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 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 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 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 Evaluation of Genetic Relationship between Trigonella-Melilotus complex Using CCMP Markers

2013 ◽  
Vol 23 (1) ◽  
Author(s):  
Amandeep Hora ◽  
C.P. Malik
Keyword(s):  
Genetic Variation ◽  
Genetic Correlation ◽  
Dna Fingerprinting ◽  
Gene Mutation ◽  
Genetic Relationship ◽  
Plant Tissue ◽  
Microsatellite Primers ◽  
Chloroplast Microsatellite ◽  
Chromosomal Alterations

To distinguish the taxa at the specific and varietal levels a range of DNA fingerprinting techniques are being employed. The objective of the current study was to establish the genetic correlation between the Trigonella-Melilotus complex i.e. M. indica, M. alba and Trigonella polyceratia using ten Consensus Chloroplast Microsatellite Primers (CCMPs). The polymorphism between the two genera indicated that they are intimately related and symbolize novel incongruity. Owing to less significant level of genetic variation, detected through CCMP, the differences between the two genera could be accredited to gene mutation or inconsequential chromosomal alterations. Plant Tissue Cult. & Biotech. 23(1): 59-66, 2013 (June)

scholarly journals Genome Sequences of Two NDM-1 Metallo-β-Lactamase-Producing Multidrug-Resistant Strains of Klebsiella pneumoniae with a High Degree of Similarity, One of Which Contains Prophage

2017 ◽  
Vol 5 (42) ◽  
Author(s):  
Nikolay V. Volozhantsev ◽  
Angelina A. Kislichkina ◽  
Anastasia I. Lev ◽  
Tatiana N. Mukhina ◽  
Alexander A. Bogun ◽  
...  
Keyword(s):  
Klebsiella Pneumoniae ◽  
Multidrug Resistant ◽  
Sequence Type ◽  
Genome Sequences ◽  
Content Type ◽  
Resistant Strains ◽  
High Degree ◽  
Degree Of Similarity

ABSTRACT We report genome sequences of two NDM-1 metallo-β-lactamase-producing multidrug-resistant Klebsiella pneumoniae isolates of sequence type 147 (ST147) from one hospital. The genomes are highly similar and differ in prophage located in the chromosome of K. pneumoniae KPB-1470/16 and in the additional plasmid-carrying bla OXA-48 gene in K. pneumoniae KPB-417/16.

scholarly journals Complete Chloroplast Genome of Japanese Larch (Larix kaempferi): Insights into Intraspecific Variation with an Isolated Northern Limit Population

Forests ◽  
2020 ◽  
Vol 11 (8) ◽  
pp. 884
Author(s):  
Shufen Chen ◽  
Wataru Ishizuka ◽  
Toshihiko Hara ◽  
Susumu Goto
Keyword(s):  
Chloroplast Genome ◽  
Intraspecific Variation ◽  
Japanese Larch ◽  
Monophyletic Group ◽  
Phylogenetic Position ◽  
Larix Kaempferi ◽  
Northern Limit ◽  
Complete Chloroplast Genome ◽  
Intraspecific Variations ◽  
Cpdna Markers

Research Highlights: The complete chloroplast genome for eight individuals of Japanese larch, including from the isolated population at the northern limit of the range (Manokami larch), revealed that Japanese larch forms a monophyletic group, within which Manokami larch can be phylogenetically placed in Japanese larch. We detected intraspecific variation for possible candidate cpDNA markers in Japanese larch. Background and Objectives: The natural distribution of Japanese larch is limited to the mountainous range in the central part of Honshu Island, Japan, with an isolated northern limit population (Manokami larch). In this study, we determined the phylogenetic position of Manokami larch within Japanese larch, characterized the chloroplast genome of Japanese larch, detected intraspecific variation, and determined candidate cpDNA markers. Materials and Methods: The complete genome sequence was determined for eight individuals, including Manokami larch, in this study. The genetic position of the northern limit population was evaluated using phylogenetic analysis. The chloroplast genome of Japanese larch was characterized by comparison with eight individuals. Furthermore, intraspecific variations were extracted to find candidate cpDNA markers. Results: The phylogenetic tree showed that Japanese larch forms a monophyletic group, within which Manokami larch can be phylogenetically placed, based on the complete chloroplast genome, with a bootstrap value of 100%. The value of nucleotide diversity (π) was calculated at 0.00004, based on SNP sites for Japanese larch, suggesting that sequences had low variation. However, we found three hyper-polymorphic regions within the cpDNA. Finally, we detected 31 intraspecific variations, including 19 single nucleotide polymorphisms, 8 simple sequence repeats, and 4 insertions or deletions. Conclusions: Using a distant genotype in a northern limit population (Manokami larch), we detected sufficient intraspecific variation for the possible candidates of cpDNA markers in Japanese larch.

The complete chloroplast genome sequences of five Miscanthus species, and comparative analyses with other grass plastomes

2021 ◽  
Vol 162 ◽  
pp. 113248
Author(s):  
Jiajing Sheng ◽  
Mi Yan ◽  
Jia Wang ◽  
Lingling Zhao ◽  
Fasong Zhou ◽  
...  
Keyword(s):  
Chloroplast Genome ◽  
Genome Sequences ◽  
Complete Chloroplast Genome ◽  
Comparative Analyses

scholarly journals Extensive Phylogenetic Analysis of Piscine Orthoreovirus Genomic Sequences Shows the Robustness of Subgenotype Classification

Pathogens ◽  
2021 ◽  
Vol 10 (1) ◽  
pp. 41
Author(s):  
Marcos Godoy ◽  
Daniel A. Medina ◽  
Rudy Suarez ◽  
Sandro Valenzuela ◽  
Jaime Romero ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Genetic Variation ◽  
Sequence Analysis ◽  
Molecular Phylogeny ◽  
Phylogenetic Trees ◽  
Genomic Segment ◽  
Double Stranded Rna ◽  
The Family ◽  
Original Classification

Piscine orthoreovirus (PRV) belongs to the family Reoviridae and has been described mainly in association with salmonid infections. The genome of PRV consists of about 23,600 bp, with 10 segments of double-stranded RNA, classified as small (S1 to S4), medium (M1, M2 and M3) and large (L1, L2 and L3); these range approximately from 1000 bp (segment S4) to 4000 bp (segment L1). How the genetic variation among PRV strains affects the virulence for salmonids is still poorly understood. The aim of this study was to describe the molecular phylogeny of PRV based on an extensive sequence analysis of the S1 and M2 segments of PRV available in the GenBank database to date (May 2020). The analysis was extended to include new PRV sequences for S1 and M2 segments. In addition, subgenotype classifications were assigned to previously published unclassified sequences. It was concluded that the phylogenetic trees are consistent with the original classification using the PRV genomic segment S1, which differentiates PRV into two major genotypes, I and II, and each of these into two subgenotypes, designated as Ia and Ib, and IIa and IIb, respectively. Moreover, some clusters of country- and host-specific PRV subgenotypes were observed in the subset of sequences used. This work strengthens the subgenotype classification of PRV based on the S1 segment and can be used to enhance research on the virulence of PRV.

Sign in / Sign up

Export Citation Format

Share Document