestor belongs remained constant in all cases of different alignment values. Non recombinant isolates, inter subtype recombinants, CRFs, URFs all followed different patterns of evolution. Non recombinant sequences were found geographically specific and subtype specific to some extent whereas, normal recombinants were subtype specific and less geographically specific. CRFs showed variation among the pattern of their evolution. At some instances the sequences occurred as sister taxa of non-recombinant or normal inter subtype recombinant sequences, while at some instances as sister taxa of other CRFs where they were geographically specific. Three CRFs existed as completely diverged sequences. URFs were four in number; two of them were Indian isolates of while other two were Japanese isolates. URFs were found to be totally geographically specific. Geography wise high rate of variation was observed in India and Japan as these two countries had sequences belonging to all of the above categories. Cameroon and South Africa have very large number isolates and a considerable amount of genetic variation among isolates but they lack URFs.

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