Synonymous Codon Usage Analysis of Thirty Two Mycobacteriophage Genomes

Synonymous codon usage of protein coding genes of thirty two completely sequenced mycobacteriophage genomes was studied using multivariate statistical analysis. One of the major factors influencing codon usage is identified to be compositional bias. Codons ending with either C or G are preferred in highly expressed genes among which C ending codons are highly preferred over G ending codons. A strong negative correlation between effective number of codons (Nc) and GC3s content was also observed, showing that the codon usage was effected by gene nucleotide composition. Translational selection is also identified to play a role in shaping the codon usage operative at the level of translational accuracy. High level of heterogeneity is seen among and between the genomes. Length of genes is also identified to influence the codon usage in 11 out of 32 phage genomes. Mycobacteriophage Cooper is identified to be the highly biased genome with better translation efficiency comparing well with the host specific tRNA genes

Synonymous Codon Usage Analysis of Thirty Two Mycobacteriophage Genomes

Synonymous codon usage of protein coding genes of thirty two completely sequenced mycobacteriophage genomes was studied using multivariate statistical analysis. One of the major factors influencing codon usage is identified to be compositional bias. Codons ending with either C or G are preferred in highly expressed genes among which C ending codons are highly preferred over G ending codons. A strong negative correlation between effective number of codons (Nc) and GC3s content was also observed, showing that the codon usage was effected by gene nucleotide composition. Translational selection is also identified to play a role in shaping the codon usage operative at the level of translational accuracy. High level of heterogeneity is seen among and between the genomes. Length of genes is also identified to influence the codon usage in 11 out of 32 phage genomes. Mycobacteriophage Cooper is identified to be the highly biased genome with better translation efficiency comparing well with the host specific tRNA genes

Adenoviruses and Their Diversity in Poultry

An investigation into the aetiology of fowl adenovirus strains and their distribution worldwide in populations of poultry flocks industry has been conducted. Pathogenic role of the viruses is not always clear. They can cause latent infection or several diseases and are the reason of economic losses in poultry flock industry. Ubiquity of adenovirus strains was commonly described, and stand-alone pathogenicity for a long time has been disputed. A globally emerging trend of adenoviruses and adenovirus-associated diseases has been increasing from year to year in all over the world. Mainly, type FAdV-4 is responsible for hydropericardium hepatitis syndrome (HP), type FAdV-1 for gizzard erosion and ulceration (GEU), and types FAdV-2, 8a, 8b, and 11 seem to be responsible for inclusion body hepatitis (IBH). Defining the spreading of the avian adenovirus strains in different types of fowl profile production, recognising their property and determining their types and molecular characterisation are very important from the epidemiological point of view and are considered as excellent basis for vaccine development and gene therapy implementation. This chapter provides a comprehensive review of FAdVs, including their epidemiology, pathogenesis, diagnostic, detection, and molecular characterisation. This comprehensive review is needed to better understand the latest progress in study of the viruses and prospects regarding disease control and implementation of gene therapy

Cluster M Mycobacteriophages Bongo, PegLeg, and Rey with Unusually Large Repertoires of tRNA Isotopes

Genomic analysis of a large set of phages infecting the common hostMycobacterium smegmatis mc2155 shows that they span considerable genetic diversity. There are more than 20 distinct types that lack nucleotide similarity with each other, and there is considerable diversity within most of the groups. Three newly isolated temperate mycobacteriophages, Bongo, PegLeg, and Rey, constitute a new group (cluster M), with the closely related phages Bongo and PegLeg forming subcluster M1 and the more distantly related Rey forming subcluster M2. The cluster M mycobacteriophages have siphoviral morphologies with unusually long tails, are homoimmune, and have larger than average genomes (80.2 to 83.7 kbp). They exhibit a variety of features not previously described in other mycobacteriophages, including noncanonical genome architectures and several unusual sets of conserved repeated sequences suggesting novel regulatory systems for both transcription and translation. In addition to containing transfer-messenger RNA and RtcB-like RNA ligase genes, their genomes encode 21 to 24 tRNA genes encompassing complete or nearly complete sets of isotypes. We predict that these tRNAs are used in late lytic growth, likely compensating for the degradation or inadequacy of host tRNAs. They may represent a complete set of tRNAs necessary for late lytic growth, especially when taken together with the apparent lack of codons in the same late genes that correspond to tRNAs that the genomes of the phages do not obviously encode

Differences in the Protein Evolutionary Rates of Arabidopsis Species and Codon Usage Biases in the Tissues of Drosophila melanogaster

Protein evolution in an organism or population is determined by a host of phenomena that affect the overall rate of change in the genome. Selection is thought to have a decreased effect in self-fertilizing plants due to decreased effective population size. Arabidopsis thaliana transitioned to self-fertilization while its congeners A. lyrata and A. halleri have retained obligatory out-crossing. The rate of protein change, measured as the nonsynonymous to synonymous divergence ratio (dN/dS), showed an increase in evolutionary rate in A. thaliana compared to A. lyrata and A. halleri, likely due to self-fertilization. Preferential codon usage is affected by translational selection, decreasing the rate of synonymous substitution. Preferred codons tend to correspond to the most abundant tRNAs. Codon usage biases differ amongst species and can be different among the tissues of an organism if relative tRNA abundances differ between the different tissues. Previous studies have found that the differences in codon usage biases may also be attributed to GC content and not only to differences in tissue specific protein expression. In the genome of Drosophila melanogaster, I have found that patterns of codon usage are different amongst proteins expressed in different tissues. Using randomized datasets, I show that these differences are always explained by which tissue these genes are expressed in, and are not due to other confounding properties of these proteins, such as GC content, protein length, or protein expression levels