Comparative analysis of codon usage patterns of FUT2 from different species

Enterotoxigenic E. coli is an important zoonotic pathogen causing diarrhea in human and newborn animals. α - (1,2) fucosyltransferase 2 (FUT2) is closely associated with the formation of pathogenic receptors of Enterotoxigenic E. coli. Codon usage bias analysis can help to better understand the molecular mechanisms and evolutionary relationships of a particular gene. In order to understand the codon usage pattern of FUT2 gene, FUT2 gene coding sequences of nine species were selected from GenBank database for calculating the nucleotide composition (GC content) and genetic indices including effective number of codons, relative synonymous codon usage and relative codon usage bias using R software, in order to analyze codon usage bias and base composition in FUT2 gene from different species. The results showed that the codon usage of FUT2 gene in different species was affected by GC bias, especially GC frequency at the third position of codon (GC3). Most of the optimal codons were biased towards the G/C-ending types. GCC, CUG, UCC, GUG and AUC showed the highest relative synonymous codon usage value among different species, belonging to the most dominant codons. The usage characteristic of the codens for FUT2 gene in Sus scrofa was similar to that of Bos taurus; Homo sapiens was similar to Pan troglodytes. Effective number of codons was significantly, negatively correlated with GC3, and the relative higher frequency of optimal codon implied that FUT2 genes from different species had a strong bias in codon usage.

BioKIT: a versatile toolkit for processing and analyzing diverse types of sequence data

Bioinformatic analysis - such as genome assembly quality assessment, alignment summary statistics, relative synonymous codon usage, paired-end aware quality trimming and filtering of sequencing reads, file format conversion, and processing and analysis - is integrated into diverse disciplines in the biological sciences. Several command-line pieces of software have been developed to conduct some of these individual analyses; however, the lack of a unified toolkit that conducts all these analyses can be a barrier in workflows. To address this obstacle, we introduce BioKIT, a versatile toolkit for the UNIX shell environment with 40 functions, several of which were community-sourced, that conduct routine and novel processing and analysis of genome assemblies, multiple sequence alignments, coding sequences, sequencing data, and more. To demonstrate the utility of BioKIT, we assessed the quality and characteristics of 901 eukaryotic genome assemblies, calculated alignment summary statistics for 10 phylogenomic data matrices, determined relative synonymous codon usage across 171 fungal genomes including those that use alternative genetic codes, and demonstrate that a novel metric, gene-wise relative synonymous codon usage, can accurately estimate gene-wise codon optimization. BioKIT will be helpful in facilitating and streamlining sequence analysis workflows. BioKIT is freely available under the MIT license from GitHub (https://github.com/JLSteenwyk/BioKIT), PyPi (https://pypi.org/project/biokit), and the Anaconda Cloud (https://anaconda.org/JLSteenwyk/biokit). Documentation, user tutorials, and instructions for requesting new features are available online (https://jlsteenwyk.com/BioKIT).

Identification Sus scrofa and Mus musculus as potential hosts of SARS-CoV-2 via phylogenetic and homologous recombination analysis

Background: Previously, most studies focus on the wild animal being sold in the Wuhan Huanan seafood wholesale market, neglecting that the livestock living around other place could also be the original hosts. Methods: First, relative synonymous codon usage was utilized to analyze the potential hosts of SARS-CoV-2; Then cluster SARS-CoV-2 and related coronavirus through the phylogenetic tree. Next, we used Recombination Detection Program to identify the possible recombination region, as well as verifying via Simplot. Results: Related coronavirus from porcine or murine sources may faciliatate the evolution and reorganization of SARS-CoV-2. Conclusions: Overall, to our knowledge, this is the first paper to illustrate that swine and mice could be probable reservoirs for the SARS-CoV-2.

Identification Sus scrofa and Mus musculus as potential hosts of SARS-CoV-2 via phylogenetic and homologous recombination analysis

Background: Wuhan Huanan seafood wholesale market is highly suspected as the original place for the outbreak of SARS-CoV-2 previously. Most studies focus on the livestock being sold in the market, neglecting that the livestock living around the city of Wuhan could also be the original hosts. Methods: First, relative synonymous codon usage was utilized to analyze the potential hosts of SARS-CoV-2; Then cluster SARS-CoV-2 and related coronavirus through the phylogenetic tree. Next, we used Recombination Detection Program to identify the possible recombination region, as well as verifying via Simplot. Results: Related coronavirus from porcine or murine sources may faciliatate the evolution and reorganization of SARS-CoV-2. Conclusions: Overall, to our knowledge, this is the first paper to illustrate that swine and mice could be probable reservoirs for the SARS-CoV-2.

Comparative Analysis of Codon Usage and tRNA in Mitochondrial Genomes of Gallus Gallus

Codon usage in mitochondrial genes of 11 Gallus gallus and two Anatidae species was analysed to determine the general patterns in codon choice of Callus gallus species. C3 contents were higher in Gallus gallus than in mammalian mitochondrial genomes that encode protein codon positions. The high C3 contents of Callus gallus might be the result of relatively strong mutational bias that occurred in the lineage of the Callus gallus species. A and C ending codons were detected as the “preferred 77 codons in Callus gallus and Anatidae. The NNR codon families are dominated by the A-ending codons, the NNY codon families are dominated by the C-ending codons and the NNN codon families are dominated by the A-ending or the C-ending codons. A comparison of the relative synonymous codon usage (RSCU) and synonymous codon families (SCF) of tRNA and proteins was made, and two groups can be classified by SCF. The codon usage in Callus gallus species indicates that codons containing A or C at the third position are used preferentially, regardless of whether corresponding tRNAs are encoded in the mtDNA. In both Callus gallus and Anatidae species mtDNA, codon usage biases are highly related to CC-ending binucleotide condons.

Differentiation of Campylobacter Populations as Demonstrated by Flagellin Short Variable Region Sequences

ABSTRACT The DNA sequence of the flaA short variable region (SVR) was used to analyze a random population of Campylobacter isolates to investigate the weakly clonal population structure of members of the genus. The SVR sequence from 197 strains of C. jejuni and C. coli isolated from humans, bovine, swine, and chickens identified a group of 43 strains containing disparate short variable region sequences compared to the rest of the population. This group contains both C. jejuni and C. coli strains but disproportionately consisted of bovine isolates. Relative synonymous codon usage analysis of the sequences identified two groups: one group typified C. jejuni, and the second group was characteristic for C. coli and the disparate alleles were not clustered. The data show that there is significant differentiation of Campylobacter populations according to the source of the isolate even without considering the disparate isolates. Even though there is significant differentiation of chicken and bovine isolates, the bovine isolates did not show any difference in ability to colonize chickens. It is possible that disparate sequences were obtained through the lateral transfer of DNA from Campylobacter species other than C. jejuni and C. coli. It is evident that recombination within the flaA SVR occurs rapidly. However, the rate of migration between populations appears to limit the distribution of sequences and results in a weakly clonal population structure.

EVOLUTION OF RELATIVE SYNONYMOUS CODON USAGE IN HUMAN IMMUNODEFICIENCY VIRUS TYPE-1

Mutation in Human Immunodeficiency Virus type-1 (HIV-1) is extremely rapid, a consequence of a low-fidelity viral reverse transcription process. The envelope gene has been shown to accumulate substitutions at a rate of approximately 1% per year and can frequently spend a long time in the host (approximately 10 years). The relative synonymous codon usage (RSCU) in HIV-1 is known to be different from that of the human host. However, by reengineering the protein coding sequences of HIV-1 to reflect the RSCU patterns observed in humans, a large increase in protein expression is observed. It is reasonable to suggest that within a host there may be a selective drive for change in the RSCU of HIV-1 towards human RSCU.To test this hypothesis we analyzed HIV-1 partial envelope sequences from eight patients sampled serially in time. For each sequence, an RSCU table was constructed. Sequences were labelled as "early" or "late" depending on whether they were sampled before or after the mid-point of the study. Using the RSCU values as descriptor variables, a Principal Components Analysis (PCA) was performed. The first three components clearly discriminated between early and late sequences. We also constructed pooled groupwise RSCU tables for early and late sequences. The viral RSCU values of each of the groups were correlated with human RSCU. If there is selection for host-adaptation in RSCU, we expect that "late" viral RSCUs would tend to be more highly correlated with human RSCU than "early" viral RSCUs. In fact, tests of significance suggest that this is the case. However, closer examination of the data revealed that the apparent trend towards human RSCU can be attributed to the homogenization of the codon usage by mutation pressure rather than host adaptation.