International Journal of Molecular Evolution and Biodiversity, 2025, Vol.15, No.1, 40-50 http://ecoevopublisher.com/index.php/ijmeb 45 5.4 Gene families and copy number variations Pineapple has 43 GRAS genes, which help control growth and signals. These genes are spread across 19 of the 25 chromosomes (Lin et al., 2024). Some of them formed through tandem duplication on the same chromosome. When comparing with other plants, scientists saw that some GRAS subfamilies, like SHR and PAT1, had their own duplication patterns in pineapple. Some gene families are reduced in copy number in pineapple-for example, the photoreceptor family is smaller compared to C3 grasses, aligning with pineapple’s adaptation to sunlit, open environments (which reduces the need for shade responses). On chromosome 3, a gene related to fruit protease has different copy numbers in different pineapple lines. Some have one copy, and others have two, which could affect how much protease the fruit makes. More genome sequencing has found many other CNVs, including in genes tied to disease resistance (like NBS-LRR), secondary metabolism, and development. Because pineapples are mostly grown from shoots and not seeds, rare gene duplications can stay in the same line for a long time. 6 Molecular Evolution of Key Gene Families 6.1 Photosynthesis-related gene families and the evolution of CAM photosynthesis CAM photosynthesis in pineapple evolved in a different way compared to some C4 plants. In C4 plants, genes like PEPC or Rubisco activase often expand a lot. But in pineapple, this did not happen. The PEPC gene family, which helps fix CO₂ at night, is small. Only a few PEPC versions exist, and there’s no sign that new ones evolved recently. Pineapple uses just one PEPC gene for CAM, and its activity is tightly controlled by the biological clock. The PEPC-activating kinase (PPCK) is also encoded by a single gene. Another important group is aquaporins. These proteins help move CO₂ in leaf tissues. Pineapple has a moderate number of aquaporin genes in the PIP1 and PIP2 groups, and some work mainly at night. Genes that control stomata, like OST1 kinase and ABA receptors, did not expand much, but their activity patterns fit well with CAM. The bHLH transcription factor family is large in pineapple, with about 121 genes (Hu et al., 2021). Some of these might help control stomata at night. In pineapple, CAM likely formed through small changes in when common photosynthesis genes are active. This was helped by promoter changes and new roles for transcription factors from the bHLH and NAC families. 6.2 Gene families related to flowering regulation and development Pineapple flowers in a unique way. It needs a long juvenile phase and often responds to ethylene to flower. Flowering in pineapple is controlled by genes seen in other plants, but it also has its own features. Main regulators include MADS-box genes, FT-like genes, and hormone-related genes. Scientists found 43 MADS-box genes in pineapple-32 type II (MIKC-type) and 11 type I. These genes match all major groups seen in flowering plants. But unlike grasses or orchids, pineapple doesn’t have many extra MADS genes. Pineapple has only one SEP gene. It works during both flower and fruit development. This shows it helps with organ fusion and ripening. Genes like AcAP1 and AcAG follow the “ABC model” and are active in sepals, petals, stamens, and carpels. Pineapple flowers are small and packed together. The thick flower stem that forms the fruit may be due to continued action of genes like AcFUL and AcAGL11 during development. CONSTANS (CO) and FT genes help plants track day length. Pineapple has at least two FT-like genes. One reacts to drought and stress, which may cause flowering during tough times (Yow et al., 2023). Pineapple also has 19 B-box (BBX) transcription factor genes (Ouyang et al., 2022). Some are like CONSTANS (COL) and help respond to light. AcBBX5 is one such gene. If you increase its expression, the plant flowers faster; if you reduce it, flowering is delayed. 6.3 Stress resistance gene families (NBS-LRR, WRKY, NAC) Pineapple has about 80~90 NBS-LRR genes, which help fight disease. This number is lower than in many
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