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.