International Journal of Molecular Evolution and Biodiversity, 2025, Vol.15, No.1, 40-50 http://ecoevopublisher.com/index.php/ijmeb 44 4.4 Stress adaptation and defense mechanisms CAM photosynthesis itself is a water-saving adaptation, but pineapple also possesses various defensive traits: tough, spiny leaves (to deter herbivores), high tissue concentrations of bromelain (a proteolytic enzyme), and metabolic responses to abiotic stress. Cysteine proteases such as bromelain and their inhibitors may help defend against pests and pathogens. In cultivated pineapple, a genomic region containing tandemly repeated bromelain inhibitor genes has undergone strong selective sweeps (Chen et al., 2019). The WRKY gene family is important for plant stress responses. Pineapple has at least 54 WRKY genes (Wai et al., 2024). When AcWRKY28 is overexpressed, the plant tolerates salt stress better. But overexpressing AcWRKY31 makes the plant less tolerant to salt and drought. Still, it improves resistance to pineapple mealybug (Dysmicoccus brevipes). 5 Genomic Duplication and Structural Variation in Pineapple 5.1 Ancestral whole-genome duplication and karyotype conservation Pineapple did not go through recent whole-genome duplication (WGD), unlike many other flowering plants. It comes from a monocot ancestor that had seven original chromosomes. Grasses went through more WGD events, but pineapple did not. As a result, its genome stayed more stable and shows less duplication. Pineapple split from grasses before the “rho” WGD event. This helped it avoid extra genome doubling and kept its chromosome number steady at 25 for millions of years. Because pineapple did not become polyploid in recent times, its genome changed more slowly. It also avoided problems like subgenome dominance or losing too many genes. The fact that it is clearly diploid makes it easier to build genetic maps and find genes linked to traits. Fewer duplicate genes also mean it is easier to see which genes cause which traits. 5.2 Structural variations and genome structural evolution High-resolution comparisons between different Ananas genomes (cultivated and wild species) have revealed differences such as insertions, deletions, inversions, and copy number variations (CNVs). A comparison between the genome of A. bracteatus CB5 and A. comosus F153 showed high overall genome synteny, but also identified several large inversions and translocations (Feng et al., 2022). In a comparison between the ornamental red pineapple (A. bracteatus tricolor variety GL1) and the wild type CB5, researchers found two genomic fragments present in CB5 but absent in GL1, one of which (~1.1 kb) contains a photosynthetic protein gene. The MD2 pineapple genome was improved using haplotype phasing. This revealed many structural variations even within this single cultivated type (Yow et al., 2022). Most of these were small insertions, deletions, or small CNVs. These differences affect gene copies and may lead to trait diversity. One example is the duplication of the AcTI gene, which codes for a trypsin inhibitor. Cultivated pineapple has more copies of this gene than wild types (Chen et al., 2019). 5.3 Transposable elements and genome dynamics In the MD2 pineapple genome, about 45% of the genome is made up of long terminal repeat (LTR) retrotransposons (Feng et al., 2022). In A. bracteatus, the Gypsy-type LTR retrotransposons are the most common, making up around 44.8%. Pineapple had a burst of transposon activity in the late Pleistocene. Many intact LTR elements in CB5 and GL1 appeared about 1.7 to 2.1 million years ago. The genome of cultivated A. comosus (F153) has fewer recent LTRs. This could be because repeat regions were not fully assembled or because domestication reduced transposon diversity. In some pineapple types, a DNA transposon from the CACTA family inserted before the AcFT gene, which may affect when the plant flowers. Pineapple uses DNA methylation to keep transposons silent. This is especially important because most pineapples are not grown from seeds, so harmful insertions are not easily removed. Studies on pineapple leaves found high CHH methylation levels, which shows active transposon silencing. Both green and white tissues have this pattern, though some differences were found (Shi et al., 2021).
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