International Journal of Molecular Ecology and Conservation, 2025, Vol.15, No.6, 286-293 http://ecoevopublisher.com/index.php/ijmec 287 species: A. comosus and A. macrodontes. This change in classification not only reflects the richness of genetic diversity of plants in this family, but also provides a basis for clarifying the systematic relationship between species (Zhang et al., 2014). In addition, the reference genome of pineapple also provides an important basis for subsequent research on the evolutionary mechanism of Bromeliaceae and the origin of CAM photosynthesis (Ming et al., 2016). 2.2 Comparative genomics of pineapple and other monocots Through genome comparison, researchers found that among all monocots, especially in the Poales group, the pineapple genome showed unique stability. Unlike most Poaceae plants that have undergone multiple rounds of whole genome duplication events, the pineapple genome has changed less during evolution. This structural "simple" provides us with a favorable entry point for inferring the original state of the early monocot genome. This type of comparison also helps scientists understand how plant genomes change over long time scales and how they are shaped by gene duplication events. Because of its relatively stable genome, pineapple can be used as a reference point for comparative studies with crops with more complex structures and higher gene redundancy (such as cereals), helping to reveal the universal laws behind genome evolution. 2.3 Key evolutionary events shaping the pineapple genome Several major changes helped shape the pineapple genome. One of the biggest is its move from C3 to CAM photosynthesis. This shift didn’t happen because the plant gained lots of new genes. Instead, it reused old ones in new ways through gene regulation. Pineapple did go through two ancient full-genome duplications, but unlike some other monocots, it didn’t have a more recent one. That’s one reason why its genome looks different. Some parts of the genome were copied in segments, and that helped grow certain gene families, like WRKY and MYB, which help the plant respond to stress and control growth (Liu et al., 2017; Xie et al., 2018). These changes made pineapple better at saving water and dealing with tough environments (Zhang et al., 2020). 3 CAM Photosynthesis and Its Genomic Basis in Pineapple 3.1 Overview of crassulacean acid metabolism (CAM) and its adaptive advantage CAM is a special type of photosynthesis. Its mechanism is to absorb CO₂ at night and close stomata during the day to reduce water evaporation. This water-saving strategy is particularly critical in arid areas. Plants like pineapples use the CAM mechanism, which "shifts" the timing of carbon absorption and photosynthesis, so that they can still grow normally in a water-deficient environment (Shi et al., 2021). 3.2 Genetic regulatory network of CAM mechanism in pineapples In pineapples, the CAM mechanism does not rely on the emergence of new genes, but regulates the function of the original C₃ photosynthesis genes. The key genes have not increased, but "new wine in old bottles" - they are activated or closed at different time periods, relying on the plant's own biological clock rhythm. This precise control of the circadian rhythm is one of the core mechanisms for the operation of CAM. The study also found that some long non-coding RNAs (lncRNAs) are also involved in the regulation process. For example, the expression of key genes such as PPCK and PEPC is regulated by these lncRNAs, which act like traffic dispatchers to maintain the coordinated operation of the entire metabolic process (Bai et al., 2019). 3.3 Comparative analysis of the genomes of pineapples and other CAM and C₃ plants The differences between pineapples and other CAM plants have also attracted the attention of researchers. Unlike some plants that have evolved CAM mechanisms through gene addition, pineapples rely more on the reshaping of existing gene expression patterns. This "using the old to make the new" strategy is its uniqueness. Although the biological clock is also highly associated with CAM rhythms in many CAM plants, the specific mechanisms vary from species to species. In the case of pineapples, this timing control is particularly tight. In addition, pineapples also have typical CAM plant morphological characteristics, such as thicker leaves and specific enzyme systems, which indicates that different plants often evolve similar solutions when adapting to arid environments (Ming et al., 2016; Heyduk et al., 2016).
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