AUTHOR=Mou Qiao-Hui , Hu Zhe , Zhang Jing , Daroch Maurycy , Tang Jie TITLE=Comparative genomics of thermosynechococcaceae and thermostichaceae: insights into codon usage bias JOURNAL=Acta Biochimica Polonica VOLUME=Volume 71 - 2024 YEAR=2025 URL=https://www.frontierspartnerships.org/journals/acta-biochimica-polonica/articles/10.3389/abp.2024.13825 DOI=10.3389/abp.2024.13825 ISSN=1734-154X ABSTRACT=Members of the family Thermosynechococcaceae and Thermostichaceae are wellknown unicellular thermophilic cyanobacteria and a non-thermophilic genus Pseudocalidococcus was newly classified into the former. Analysis of codon usage bias (CUB) of cyanobacterial species inhabiting different thermal and non-thermal niches will benefit the understanding of their genetic and evolutionary characteristics. Herein, the CUB and codon context patterns of protein-coding genes were systematically analyzed and compared among members of the two families. Overall, the nucleotide composition and CUB indices are distinct between the thermophiles and non-thermophiles. The thermophiles show higher G/C content in the codon base composition and tend to end with G/C, compared to the non-thermophile.Correlation analysis indicates significant associations between codon base composition and CUB indices. The results of the effective number of codons, parity-rule 2, neutral and correspondence analysis indicate that mutational pressure and natural selection primarily account for CUB in these cyanobacterial species, but the primary driving forces exhibit variation among genera. Moreover, the optimal codons identified based on relative synonymous codon usage values are distinct among the genera and even within the genus. In addition, codon context pattern analysis reveals the specificity of the sequence context of start and stop codons among the genera. Intriguingly, the clustering of codon context patterns appears to be more related to thermotolerance than to phylogenomic relationships. Conclusively, this study facilitates the understanding of characteristics and variation sources of CUB and the evolution of the surveyed cyanobacterial clades with different thermotolerance and provides insights into their adaptation to different environments.