Background: The transcription factors (TFs) in thermophilic cyanobacteria might represent a uniquely evolved gene repertoire in light of the strong selective pressure caused by hostile habitats. Understanding the molecular composition of the TF genes in thermophilic cyanobacteria will facilitate further studies regarding verifying their exact biochemical functions and genetic engineering. However, limited information is available on the TFs of thermophilic cyanobacteria. Herein, a thorough investigation and comparative analysis were performed to gain insights into the molecular composition of the TFs in 22 thermophilic cyanobacteria. Results: The results suggested a fascinating diversity of the TFs among these thermophiles. The abundance and type of TF genes were diversified in these genomes. The identified TFs are speculated to play various roles in biological regulations. Further comparative and evolutionary genomic analyses revealed that HGT may be associated with the genomic plasticity of TF genes in Thermostichus and Thermosynechococcus strains. Comparative analyses also indicated different pattern of TF composition between thermophiles and corresponding mesophilic reference cyanobacteria. Moreover, the identified unique TFs of thermophiles are putatively involved in various biological regulations, mainly as responses to ambient changes, may facilitating the thermophiles to survive in hot springs. Conclusion: The findings herein shed light on the TFs of thermophilic cyanobacteria and fundamental knowledge for further research regarding thermophilic cyanobacteria with a broad potential for transcription regulations in responses to environmental fluctuations.

Members of the families Thermosynechococcaceae and Thermostichaceae are well-known unicellular thermophilic cyanobacteria and a non-thermophilic genus Pseudocalidococcus was newly classified into the former. Analysis of the 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 between members of the two families. Overall, the nucleotide composition and CUB indices were found to differ between thermophiles and non-thermophiles. The thermophiles showed a higher G/C content in the codon base composition and tended to end with G/C compared to the non-thermophiles. Correlation analysis indicated significant associations between codon base composition and CUB indices. The results of the effective number of codons, parity-rule 2, neutral and correspondence analyses indicated 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 were found to differ among genera and even within genera. In addition, codon context pattern analysis revealed the specificity of the sequence context of start and stop codons among genera. Intriguingly, the clustering of codon context patterns appeared to be more related to thermotolerance than to phylogenomic relationships. In conclusion, this study facilitates the understanding of the characteristics and sources of variation of CUB and the evolution of the surveyed cyanobacterial clades with different thermotolerance and provides insights into their adaptation to different environments.

Porcine epidemic diarrhea virus (PEDV) and porcine deltacoronavirus (PDCoV) cause severe diarrhoea in piglets, requiring rapid laboratory differentiation. In this technical note, we evaluated primer–probe sets from Chinese quarantine industry standards on the Coyote Flash10 cartridge-based POCT combined primer–probe RT qPCR platform. Assays were characterised using a digitally PCR-quantified single-target in vitro transcribed viral RNA and RNA-spiked porcine faecal matrix. Exploratory low-concentration amplifications were observed at 3.222 copies/μL (PEDV) and 2.28 copies/μL (PDCoV); however, the corresponding Ct values fell within an indeterminate range, and no statistically validated limits of detection were established. The PEDV standard curve included concentrations with mean Ct values in the indeterminate and negative ranges, so its apparent efficiency was not considered a validated performance metric. PDCoV efficiency was sub-optimal (~77.7%). Low intra run Ct variability (CV < 3%) was observed in spiked matrix tests. No cross amplification was detected against four selected swine pathogens under the tested conditions. Notably, mixed-ratio co-template viral RNA experiments simulating co-infection were not performed. The proprietary internal control (IC) was recorded descriptively and was not used to assess extraction efficiency or sample validity. This work demonstrates preliminary analytical feasibility of this primer–probe combination on the Flash10 platform; full clinical diagnostic performance remains to be validated in further studies.