Chestnuts are popular edible nuts that are rich in starch. In order to enhance the transcriptomic resources and further understand starch and sucrose metabolism in maturing chestnuts, a comparative transcriptomic study of Chinese chestnut kernels was conducted at three ripening stages (70, 82, and 94 DAF). At 82 and 94 days after flowering (DAF), starch continued to accumulate, and the amylopectin/amylose ratio increased. Transcriptomic profiling of kernels at 70 (stage I), 82 (stage II), and 94 DAF (stage III) indicated that soluble starch synthase and α-1,4-glucan branching enzyme genes are actively expressed at 82 and 94 DAF. The starch degradation enzymes amylase, phosphoglucan phosphatase DSP4, and maltose exporter did not show differential gene expression, while glycogen phosphorylase-encoding unigenes were significantly down-regulated at 94 DAF. In addition to starch and sucrose metabolism, RNA transport, RNA degradation, pyrimidine metabolism, purine metabolism, plant hormone signal transduction, plant–pathogen interactions, and glycerophospholipid metabolism were found to be significantly enriched in all comparisons included in the study. As Chinese chestnut matured, the unique enriched pathways switched from ribosomal biogenesis and RNA polymerase of eukaryotes to endocytosis and spliceosomes. These genomic resources and findings are valuable for further understanding starch and sucrose metabolism in the Chinese chestnut.

Seed germination is a crucial developmental event in the plant life cycle. Proper germination significantly impacts the yield and quality. This study focuses on macadamia nuts, exploring the physiological, metabolic, and molecular biological characteristics during seed germination. The water content of macadamia seeds reached a peak in the seed imbibition stage, followed by a gradual decline. Key components such as fats, proteins, and soluble sugars decreased consistently. The enzyme activities of superoxide dismutase (SOD), peroxidase (POD), catalase (CAT), and glutathione peroxidase (GPX) increased throughout seed germination, reaching peak levels in leaf growth stages. A total of 1523 metabolites and 13,035 differentially expressed genes (DEGs) were detected by transcriptomic and metabolomic analyses, among which 1320 were transcription factors. The transcriptome and metabolome integration analysis showed significant overlaps between DEGs and differential metabolites in pathways such as phenylpropanoid biosynthesis. Quercetin, trifolin, rutin, myricetin, and quercetin 3-beta-D-sophoroside may play important roles in seed germination. FG2 and CYP75A/CYP75B1 were key genes in the flavonoid pathway. Hormones such as auxin (IAA), cytokinin (CTK), gibberellin (GA), and abscisic acid (ABA) exhibited stage-specific changes during germination. This study provided important theoretical basis and practical guidance for optimizing seed germination rates and enhancing stress resistance capabilities.

Severe physiological fruit abscission significantly limits yield potential in macadamia. Polygalacturonase (PG), a key hydrolytic enzyme in pectin degradation, plays a critical role in fruit abscission. However, in the macadamia genome, the PG gene family and the members involved in fruit abscission remain poorly understood. In this study, 56 PG gene family members, which were unevenly distributed across 13 of the 14 chromosomes, were identified in the macadamia genome. Phylogenetic analysis clustered these genes into seven clades, with most members found in clades D and E. The MiPGs contained 3–11 exons and 2–10 introns, and except for those in clades E and G, most contained conserved domains I–IV and were predicted to be localized exclusively to the cell membrane. MiPG promoter analysis revealed numerous light-, phytohormone-, and stress-responsive cis-elements. Expression profiling during fruit development showed that twelve MiPGs were either undetectable or expressed at low levels in the fruit abscission zone, whereas eight were highly expressed. MiPG9, MiPG37, and MiPG53 were significantly upregulated during abscission induced by a combination of girdling with defoliation and ethephon treatments. Moreover, transient MiPG37 overexpression in lily petals promoted premature abscission, suggesting that this gene plays a pivotal role in macadamia fruit abscission. These findings advance the functional characterization of macadamia PG genes and highlight a subset of candidate genes for further genetic manipulation to improve fruit retention.

Color serves as a crucial visual signal for attracting pollinating insects and directly affects the fruit set rate in woody crops. This study investigated the molecular mechanisms underlying flower color formation in macadamia. The results demonstrated that darker flower colors were associated with higher fruit set rates: the rates for purple, pink, pinkish-white, and white flowers were 2.78, 1.99, 1.35, and 1.31, respectively. High-throughput sequencing identified 1359 differentially accumulated metabolites, including benzoic acid, 4-hydroxybenzaldehyde, and isorhamnetin. Transcriptional regulators such as ERF, MYB, and WRKY were significantly up-regulated in darker flowers. KEGG analysis revealed two key metabolic pathways, in which genes including HCT (shikimate hydroxycinnamoyl transferase) and F3GalTase (flavonol 3-O-galactosyltransferase), as well as related metabolites such as p-coumaric acid, chlorogenic acid, and myricetin, showed higher expression levels in darker flowers. Anthocyanin content was highest in pink and pinkish-purple varieties (462.79 and 446.35 μg/g, respectively), and lower in white and light pink varieties (140.52 and 167.97 μg/g). In conclusion, flower color intensity is positively correlated with both fruit set rate and anthocyanin content. Genes involved in the flavonoid and phenylpropanoid pathways, along with transcription factors such as WRKY and MYB, collectively regulate flower color formation. This study provides a theoretical basis for macadamia flower color breeding.

The pericarp of Macadamia integrifolia represents a promising but underexplored source of functional flavonoids. To systematically elucidate their biosynthesis and enhance the industrial potential of this by-product, we conducted integrated transcriptomic and metabolomic profiling of pericarps across five developmental stages (50, 80, 110, 140, and 170 days after flowering). Our analysis reveals, for the first time, a distinct temporal shift in both gene expression and metabolite accumulation. Early stages were characterized by high expression of PAL, 4CL, CHS, and FLS, coupled with abundant flavonols and anthocyanins. In contrast, late stages exhibited upregulation of CHI and F3’5’H, redirecting the metabolic flux toward flavanones and isoflavones. This dynamic profile was closely associated with jasmonate and gibberellin signaling pathways and was likely regulated by key transcription factors (MYB, NAC, bHLH). These findings provide a multi-omics framework that elucidates the temporal flavonoid biosynthesis in macadamia pericarp, thereby laying the groundwork for its future industrial valorization.

Despite Macadamia’s global economic importance as a nutrient-dense nut crop, the structural and evolutionary characteristics of its chloroplast genomes (plastomes) remain underexplored. Here, we present the first comprehensive plastomic analysis of 185 cultivated Macadamia accessions from a Chinese germplasm collection. These plastomes exhibited conserved quadripartite structures (159,195–159,726 bp), comprising a large single-copy (LSC, 87,651–88,107 bp), a small single-copy (SSC, 18,743–18,819 bp), and inverted repeats (IRs, 26,378–26,422 bp). All plastomes maintained 115 functional genes (81 protein-coding, 30 tRNA, 4 rRNA) and were classified into 23 unique haplotypes. We identified 573 SNPs, 577 long repeats, and five hypervariable regions (trnS–trnG-exon1, ndhD–psaC, trnH–psbA, petA–psbL, and psbC–psbZ), with nucleotide diversity (Pi) values > 0.01. Phylogenetic reconstruction based on whole plastomes resolved maternal lineages and revealed distinct clustering patterns between ancestral and modern cultivars, with first-generation hybrids demonstrating significant plastomic uniformity. Notably, three accessions (‘Bailahe1’, ‘JingG6’, ‘Jing40’) showed ambiguous phylogenetic placement, warranting further investigation. Our findings provide critical plastomic resources for cultivar authentication, evolutionary studies, and the strategic expansion of genetic diversity in Macadamia breeding programs, particularly valuable given the crop’s recent domestication history and narrow genetic base.