Background Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an emerging disease with fatal outcomes. In this study, a fundamental knowledge gap question is to be resolved by evaluating the differences in biological and pathogenic aspects of SARS-CoV-2 and the changes in SARS-CoV-2 in comparison with the two prior major COV epidemics, SARS and Middle East respiratory syndrome (MERS) coronaviruses. Methods The genome composition, nucleotide analysis, codon usage indices, relative synonymous codons usage, and effective number of codons (ENc) were analyzed in the four structural genes; Spike (S), Envelope (E), membrane (M), and Nucleocapsid (N) genes, and two of the most important nonstructural genes comprising RNA-dependent RNA polymerase and main protease (Mpro) of SARS-CoV-2, Beta-CoV from pangolins, bat SARS, MERS, and SARS CoVs. Results SARS-CoV-2 prefers pyrimidine rich codons to purines. Most high-frequency codons were ending with A or T, while the low frequency and rare codons were ending with G or C. SARS-CoV-2 structural proteins showed 5 to 20 lower ENc values, compared with SARS, bat SARS, and MERS CoVs. This implies higher codon bias and higher gene expression efficiency of SARS-CoV-2 structural proteins. SARS-CoV-2 encoded the highest number of over-biased and negatively biased codons. Pangolin Beta-CoV showed little differences with SARS-CoV-2 ENc values, compared with SARS, bat SARS, and MERS CoV. Conclusion Extreme bias and lower ENc values of SARS-CoV-2, especially in Spike, Envelope, and Mpro genes, are suggestive for higher gene expression efficiency, compared with SARS, bat SARS, and MERS CoVs.

https://onlinelibrary.wiley.com/doi/pdf/10.1002/jmv.25754

From SARS and MERS CoVs to SARS-CoV-2: Moving toward more biased codon usage in viral structural and nonstructural genes.

Ethnobotanical study of Kani tribes in Thoduhills of Kerala, South India

Codon usage and codon pair patterns in non-grass monocot genomes.

Codon usage pattern and prediction of gene expression level in Bungarus species.

Enhanced micropropagation protocol of Morinda citrifolia L. through nodal explants

Comparative study of synonymous codon usage variations and factors influencing its diversification in α - cyanobacterial descendant Paulinella chromatophora and β - cyanobacterium Synechococcus elongatus PCC6301 has not been reported so far In the present study, we investigated various factors associated with synonymous codon usage in the genomes of P chromatophora and S elongatus PCC6301 and findings were discussed Mutational pressure was identified as the major force behind codon usage variation in both genomes However, correspondence analysis revealed that intensity of mutational pressure was higher in S elongatus than in P chromatophora Living habitats were also found to determine synonymous codon usage variations across the genomes of P chromatophora and S elongatus Whole genome sequencing of α-cyanobacteria in the cyanobium clade would certainly facilitate the understanding of synonymous codon usage patterns and factors contributing its diversification in presumed ancestors of photosynthetic endosymbionts of P chromatophora

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Mutational pressure dictates synonymous codon usage in freshwater unicellular α - cyanobacterial descendant Paulinella chromatophora and β - cyanobacterium Synechococcus elongatus PCC6301

Morinda reticulata Gamble is a highly endangered medicinal plant of Southern Western Ghats of India. Since conventional propagation methods are not effective, in vitro propagation was attempted for the first time using nodal explants. Year long experiment on responses of apical bud and nodal explants revealed that summer season (March - May ) induced early bud break and faster shoot regeneration than in the other seasons. MS medium supplemented with 6-benzylaminopurine (BAP) and kinetin (KN) were tested at various concentrations ranging from 2.2muM - 46 muM. The maximum response of explants (62.7%) with longest mean shoot length (6.7 cm) was obtained with 4.4 muM BAP. The number of shoots per explant never increased beyond four even at higher levels of cytokinin However, healthy microshoots with uniform shoot development from the nodal segments led to the establishment of a large number of shoots. A combination of 0.12 mM silver nitrate with 22 muM BAP resulted in 4-5 shoots per nodal explant. However, the shoots were smaller with shorter internodes. Shoots regenerated in presence of BAP were converted into plantlets by in vitro rooting using 1-naphthaleneacetic acid (NAA), indole-3-butyric acid (IBA) and BAP. About 80% of the micropropagated plants were acclimatized for field conditions.

/pdf/conservation-and-in-vitro-multiplication-of-highly-q3xvxwd08p.pdf

Conservation and in vitro multiplication of highly endangered Indian traditional medicinal plant (Morinda reticulata Gamble) through nodal explants

Background: Most of the amino acids are encoded by more than one codon, termed as synonymous codons. Synonymous codon usage is not random as it is unique to species. In each amino acid family, some synonymous codons are preferred and this is referred to as synonymous codon usage bias (SCUB). Trends associated with evolution of SCUB and factors influencing its diversification in plastomes of genetically distinct Oenothera plastomes have not been investigated so far. Objectives: In the present study, major forces that shape SCUB in Oenothera plastomes and putative preferred codons in the protein coding genes (PCG) of plastomes were identified. Materials and Methods: To unravel various features of SCUB across selected Oenothera plastomes, commonly used codon usage indices such as relative synonymous codon usage (RSCU), synonymous codon usage order (SCUO), effective number of codons (ENC) and codon adaptation index (CAI) were calculated. Correspondence analysis (COA) on RSCU was performed to identify various characteristics of SCUB across different PCG in Oenothera plastomes. Spearman’s rank correlation analysis was adopted to correlate nucleotide contents, codon usage indices and major axes of COA to find out critical parameters in shaping SCUB. Results: Mutational bias due to compositional constraints played crucial role in shaping SCUB as T3 and GC3 contents were in strong negative correlation with all axes of COA. Nevertheless, significant negative correlations between axis 1 and 3 with ENC and CAI respectively, in all species, and narrow distribution of GC contents in neutrality plot, indicate the role of natural selection. Hydropathy score of proteins was found to be influencing SCUB in O. glazioviana as it showed strong negative correlation with axis 2. Conclusion: We concluded that mutational pressure coupled with weak selection influenced SCUB in the examined plastomes of Oenothera. In addition, all examined species of Oenothera exist as disjunct populations in different parts of North America and these populations might have experienced genetic drift as random mutations in small populations that have been fixed over a period of time.

http://www.ijbiotech.com/article_7934_2268840fb3001202e6af4b0b6b680abc.pdf

Mutational Pressure Drives Evolution of Synonymous Codon Usage in Genetically Distinct Oenothera plastomes

https://link.springer.com/content/pdf/10.1186/s43141-021-00277-1.pdf

Ganesh Doss

Papers

Mutational pressure dictates synonymous codon usage in freshwater unicellular α - cyanobacterial descendant Paulinella chromatophora and β - cyanobacterium Synechococcus elongatus PCC6301

Conservation and in vitro multiplication of highly endangered Indian traditional medicinal plant (Morinda reticulata Gamble) through nodal explants

Mutational Pressure Drives Evolution of Synonymous Codon Usage in Genetically Distinct Oenothera plastomes

Molecular marker for characterization of traditional and hybrid derivatives of Eleusine coracana (L.) using ISSR marker.

Improved protocol for isolation of genomic dna from leaf tissues of phyllanthus emblica gaertn ?(short communication)