A physiological disease of the pineapple fruit called pineapple translucency causes the pulp to become water-soaked, which affects the fruit’s taste, flavor, shelf life, and integrity. In the present study, we analyzed seven pineapple varieties, of which three were watery and four were non-watery. There were no apparent macronutritional (K, P, or N) differences in their pulp, but the non-watery pineapple varieties had higher dry matter and soluble sugar content. The metabolomic analysis found 641 metabolites and revealed differential expression of alkaloids, phenolic acids, nucleotide derivatives, lipids, and other metabolites among the seven species. Transcriptome analysis and further KEGG enrichment showed downregulation of ‘flavonoid biosynthesis’ pathways, differential expression of metabolic pathways, secondary metabolites biosynthesis, plant–pathogen interaction, and plant hormone signal transduction. We believe this study will provide critical molecular data supporting a deeper understanding of pineapple translucency formation and greatly benefit future research on this commercially important crop.

Macadamia is an economically significant crop, with its kernel oil being abundant in monounsaturated fatty acids (MUFA). Analyzing the expression of genes related to MUFA biosynthesis is essential for understanding the complex regulatory networks in Macadamia. However, there are few reports on the identification of suitable reference genes for use as internal controls in this species. Consequently, selecting a reliable reference gene for gene expression studies under various conditions is critical. In this study, we evaluated the expression stability of 11 traditional housekeeping genes: α-tubulin (TUBa), β-tubulin (TUBb), malate dehydrogenase (MDH), 18S ribosomal RNA (18S), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), α-elongation factor 1 (EF1a), β-elongation factor 1 (EF1b), ubiquitin (UBQ), ubiquitin-conjugating enzyme (UBC), cyclophilin (CYP), and actin (ACT) under abiotic stresses, hormonal treatments and in variety of plant tissues using the online tool RefFinder, which integrates four commonly used software programs: ΔCt, geNorm (version 3.4), NormFinder (version 0953), and BestKeeper (version 1.0). A comprehensive expression stability ranking was established by integrating results from these four methods based on the geometric mean. The findings indicated that ACT was the most stable gene across all samples, including those subjected to cold stress, NaCl stress, PEG stress, ABA treatment, MeJA treatment, and both stem and leaf tissues. EF1b was identified as the most stable gene in GA treatment and heat stress samples, while UBC and CYP were ranked highest in ethrel treatment and root tissue samples, respectively. Finally, the reliability of these findings was further validated using the target gene SAD through qRT-PCR. In summary, this study evaluated and validated appropriate reference genes for qRT-PCR, which will facilitate future investigations into the molecular mechanisms in Macadamia.

Macadamia is an emerging woody nut with high economic value. Although genome assemblies are now available for all four species, a comprehensive evolutionary analysis integrating divergence time estimation, lineage-specific gene family dynamics, and whole-genome duplication (WGD) history has not yet been undertaken. Here, we performed a comparative genomic analysis of four macadamia species (M. integrifolia, M. tetraphylla, M. jansenii, and M. ternifolia) alongside 11 other plant species. A total of 72,992 gene families were identified, with species-specific gene families numbering 277 in M. integrifolia, 234 in M. tetraphylla, 236 in M. ternifolia, and 183 in M. jansenii. KEGG enrichment analysis revealed that M. integrifolia-unique genes were enriched in terpenoid biosynthesis and ABC transporter pathways, whereas the unique genes of the other three species were predominantly associated with phenylpropanoid biosynthesis and amino acid/carbohydrate metabolism. Phylogenetic analysis revealed a well-supported monophyletic macadamia clade, with M. integrifolia and M. tetraphylla forming one subclade, and M. ternifolia and M. jansenii forming another. Divergence time estimation indicated that the genus diverged approximately 10.3 million years ago (Mya), with species-level divergences occurring at 7.8–8.4 Mya. Genomic synteny analysis revealed a conserved genomic architecture, with 57.36%–59.68% of genes being shared in syntenic blocks among species. Gene family dynamics revealed lineage-enriched patterns in the terpenoid biosynthesis pathways: expansion in M. integrifolia but contraction in the other three species. WGD analysis detected two WGD events. On a relative Ks scale, the more recent WGD event overlapped with the species-level divergence, whereas the older WGD event was shared by the common ancestor of the genus. These findings provide a comprehensive genomic foundation for understanding macadamia evolution and may facilitate breeding and conservation efforts.