Baccaurea ramiflora Lour., an evergreen tree of the Baccaurea genus of the Phyllanthaceae family, is primarily distributed in South Asia, Southeast Asia, and southern China, including southern Yunnan Province. It is a wild or semi-cultivated tree species with ornamental, edible, and medicinal value, exhibiting significant development potential. In this study, we present the whole-genome sequencing of B. ramiflora, employing a combination of PacBio SMRT and Illumina HiSeq 2500 sequencing techniques. The assembled genome size was 975.8 Mb, with a contig N50 of 509.33 kb and the longest contig measuring 7.74 Mb. The genome comprises approximately 73.47% highly repetitive sequences, of which 52.1% are long terminal repeat–retrotransposon sequences. A total of 29,172 protein-coding genes were predicted, of which 25,980 (89.06%) have been annotated, Additionally, 3452 non-coding RNAs were identified. Comparative genomic analysis revealed a close relationship between B. ramiflora and the Euphorbiaceae family, with both being sister groups that diverged approximately 59.9 million years ago. During the evolutionary process, B. ramiflora exhibited positive selection in 278 candidate genes. Synonymous substitution rate and collinearity analysis demonstrated that B. ramiflora underwent a single ancient genome-wide triploidization event, without recent genome-wide duplication events. This high-quality B. ramiflora genome provides a valuable resource for basic research and tree improvement programs focusing on the Phyllanthaceae family.

Background: Mangrove plants are a core component of coastal ecosystems, directly influencing biodiversity and shoreline stability. However, in recent years, due to the combined pressures of human activities and climate change, nearly half of the mangrove species in China are endangered and require urgent conservation measures. This study analyzed the population dynamics and stress factors affecting four rare and endangered mangrove species—Lumnitzera racemosa, Ceriops tagal, Barringtonia racemosa, and Heritiera littoralis—on the Leizhou Peninsula, providing scientific evidence for their conservation. Methods: Field surveys and plot investigations were conducted, with population dynamics and structure quantified using static life tables, survival rates, mortality rates, and disappearance curves. Additionally, the MaxEnt species distribution model and GIS technology were applied to predict the potentially suitable distribution areas. Results: The findings revealed that the population of L. racemosa exhibits an atypical pyramid structure, with few seedlings and constraining population growth potential. The C. tagal population follows an irregular pyramid structure, with abundant seedlings but fewer mature individuals, suggesting a rapid decline followed by stability. The B. racemosa population also follows an irregular pyramid structure, with many seedlings and a greater proportion of middle-aged and older individuals, facing the risk of early mortality. The H. littoralis population is also in decline, with few seedlings and a severe risk of local extinction. MaxEnt model predictions indicated that temperature is the primary environmental factor, with Area Under the Curve (AUC) values for all species exceeding 0.8, indicating strong predictive ability. The predicted potential suitable areas showed an expanded distribution range compared to current distribution points, providing valuable references for species introduction and propagation. Conclusions: This study described the population structure of the four mangrove species on the Leizhou Peninsula and assessed their primary stress factors. The results provided a theoretical basis for the conservation and restoration of endangered mangrove species and offer important guidance for developing effective conservation strategies in southern China.

Introduction: The taste differences between sour-tasting (LR) and sweet-tasting (BR) fruits of Baccaurea ramiflora Lour. are pronounced, but the underlying molecular mechanisms remain unclear. Methods: This study employed a combined metabolomic and transcriptomic analysis to elucidate the metabolic pathways governing this flavour variation. Results: Metabolomic profiling identified D-(+)-glucose and citric acid as the key taste determinants, with BR fruits exhibiting a significantly higher sugar-to-acid ratio than LR fruits. Transcriptomic data revealed that invertase ( INV ) activity correlated with D-glucose levels, whereas sucrose synthase ( SUS ) and sucrose-phosphate synthase ( SPS ) were associated with sucrose accumulation. In fully mature BR fruits, the suppressed expression of INV suggested that reduced sucrose hydrolysis contributes to their enhanced sweetness. Conversely, in LR fruits, elevated expression of hexokinase ( HK ) indicated higher glucose utilization. Furthermore, the expression of genes involved in organic acid metabolism—including citrate synthase ( CS ), aconitase ( ACO ), and NADP-malic enzyme ( NADP-ME )—was found to regulate the content of citric and malic acids. Discussion: These findings advance our understanding of the molecular basis of flavour formation in B. ramiflora , and provide potential targets for the breeding and biotechnological improvement of fruit taste.

Baccaurea ramiflora Lour., an evergreen tree of the Baccaurea genus of the Phyllanthaceae family, is mainly distributed in South Asia, Southeast Asia, and southern China, including southern Yunnan Province. It is a wild or semicultivated tree species of ornamental, edible, and medicinal value, with important development potential. Here, we report the whole-genome sequencing of B. ramiflora through the combination of PacBio SMRT and Illumina HiSeq 2500 sequencing techniques. The size of the assembled genome is 975.8 Mb, with a contig N50 of 509.33 kb and a longest contig of 7.74 Mb. Highly repetitive sequences make up 73.47% of the genome, of which 52.1% are long terminal repeat–retrotransposon sequences. A total of 29,172 protein-coding genes are predicted, of which 25,980 (89.06%) have been annotated, while 3,452 noncoding RNAs are found. Comparative genomic analysis indicates that B. ramiflora is closely related to the family Euphorbiaceae, being sister groups to each other that diverged approximately 59.9 Mya. During the evolutionary process, B. ramiflora has 278 candidate genes under positive selection. The synonymous substitution rate and collinearity analysis show that B. ramiflora only underwent one ancient genome-wide triploidization event and no recent genome-wide duplication event. This high-quality B. ramiflora genome provides a valuable resource for basic research and tree improvement programs of the Phyllanthaceae family.

Phyllanthus emblica is valued for its nutritional and medicinal properties, yet the genomic divergence between localized and widespread cultivars remains poorly understood. We investigated the genomes of two individuals from the endemic cultivar ‘Hongguang’ (HG), propagated via regional grafting, and the commercially widespread ‘Dongkeng’ (DK), known for its superior protein content. Using whole-genome sequencing, we reconstructed phylogenies from two nuclear markers, profiled genome-wide variations, assembled chloroplast genomes, and verified relative plastid copy numbers via real-time quantitative PCRs (qPCRs). Nuclear internal transcribed spacer (ITS) and phytochrome C (PHYC) phylogenies confirmed both samples belonged to the P. emblica lineage, while revealing a distinct genetic identity for the HG individual. Genome-wide variant profiling of the two individuals identified KEGG enrichment in plant hormone signaling pathways; DK variants mapped to the canonical auxin axis, while HG variants were annotated to reversible protein phosphorylation. Comparative chloroplast genomics demonstrated shared maternal inheritance and shared mutations in key photosynthetic genes (psaB, petA, and the ndh cluster) between the two genomes, though qPCR validation revealed a higher relative chloroplast DNA copy number in the DK sample. Despite the two-individual limitation, these findings revealed preliminary genomic variations, offering candidate molecular markers for future population studies and marker-assisted breeding.