Bioscience Methods 2026, Vol.17, No.1, 9-22 http://bioscipublisher.com/index.php/bm 11 It showed a genome size of about 526–563 Mb, with 25 chromosomes (2n = 50) (Figure 1) (Yow et al., 2021). Pineapple had fewer whole-genome duplication events than crops like grasses, so it has a smaller gene set. Around 27,000 protein-coding genes were found. The first genome gave useful data on traits such as CAM photosynthesis, but the sequence continuity was low (contig N50 < 100 kb). Figure 1 Karyotype structure and chromosome composition of the pineapple genome (Adapted from Ming et al., 2015) In 2022, researchers built a better genome assembly for the MD2 cultivar using PacBio long-read sequencing and Hi-C scaffolding. In the MD2 v2 version, 99.7% of the sequence was placed on 25 pseudochromosomes. The contig N50 was over 1 Mb. This work confirmed that the haploid genome size is about 563 Mb and that MD2 has high allelic heterozygosity (Yow et al., 2021). Genome annotation has also improved. Many genes now have predicted roles, and big gene families, such as transcription factors and enzymes, have been listed. Studies show that pineapple has kept many single-copy genes even though it did not have recent whole-genome duplications (Ming et al., 2015). RNA sequencing from different plant tissues has helped scientists predict gene models and spot genes linked to disease. At present, pineapple has a solid reference genome and detailed annotation data (Yow et al., 2021). These resources make it easier to find resistance genes and plan CRISPR strategies based on its genetic map. 2.2 Identified disease resistance genes in pineapple Research on pineapple disease-related genes is still limited, but some have been found. Pineapple carries NBS-LRR resistance (R) genes, which help recognize pathogen effectors. However, it has far fewer of these genes than many other crops. One study showed that pineapple has far fewer NBS-LRR genes than grasses, likely because it missed the whole-genome duplication events that expanded these genes in cereals (Chen et al., 2019). Pineapple may have only a few dozen, while rice and maize have hundreds (Zhou et al., 2024). Some pineapple R genes belong to known groups, such as coiled-coil NBS-LRRs, and are close to those in resistant monocots.
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