Comparative genomics of a few members of the family Aquificaceae on the basis of their codon usage profile

Gene Reports ◽  
2019 ◽  
Vol 14 ◽  
pp. 54-64 ◽  
Author(s):  
Debadin Bose ◽  
Subhasis Mukhopadhyay
Keyword(s):  
Comparative Genomics ◽  
Codon Usage ◽  
The Family

Comparative genomics: tracking chromosome evolution in the family Ursidae using reciprocal chromosome painting

1998 ◽  
Vol 83 (3-4) ◽  
pp. 182-192 ◽  
Author(s):  
W.G. Nash ◽  
J. Wienberg ◽  
M.A. Ferguson-Smith ◽  
J.C. Menninger ◽  
S.J. O’Brien
Keyword(s):  
Comparative Genomics ◽  
Chromosome Painting ◽  
Chromosome Evolution ◽  
Reciprocal Chromosome Painting ◽  
The Family

scholarly journals Codon Usage in the Iflaviridae Family Is Not Diverse Though the Family Members Are Isolated from Diverse Host Taxa

Viruses ◽  
2019 ◽  
Vol 11 (12) ◽  
pp. 1087 ◽  
Author(s):  
Sheng-Lin Shi ◽  
Run-Xi Xia
Keyword(s):  
Codon Usage ◽  
Codon Usage Bias ◽  
Synonymous Codon ◽  
Nucleotide Composition ◽  
Effective Number ◽  
Bias Analysis ◽  
The Family ◽  
Usage Patterns ◽  
Codon Positions ◽  
Effective Number Of Codons

All iflavirus members belong to the unique genus, Iflavirus, of the family, Iflaviridae. The host taxa and sequence identities of these viruses are diverse. A codon usage bias, maintained by a balance between selection, mutation, and genetic drift, exists in a wide variety of organisms. We characterized the codon usage patterns of 44 iflavirus genomes that were isolated from the classes, Insecta, Arachnida, Mammalia, and Malacostraca. Iflaviruses lack a strong codon usage bias when they are evaluated using an effective number of codons. The odds ratios of the majority of dinucleotides are within the normal range. However, the dinucleotides at the 1st–2nd codon positions are more biased than those at the 2nd–3rd codon positions. Plots of effective numbers of codons, relative neutrality analysis, and PR2 bias analysis all indicate that selection pressure dominates mutations in shaping codon usage patterns in the family, Iflaviridae. When these viruses were grouped into their host taxa, we found that the indices, including the nucleotide composition, effective number of codons, relative synonymous codon usage, and the influencing factors behind the codon usage patterns, all show that there are non-significant differences between the six host-taxa-groups. Our results disagree with our assumption that diverse viruses should possess diverse codon usage patterns, suggesting that the nucleotide composition and codon usage in the family, Iflaviridae, are not host taxa-specific signatures.

scholarly journals A Comparative Genomics, Network-Based Approach to Understanding Virulence in Vibrio cholerae

2009 ◽  
Vol 191 (20) ◽  
pp. 6262-6272 ◽  
Author(s):  
Jianying Gu ◽  
Yufeng Wang ◽  
Timothy Lilburn
Keyword(s):  
Comparative Genomics ◽  
Vibrio Cholerae ◽  
Confidence Score ◽  
Online Data ◽  
The Family ◽  
Associated Proteins ◽  
Core Proteome ◽  
Functional Association Network ◽  
El Tor ◽  
The Relationship

ABSTRACT Our views of the genes that drive phenotypes have generally been built up one locus or operon at a time. However, a given phenotype, such as virulence, is a multilocus phenomenon. To gain a more comprehensive view of the genes and interactions underlying a phenotype, we propose an approach that incorporates information from comparative genomics and network biology and illustrate it by examining the virulence phenotype of Vibrio cholerae O1 El Tor N16961. We assessed the associations among the virulence-associated proteins from Vibrio cholerae and all the other proteins from this bacterium using a functional-association network map. In the context of this map, we were able to identify 262 proteins that are functionally linked to the virulence-associated genes more closely than is typical of the proteins in this strain and 240 proteins that are functionally linked to the virulence-associated proteins with a confidence score greater than 0.9. The roles of these genes were investigated using functional information from online data sources, comparative genomics, and the relationships shown by the protein association map. We also incorporated core proteome data from the family Vibrionaceae; 35% of the virulence-associated proteins have orthologs among the 1,822 orthologous groups of proteins in the core proteome, indicating that they may be dual-role virulence genes or encode functions that have value outside the human host. This approach is a valuable tool in searching for novel functional associations and in investigating the relationship between genotype and phenotype.

scholarly journals Updated phylogeny of Chikungunya virus suggests lineage-specific RNA architecture

2019 ◽  
Author(s):  
Adriano de Bernardi Schneider ◽  
Roman Ochsenreiter ◽  
Reilly Hostager ◽  
Ivo L. Hofacker ◽  
Daniel Janies ◽  
...  
Keyword(s):  
Comparative Genomics ◽  
Chikungunya Virus ◽  
Genetic Data ◽  
Untranslated Regions ◽  
Current Status ◽  
The Public ◽  
Coding Regions ◽  
Evolutionarily Conserved ◽  
The Family ◽  
Duplication Events

AbstractChikungunya virus (CHIKV), a mosquito-borne alphavirus of the family Togaviridae, has recently emerged in the Americas from lineages from two continents, Asia and Africa. Historically, CHIKV circulated as at least four lineages worldwide with both enzootic and epidemic transmission cycles. To understand the recent patterns of emergence and the current status of the CHIKV spread, updated analyses of the viral genetic data and metadata are needed. Here, we performed phylogenetic and comparative genomics screens of CHIKV genomes, taking advantage of the public availability of many recently sequenced isolates. Based on these new data and analyses, we derive a revised phylogeny from nucleotide sequences in coding regions. Using this phylogeny, we uncover the presence of several distinct lineages in Africa that were previously considered a single one. In parallel, we performed thermodynamic modeling of CHIKV untranslated regions (UTRs), which revealed evolutionarily conserved structured and unstructured RNA elements in the 3’UTR. We provide evidence for duplication events in recently emerged American isolates of the Asian CHIKV lineage and propose the existence of a flexible 3’UTR architecture among different CHIKV lineages.

scholarly journals Updated Phylogeny of Chikungunya Virus Suggests Lineage-Specific RNA Architecture

Viruses ◽  
2019 ◽  
Vol 11 (9) ◽  
pp. 798 ◽  
Author(s):  
Adriano de Bernardi Schneider ◽  
Roman Ochsenreiter ◽  
Reilly Hostager ◽  
Ivo L. Hofacker ◽  
Daniel Janies ◽  
...  
Keyword(s):  
Comparative Genomics ◽  
Chikungunya Virus ◽  
Genetic Data ◽  
Untranslated Regions ◽  
Current Status ◽  
The Public ◽  
Coding Regions ◽  
Evolutionarily Conserved ◽  
The Family ◽  
Duplication Events

Chikungunya virus (CHIKV), a mosquito-borne alphavirus of the family Togaviridae, has recently emerged in the Americas from lineages from two continents: Asia and Africa. Historically, CHIKV circulated as at least four lineages worldwide with both enzootic and epidemic transmission cycles. To understand the recent patterns of emergence and the current status of the CHIKV spread, updated analyses of the viral genetic data and metadata are needed. Here, we performed phylogenetic and comparative genomics screens of CHIKV genomes, taking advantage of the public availability of many recently sequenced isolates. Based on these new data and analyses, we derive a revised phylogeny from nucleotide sequences in coding regions. Using this phylogeny, we uncover the presence of several distinct lineages in Africa that were previously considered a single one. In parallel, we performed thermodynamic modeling of CHIKV untranslated regions (UTRs), which revealed evolutionarily conserved structured and unstructured RNA elements in the 3’UTR. We provide evidence for duplication events in recently emerged American isolates of the Asian CHIKV lineage and propose the existence of a flexible 3’UTR architecture among different CHIKV lineages.

scholarly journals A comparative genomics-based study of positive strand RNA viruses emphasizing on SARS-CoV-2 utilizing dinucleotide signature, codon usage and codon context analyses

Gene Reports ◽  
2021 ◽  
Vol 23 ◽  
pp. 101055 ◽  
Author(s):  
Jayanti Saha ◽  
Sukanya Bhattacharjee ◽  
Monalisha Pal Sarkar ◽  
Barnan Kumar Saha ◽  
Hriday Kumar Basak ◽  
...  
Keyword(s):  
Comparative Genomics ◽  
Codon Usage ◽  
Rna Viruses ◽  
Positive Strand ◽  
Codon Context ◽  
Positive Strand Rna
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