Jaboticaba is a typical tropical plant that blossoms and bears fruit on the tree trunks and branches. The fruits resemble grapes in appearance and texture and are also known as “treegrapes”. Currently, research on the genomics of jaboticaba is lacking. In this study, we constructed an integrated, telomere-to-telomere (T2T) gap-free reference genome and two nearly complete haploid genomes, thereby providing a high-quality genomic resource. Furthermore, we unveiled the evolutionary history of several species within the Myrtaceae family, highlighting significant expansions in metabolic pathways such as the citric acid cycle, glycolysis/gluconeogenesis, and phenylpropanoid biosynthesis throughout their evolutionary process. Transcriptome analysis of jaboticaba fruits of different colors revealed that the development of fruit skin color in jaboticaba is associated with the phenylpropanoid and flavonoid biosynthesis pathways, with the flavanone 3-hydroxylase (F3H) gene potentially regulating fruit skin color. Additionally, by constructing the regulatory pathway of the citric acid cycle, we found that low citric acid content is correlated with high expression levels of genes such as thiamin diphosphate (ThDP) and low expression of phosphoenolpyruvate carboxykinase (PEPCK), indicating that PEPCK positively regulates citric acid content. These T2T genomic resources will accelerate jaboticaba pepper genetic improvement and help to understand jaboticaba genome evolution.

Plant height is an important characteristic, the modification of which can improve the ability of stress adaptation as well as the yield. In this study, genome-wide association analysis was performed for plant height traits in 370 potato cultivars using the tetraploid potato genome as a reference. A total of 92 significant single nucleotide polymorphism (SNP) loci for plant height were obtained, which were particularly significant in haplotypes A3 and A4 on chromosome 1 and A1, A2, and A4 on chromosome 5. Thirty-five candidate genes were identified that were mainly involved in the gibberellin and brassinolide signal transduction pathways, including the FAR1 gene, methyltransferase, ethylene response factor, and ubiquitin protein ligase. Among them, PIF3 and GID1a were only present on chromosome 1, with PIF3 in all four haplotypes and GID1a in haplotype A3. This could lead to more effective genetic loci for molecular marker-assisted selection breeding as well as more precise localization and cloning of genes for plant height traits in potatoes.

The timing of potato tuberization is affected by potato ripeness, environmental factors, and polygene regulation. The accurate control of the transition to tuberization has both scientific and practical production value, but the key factors regulating this transition remain unclear. This study grafted an early-maturing potato variety (Favorita) scion to the late-maturing Qingshu 9 variety and demonstrated that a heterologous early-maturing scion can induce early potato formation on a late-maturing rootstock. The transcriptome of functional leaves and stolons of grafted plants was comprehensively analyzed and 593 differentially expressed genes (DEGs) were identified, including 38 transcription factors. Based on gene molecular function analysis and previous reports, we propose that PIF5, bHLH93, CBF3, ERF109, TCP19, and YABBY1 are the key DEGs that induce tuber formation in early- and late-maturing potatoes. The YABBY1 gene was subjected to functional verification. The leaf area of StYABBY1-overexpressing plants was smaller than the wild type and no potato tubercles were formed, while an RNA interference plant line showed no change in leaf area and formed tubers, indicating that StYABBY1 has a role in leaf size regulation and tuber formation.

PYR/PYL (pyrroloquinoline quinone resistance/PYR1-like) are receptors for abscisic acid (ABA) in plants and play a crucial role in responses to abiotic stress. In this study, we identified 63 members of the StPYL gene family at the tetraploid whole-genome level in potatoes. We analyzed the physicochemical properties of these 63 StPYLs and constructed a phylogenetic tree using Arabidopsis thaliana and potato (Solanum tuberosum L.) cultivar ‘DM’ as the reference. By examining gene structure, conserved protein motifs, and collinearity, we found that StPYLs are highly conserved throughout evolution. The gene expression heat map under salt stress revealed that 57 StPYL genes are involved in the salt stress response. Among them, the expression level of StPYL9a-like changed significantly under salt stress. Through genetic transformation, we observed that overexpression of StPYL9a-like enhanced the growth and survival of potato plants under salt stress compared to the wild type. The contents of proline (Pro), superoxide dismutase (SOD), and chlorophyll in the leaves of overexpressing plants increased, while malondialdehyde (MDA) levels decreased. This suggests that StPYL9a-like positively regulates salt tolerance by affecting antioxidant enzyme activity and osmotic adjustment substances in potatoes. Subcellular localization demonstrated that StPYL9a-like is localized in the nucleus. This study provides a reference for the functional research of PYLs in potatoes, offers a basis for screening potato genes related to salt stress, and lays a foundation for developing salt-tolerant potato varieties.

The color change in the peel of Jaboticaba (Myrciaria cauliflora Berg) ‘Essart’ is primarily driven by the spatiotemporal regulation of anthocyanin biosynthesis, but its molecular mechanism remains unclear. This study employed a multi-omics integrated analysis approach, combining targeted metabolomics, transcriptomics, and small RNA sequencing, to systematically elucidate the regulatory mechanism underlying color change during Jaboticaba fruit peel development. The results showed that during the color-turning stage, the content of most anthocyanins tended to decrease, while the content of Cyanidin significantly increased during the fully ripe stage. Weighted Gene Co-expression Network Analysis (WGCNA) identified the brown module as a highly relevant module for anthocyanin accumulation, which includes a co-expression network of 98 transcription factors and 6 structural genes (F3H, CHI, ANS, CHS). Furthermore, small RNA sequencing results discovered a novel regulatory relationship: plant-MIR408-4—McMYB88. This regulatory relationship exhibited precise temporal dynamics: during the green fruit stage, plant-MIR408-4 was highly expressed and McMYB88 was lowly expressed, thereby inhibiting anthocyanin synthesis; however, during the fully ripe stage, plant-MIR408-4 expression decreased and McMYB88 expression increased, promoting anthocyanin accumulation. In summary, this study revealed the molecular regulatory mechanism of color formation in Jaboticaba fruit peel, providing an important theoretical basis for its color improvement and molecular breeding.

Coconut (Cocos nucifera L.) plays a vital economic and cultural role in many tropical and subtropical regions. A comprehensive review of the existing literature underscores that advanced biotechnologies are pivotal in unlocking the full potential of coconut germplasm exchange, which is crucial for the future sustainability of this crop. While traditional exchange methods are hampered by phytosanitary risks and logistical burdens, biotechnological interventions such as in vitro conservation and cryopreservation present targeted solutions to overcome these bottlenecks. The exchange, facilitated by these technologies, allows for the efficient introduction of desirable traits. We indicate that diversification and germplasm exchange hold the key to improving coconut quality and yield, developing varieties resistant to pests and diseases, and ensuring long-term conservation of coconut genetic diversity. This review highlights the potential to overcome the challenges faced by regional breeding programs often hindered by restricted genetic resources. Furthermore, by examining past successes and challenges in coconut germplasm identification and exchange, we offer perspectives on optimizing strategies to conserve diversity. This work emphasizes that germplasm exchange paves the way for coconut varieties that can thrive under changing environmental conditions, securing the future of this highly valuable crop.