Genome-Wide Relative Analysis of Codon Usage Bias and Codon Context Pattern in the Bacteria Salinibacter Ruber, Chromohalobacter Salexigens and Rhizobium Etli

Farooqi, Mohammad Samir

doi:10.4172/2161-1009.1000257

Cited by 1 publication

(3 citation statements)

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“…It is widely known that synonymous codon usage varies among organisms and that it is related to differences in G+C content, replication strand skew, or gene expression ( Suzuki et al, 2008 ; Farooqi et al, 2016 ). The interaction of these factors may vary among species depending on their evolutionary process ( Ma et al, 2015 ).…”

Section: Resultsmentioning

confidence: 99%

“…It has also been suggested that the extent of codon usage bias plays a role in the adaptation of prokaryotic organisms to their environments and lifestyles ( Botzman and Margalit, 2011 ). To analyze the overall codon usage trends of the Arcobacter species, the frequencies of the different codons were obtained from the whole genomes and the RSCU was computed using the CAI, which is a useful tool for estimating codon usage bias ( Ma et al, 2015 ; Farooqi et al, 2016 ). A first finding was that all the Arcobacter species presented a preferential use of the codons finishing in A or T ( Supplementary Figure S5 ), which might be expected due to their low G+C% content.…”

Section: Resultsmentioning

confidence: 99%

“…A percentage of Average Amino-acid Identity (AAI) ranging from 60 to 80% between the compared genomes of species or strains and a Percentage of Conserved Proteins (POCPs) above 50% has been proposed if they are to belong to the same genus ( Konstantinidis and Tiedje, 2005 ; Qin et al, 2014 ). Finally, the Relative Synonymous Codon Usage (RSCU) has also been used by some authors to infer evolutionary and ecological links among bacterial species ( Ma et al, 2015 ; Farooqi et al, 2016 ).…”

Section: Introductionmentioning

confidence: 99%

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Revisiting the Taxonomy of the Genus Arcobacter: Getting Order From the Chaos

et al. 2018

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Since the description of the genus Arcobacter in 1991, a total of 27 species have been described, although some species have shown 16S rRNA similarities below 95%, which is the cut-off that usually separates species that belong to different genera. The objective of the present study was to reassess the taxonomy of the genus Arcobacter using information derived from the core genome (286 genes), a Multilocus Sequence Analysis (MLSA) with 13 housekeeping genes, as well as different genomic indexes like Average Nucleotide Identity (ANI), in silico DNA–DNA hybridization (isDDH), Average Amino-acid Identity (AAI), Percentage of Conserved Proteins (POCPs), and Relative Synonymous Codon Usage (RSCU). The study included a total of 39 strains that represent all the 27 species included in the genus Arcobacter together with 13 strains that are potentially new species, and the analysis of 57 genomes. The different phylogenetic analyses showed that the Arcobacter species grouped into four clusters. In addition, A. lekithochrous and the candidatus species ‘A. aquaticus’ appeared, as did A. nitrofigilis, the type species of the genus, in separate branches. Furthermore, the genomic indices ANI and isDDH not only confirmed that all the species were well-defined, but also the coherence of the clusters. The AAI and POCP values showed intra-cluster ranges above the respective cut-off values of 60% and 50% described for species belonging to the same genus. Phenotypic analysis showed that certain test combinations could allow the differentiation of the four clusters and the three orphan species established by the phylogenetic and genomic analyses. The origin of the strains showed that each of the clusters embraced species recovered from a common or related environment. The results obtained enable the division of the current genus Arcobacter in at least seven different genera, for which the names Arcobacter, Aliarcobacter gen. nov., Pseudoarcobacter gen. nov., Haloarcobacter gen. nov., Malacobacter gen. nov., Poseidonibacter gen. nov., and Candidate ‘Arcomarinus’ gen. nov. are proposed.

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Section: Resultsmentioning

confidence: 99%