International Journal of Molecular Ecology and Conservation, 2025, Vol.15, No.6, 286-293 http://ecoevopublisher.com/index.php/ijmec 291 Genome comparison found that pineapple has experienced fewer whole genome duplication (WGD) events than Gramineae plants, and its chromosome number has remained stable for a long time, with only 7 chromosomes. For this reason, pineapple is often used as an "outgroup reference" to track the historical trajectory of monocot genome evolution and the mechanism of duplication events. 7.2 Evolutionary inspiration from colinearity and orthologous gene analysis With the help of colinearity analysis, researchers further revealed that the evolution of CAM photosynthesis does not rely on the generation of new genes, but rather reconstructs the regulation of the original C₃ photosynthetic genes. Comparison of orthologous genes showed that many important non-coding region sequences are highly conserved in different species, and these regions may be the key to determining the biological characteristics of pineapples. The study also found that some genes involved in the CAM mechanism have obvious expression fluctuations in the circadian rhythm, and this temporal change is precisely controlled by the internal biological clock of the plant (Zhu et al., 2018). This shows that the co-evolution of gene duplication and expression pattern jointly promoted the formation of the CAM mechanism. 7.3 The role of natural selection and domestication in pineapple evolution The formation of the pineapple genome is not entirely dependent on mutation and duplication, and the intervention of natural selection and artificial domestication cannot be ignored. The emergence of CAM photosynthesis is likely the result of plant adaptation to arid and low CO₂ environments, allowing pineapples to survive in resource-limited niches (De La Harpe et al., 2020). DNA marker studies also show that there are significant genetic differences between different types of pineapple germplasm resources, which prompted the scientific community to update the classification system of pineapples (Zhang et al., 2014). During the domestication process, humans may have preferred to select plants with efficient water use, thereby strengthening CAM-related traits. The superposition of all these factors - natural selection, gene duplication, and regulatory reconstruction - jointly shaped the adaptive characteristics of pineapple today. 8 Conclusion and Future Prospects This study systematically analyzed the evolutionary characteristics and molecular mechanisms of the pineapple genome, focusing on its unique evolutionary position in monocots, the transition from C₃ to CAM photosynthesis, the structural stability of chromosomes, and the expansion pattern of gene families. Compared with typical monocots such as rice and orchids, pineapples have experienced significantly fewer whole genome duplication events, always maintaining a conservative karyotype of seven chromosomes, and achieving gene function diversification through segmental duplication and chromosome rearrangement. This "low replication, high conservation" evolutionary strategy not only ensures the stability of gene expression, but also provides a genetic basis for its adaptation to extreme environments such as drought and low CO₂. In addition, as a model plant for studying the origin and regulatory mechanism of CAM photosynthesis, pineapple exhibits a complex regulatory network with circadian rhythm as the core, involving a variety of long non-coding RNAs (lncRNAs) and regulatory elements. These characteristics reveal the molecular logic behind the transition from C₃ to CAM, that is, the new functions of old genes (regulatory remodeling) play a greater role in this process than the acquisition of new genes. Colinearity and homology analysis further confirmed that the main driving force for CAM functional innovation comes from changes in gene expression patterns rather than changes in gene content. Looking to the future, pineapple genome research not only provides important clues to the evolutionary history of monocots, but also provides theoretical support and gene resources for crop drought resistance breeding. With the development of gene editing and synthetic biology, the key CAM genes found in pineapples are expected to be introduced into C₃ crops to enhance their adaptability under climate change conditions and achieve sustainable agricultural development. At the same time, in-depth exploration of the genetic diversity and domestication history of pineapples will also open up new paths for biodiversity conservation and precision breeding.
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