International Journal of Molecular Ecology and Conservation, 2025, Vol.15, No.1, 19-29 http://ecoevopublisher.com/index.php/ijmec 23 from bacteria and archaea, of which more than 75% were carbohydrate metabolism-related genes. These horizontally acquired bacterial enzymes (such as cellulases, hemicellulases, etc.) greatly enhanced the ability of ciliates to decompose complex plant polysaccharides, allowing them to thrive in the fiber-filled rumen environment. The metabolic functions acquired by ciliates through HGT are further converted into nutritional benefits for the host goats: volatile fatty acids and other nutrients produced by rumen microbial fermentation are absorbed and utilized by goats, enabling goats to digest high-fiber, low-quality plant materials. 3.3 Potential mechanism of HGT in environmental adaptation of goats HGT gives the host new physiological functions. Through HGT, goats may acquire functional genes that their ancestors never had, expanding their range of adaptation from scratch (Dai et al., 2021). For example, if an ancestor of goats ingested a microorganism containing a gene for antivenom, and the gene was integrated through intestinal HGT, and antivenom was produced in goat serum, then the survival rate of this population in an environment with snakes would be significantly improved. HGT can also accelerate the rate of adaptive evolution. Compared with the traditional mutation-selection process, HGT is equivalent to directly "copying" a ready-made adaptation plan from another species, greatly shortening the generation time to reach an adaptive phenotype (Nakaya and Miyazawa, 2015). When the environment changes suddenly or a new ecosystem expands, the genes provided by HGT may allow goats to quickly break through the limitations. HGT can provide the raw materials for genetic innovation. Even if an HGT event does not bring significant adaptive advantages at the moment, the new genes introduced may become the starting point of innovation through gene duplication, recombination, etc. in subsequent evolution (Burmeister, 2015; Ravenhall et al., 2015). For example, a silent bacterial gene in the goat genome may confer a new phenotype if structural variation occurs in the offspring to activate its expression. In addition, HGT can also cooperate with structural variation to improve adaptability. Simply put, if a gene acquired through HGT undergoes structural variation such as gene duplication, it can further expand production or multifunctionality and improve environmental adaptability (Dai et al., 2021). 4 The Key Role of Structural Variation (SV) in Goat Adaptation 4.1 Progress in identification technology of structural variation in goat genome Since 2019, with the rise of third-generation sequencing and graphical pan-genome concepts, scientists have conducted systematic research on goat SV (Bian et al., 2024). After 2020, PacBio high-fidelity long-read sequencing (HiFi) and Oxford Nanopore sequencing were successively applied to goats. In 2024, Bian et al. (2024) constructed the world's first goat graphical pan-genome using de-chimeric diploid assembly of 8 representative goat breeds. Compared with traditional references, the pan-genome adds about 113 Mb of new sequences, including many structural variations that have not been included before. For goat populations with rich genetic diversity, pan-genome + long read length is an effective means to fully capture SV. In addition to long read length, complementary technologies such as chromosome conformation capture (Hi-C) are also used to assemble and verify large-scale structural variations, and optical mapping technology (Bionano) helps detect ultra-long repeats and translocations. In order to identify the selected functional SVs, researchers usually combine SVs with population genetics statistics. For example, XP-CLR, F_ST, Pi ratio, etc. are used to compare the differences in SV frequency among different ecotypes or breeds. At the same time, functional annotation methods are also being followed up: SVs are located to genes or regulatory regions to evaluate the gene functions that may be affected. In addition, RNA sequencing can be used to detect the effects of SVs on gene expression, thereby inferring their biological significance (Zhang et al., 2024). 4.2 Research findings on the influence of structural variation on goat adaptability A large amount of evidence supports that structural variation has a profound impact on the adaptive traits of goats, from coat warmth, reproduction patterns to immune resistance, etc., all of which leave traces of SVs. Under multiple selection pressures, the convergent evolution process of sheep and goat animals in morphological traits and adaptability, structural variation (SV) candidate genes played an important role in domestication and improvement (Figure 2) (Yang et al., 2024). These variations shape phenotypes by changing gene dosage (such as gene duplication or deletion changing the number of products) or changing gene regulation (such as
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