Computational Molecular Biology 2025, Vol.15, No.6, 273-281 http://bioscipublisher.com/index.php/cmb 277 pathways and resistance mechanisms can be unearthed, which are all evidence of their "solo" operation in the ecological niche (Gonzalez-Torres and Gabaldon, 2018). In other words, the changes in gene families have written their "evolutionary diaries" of adapting to the environment. 6 Phylogenetic and Evolutionary Analysis 6.1 Phylogenetic tree construction based on 16S rRNA and single-copy core genes To determine which branch the newly discovered extreme thermophilic bacteria belong to in the systematic classification, relying solely on traditional markers such as 16S rRNA is often not detailed enough. However, as an "old tool" for bacterial classification, it has not been phased out, especially when combined with multiple single-copy core genes for analysis, it can fill many resolution gaps. The phylogenetic relationships revealed in this way can not only identify kinship but are also often linked to the ecological adaptability of the bacterial species. The new strain forms a stable branch with other thermophilic bacteria that live in similar extreme environments. It is worth noting that some "traces" left by horizontal gene transfer can still be faintly seen in this clustering - they might be the driving forces behind the diversification of metabolic capabilities (Cooper et al., 2022; Shen et al., 2024). 6.2 Synteny analysis and detection of genome rearrangement events Sometimes, when phylogenetic trees fail to tell us something, genomic structure can make up for it. In the collinearity comparison of this strain with other extremophiles, the gene arrangement in some regions was highly consistent, but many regions were disrupted, such as inversions, insertions, and even large-scale translocations. This kind of rearrangement is not merely about "different arrangements"; in many cases, it actually reflects a shift in evolutionary strategies. For instance, genomic islands and movable elements often cluster in these rearrangement regions. Many studies suspect that they are related to the flexibility of the genome - especially when facing environmental stress, they may be the "accelerators" of rapid evolution (Li et al., 2020; Neubert et al., 2021). 6.3 Adaptive evolution and identification of positively selected genes Genome-wide screening sometimes reveals some "restless" genes that are particularly active in metabolism, stress response or perception of environmental changes, and often bear traces of positive selection. For instance, some genes related to heavy metal resistance or osmotic pressure tolerance are significantly more prone to mutation than other conserved regions, which precisely explains why these microorganisms can thrive in extreme environments. Furthermore, some genes are not inherited vertically but are "borrowed" from other microorganisms. That is to say, horizontal transfer is also involved in the rapid process of functional innovation. Overall, vertical genetics, horizontal transfer and natural selection interweave like three forces, jointly shaping the evolutionary profile of these extreme microorganisms (Safari et al., 2025). 7 Case Studies: Applications of Extremophile Genomes 7.1 Industrial enzyme development from hot spring or salt lake strains Some microorganisms from hot springs or salt lakes, which originally live in extreme environments, have enzymes in their bodies that possess extraordinary "resistance" properties: they can withstand high temperatures, endure strong salt, and remain calm even at extreme pH values. This characteristic precisely meets some industrial demands, such as high-demand scenarios like biofuels, food processing and pharmaceuticals. In fact, many heat-resistant proteases, lipases and amylases that are currently in use were initially discovered through genomic analysis. Especially after the quality of genome assembly has improved, researchers can not only locate the genes of these enzymes, but also identify the regulatory regions that co-occur with them and even complete expression modules. Interestingly, some microorganisms from soda lakes have surprisingly demonstrated carbohydrate metabolism pathways adapted to high-salt conditions, and even metagenomic data can reveal their catalytic potential (Verma et al., 2022; Mangoma et al., 2024). 7.2 Engineering microorganisms using stress-resistance genes from extreme environments Not all microorganisms can survive in environments with high salt or heavy metals. Those that can withstand them mostly carry specific anti-stress genes in their bodies. Such genes are now increasingly being "borrowed" to
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