Computational Molecular Biology 2025, Vol.15, No.6, 273-281 http://bioscipublisher.com/index.php/cmb 276 on a unique evolutionary path. Especially with the high-quality genomes pieced together by hybrid sequencing, structural changes such as insertions, deletions, and even gene rearrangements become particularly clear. For instance, the consensus pan-chromosome assembly method of Acinetobacter baumannii has revealed "flexible regions" related to environmental adaptability. Such strategies are also applicable to the study of microorganisms living in extreme environments (Chan et al., 2015; Gould and Henderson, 2023). Often, it is those easily overlooked genomic islands and resistance elements that are truly the key to explaining adaptability. 5.2 Identification of core and variable genomic regions The requirements for bacteria in extreme environments are not merely to "survive", but to "survive and live well". So, in their genomes, apart from the core areas that maintain basic life activities, there are also many "mobile" modules hidden. These variable regions are not present in every strain; they are more like "additional configurations" tailored for certain ecological conditions. Polar bacilli such as Haemophilus erythrosalis exhibit an open pan-genome - the stable core region is maintained by homologous recombination, while the dynamic helper parts are strongly influenced by horizontal gene transfer, including many fragments from plasmids or gene islands (Figure 1) (González-Torres and Gabaldon, 2018). These "mobile components" may not be used every day, but once the environment changes, they become the trump card for survival. Figure 1 Genome dynamics and ecological models (Adopted from González-Torres and Gabaldón, 2018) 5.3 Gene family expansion, contraction, and species-specific gene analysis Not all genetic families remain unchanged during evolution; some grow stronger while others gradually fade away. For instance, those gene groups related to heat resistance, metal resistance or osmotic pressure regulation often become "expansion households" in extremophiles. However, in contrast, some less necessary pathways will also experience functional contraction. This contractional-expansion is not random but closely related to the selective pressure of the environment. By comparing the genomes of different species, some species-specific metabolic
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