Analysis of codon usage pattern of mitochondrial protein-coding genes in different hookworms

Identification and analysis of putative tRNA genes in baculovirus genomes

Transfer RNAs (tRNAs) genes are both coded for and arranged along some viral genomes representing the entire virosphere and seem to play different biological functions during infection, other than transferring the correct amino acid to a growing peptide chain. Baculovirus genome description and annotation has focused mostly on protein-coding genes, microRNA, and homologous regions. Here we carried out a large-scale in silico search for putative tRNA genes in baculovirus genomes. Ninety-six of 257 baculovirus genomes analyzed was found to contain at least one putative tRNA gene. We found great diversity in primary and secondary structure, in location within the genome, in intron presence and size, and in anti-codon identity. In some cases, genes of tRNA-containing genomes were found to have a bias for the codons specified by the tRNAs present in such genomes. Moreover, analysis revealed that most of the putative tRNA genes possessed conserved motifs for tRNA type 2 promoters, including the A-box and B-box motifs with few mismatches from the eukaryotic canonical motifs. From publicly available small RNA deep sequencing datasets of baculovirus-infected insect cells, we found evidence that a putative Autographa californica multiple nucleopolyhedrovirus Gln-tRNA gene was transcribed and modified with the addition of the non-templated 3'-CCA tail found at the end of all tRNAs. Further research is needed to determine the expression and functionality of these viral tRNAs.

Influencing elements of codon usage bias in Birnaviridae and its evolutionary analysis

Birnaviridae is a family of double stranded (ds) RNA virus with non-enveloped virions and 2-segmented genomes. These viruses are known to cause diseases in many hosts. Virus of this family has affected the fish and poultry economy in a wide sector. Unevenness in the use of synonymous codons for a particular amino acid in the coding strand of DNA is known as codon usage bias (CUB). Codons that code the same amino acid are used with variable frequency in a variety of life forms. To understand the pattern of CUB in Birnaviridae, we carried out bioinformatics study to understand the properties of coding sequences of proteins. ENC value of Birnaviridae suggested low CUB. Nucleotide analysis revealed high GC content. Parameters such as RSCU values, nucleotide skewness, translational selection, parity plot and neutrality plot were studied to investigate the pattern of codon use and it was clear that both mutational pressure and natural selection contributed to the designing of CUB in Birnaviridae family. The neutrality plot revealed natural selection to dominate the structuring of CUB and hence remained the major CUB determinant in Birnaviridae. Outcome of our study exemplified the pattern of codon use in the Birnaviridae genomes and contributed the basic primary data for fundamental evolutionary research on them.

Analysis of codon usage of Horseshoe Bat Hepatitis B virus and its host

In the present analysis, codon usage strategies and base distribution of Horseshoe bat hepatitis B virus (HBHBV) were analyzed and compared with its host Rhinolophus sinicus, as no work was yet reported. The magnitude of synonymous codon usage bias (CUB) in the virus and its host was low with higher proportion of the base C. Notably, 21 more frequently used codons, 19 less frequently used codons and 3 underrepresented codons (TCG, ACG and GCG) were found to be similar in both virus and its host coding sequences. Neutrality plot analysis reported greater role of natural selection in HBHBV (67.84%) and R. sinicus (76.90%) over mutation pressure. Base skewness and protein properties also influenced the CUB of genes. Further, codon usage analysis depicted, HBHBV and R. sinicus had many similarities in codon usage patterns that might reflect viral adaptation to its host.

Composition, codon usage pattern, protein properties, and influencing factors in the genomes of members of the family Anelloviridae

The present study was carried out on 62 genome sequences of members of the family Anelloviridae, as there have been no reports of genome analysis of these DNA viruses using a bioinformatics approach. The genes were found to be rich in AC content with low codon usage bias (CUB). Relative synonymous codon usage (RSCU) values identified the preferred codons for each amino acid in the family. The codon AGA was overrepresented, while the codons TCG, TTG, CGG, CGT, ACG, GCG and GAT were underrepresented in all of the genomes. A significant correlation was found between the effective number of codons (ENC) and base constraints, indicating that compositional properties might have influenced the CUB. A highly significant correlation was observed between the overall base content and the base content at the third codon position, indicating that mutations might have affected the CUB. A highly significant positive correlation was observed between GC12 and GC3 (r = 0.904, p < 0.01), which indicated that directional mutation pressure influenced all three codon positions. A neutrality plot revealed that the contribution of mutation and natural selection in determining the CUB was 58.6% and 41.4%, respectively.

Genome-wide analysis of codon usage pattern in herpesviruses and its relation to evolution

The preferential use of a specific codon, out of a group of synonymous codons encoding the same amino acid, in a gene transcript results from the bias in codon choice. Various evolutionary forces namely mutation pressure and natural selection influence the pattern of codon usage i.e. distinct for each gene/genome. We investigated the pattern of codon usage of eight human herpesvirus genomes and compared them with two other herpesvirus genomes namely murine herpesvirus 68 and bovine herpesvirus type 1.1 to elucidate its compositional features, pattern of codon usage across the genomes and report the differences of codon usage pattern of human herpesviruses from that of other two other viruses. We also identified the similarity of the codon usage of human herpesviruses with its host (human). The genes were found to be CG rich in HHV2, HHV3, HHV4, HHV6, HHV7 and BH genomes while TA rich in HHV1, HHV5, HHV8 and MH genomes. The codon usage bias (CUB) of genes was low. A highly significant correlation was found among compositional contents depicting the role of mutational pressure along with natural selection in framing CUB. Several more frequently used codons as well as less frequently used codons were identified to be similar between each human virus and its host (human), while murine herpesvirus 68 and bovine herpesvirus type 1.1 genomes did not possess similar adaptation strategy as human herpesviruses to human (host), thus we could conclude that viral CUB might have been shaped as per their host's nature for better surveillance. Neutrality plot revealed mutational pressure mostly influenced the CUB of HHV1, HHV8 and MH viruses, while natural selection had a major impact in the CUB of HHV2, HHV3, HHV4, HHV5, HHV6, HHV7 and BH genomes.

Codon usage pattern and evolutionary forces of mitochondrial ND genes among orders of class Amphibia

In this study, we used a bioinformatics approach to analyze the nucleotide composition and pattern of synonymous codon usage in mitochondrial ND genes in three amphibian groups, that is, orders Anura, Caudata, and Gymnophiona to identify the commonality and the differences of codon usage as no research work was reported yet. The high value of the effective number of codons revealed that the codon usage bias (CUB) was low in mitochondrial ND genes among the orders. Nucleotide composition analysis suggested that for each gene, the compositional features differed among Anura, Caudata, and Gymnophiona and the GC content was lower than AT content. Furthermore, a highly significant difference (p < .05) for GC content was found in each gene among the orders. The heat map showed contrasting patterns of codon usage among different ND genes. The regression of GC12 on GC3 suggested a narrow range of GC3 distribution and some points were located in the diagonal, indicating both mutation pressure and natural selection might influence the CUB. Moreover, the slope of the regression line was less than 0.5 in all ND genes among orders, indicating natural selection might have played the dominant role whereas mutation pressure had played a minor role in shaping CUB of ND genes across orders.

Allele frequency analysis of GALC gene causing Krabbe disease in human and its codon usage

Krabbe disease is one of the rarest autosomal recessive disorders in human, caused by mutation in the GALC (β-galactosylceramidase) gene, resulting in several mental and physical health issues. Due to its rarity and phenotypic heterogeneity, diagnosis rate of this disease is very low. This study generated information on the recessive allele frequency dynamics of GALC gene across 15 global populations, with the highest frequency detected in Druze (Israel) population and the lowest frequency in Turkey and the United States. The recessive allele would take more time period (about 24,975 years) to be completely removed from the population having the lowest frequency and vice versa. The codon usage patterns of four isoforms of GALC gene revealed that a few synonymous codons were used more frequently than others in the isoforms. The codon AGA (arginine) was found to be overrepresented in GALC gene, except for galactocerebrosidase isoform a precursor. Further, GALC gene showed low codon usage bias (CUB) as evident from high ENC values (55.7-58.2), with A/T ending codons more preferred to G/C ending codons. CUB analysis elucidated the dual role of mutational pressure (major role) and natural selection (minor role) in GALC gene evolution.

Codon usage pattern and its influencing factors in different genomes of hepadnaviruses

Codon usage bias (CUB) arises from the preference for a codon over codons for the same amino acid. The major factors contributing to CUB are evolutionary forces, compositional properties, gene expression, and protein properties. The present analysis was performed to investigate the compositional properties and the extent of CUB across the genomes of members of the family Hepadnaviridae, as previously no work using bioinformatic tools has been reported. The viral genes were found to be AT rich with low CUB. Analysis of relative synonymous codon usage (RSCU) was used to identify overrepresented and underrepresented codons for each amino acid. Correlation analysis of overall nucleotide composition and its composition at the third codon position suggested that mutation pressure might influence the CUB. A highly significant correlation was observed between GC12 and GC3 (r = 0.910, p < 0.01), indicating that directional mutation affected all three codon positions across the genome. Translational selection (P2) and mutational responsive index (MRI) values of genes suggested that mutation plays a more important role than translational selection in members of the family Hepadnaviridae.

Analysis of codon usage patterns and influencing factors in Nipah virus

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Nipah virus (NiV) genes are AT-rich.

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Codon usage bias of NiV genes is low.

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Patterns of codon usage bias differ across the genomes of NiV.

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Both mutation pressure and natural selection influenced codon usage bias of NiV genes.

Codon usage bias (CUB) is the unequal usage of synonymous codons of an amino acid in which some codons are used more often than others and is widely used in understanding molecular biology, genetics, and functional regulation of gene expression. Nipah virus (NiV) is an emerging zoonotic paramyxovirus that causes fatal disease in both humans and animals. NiV was first identified during an outbreak of a disease in Malaysia in 1998 and then occurred periodically since 2001 in India, Bangladesh, and the Philippines. We used bioinformatics tools to analyze the codon usage patterns in a genome-wide manner among 11 genomes of NiV as no work was reported yet. The compositional properties revealed that the overall GC and AT contents were 41.96 and 58.04%, respectively i.e. Nipah virus genes were AT-rich. Correlation analysis between overall nucleotide composition and its 3^rd codon position suggested that both mutation pressure and natural selection might influence the CUB across Nipah genomes. Neutrality plot revealed natural selection might have played a major role while mutation pressure had a minor role in shaping the codon usage bias in NiV genomes.