GO categories of specific Eugenia uniflora genes.

Pitanga (Eugenia uniflora L.), a member of the Myrtaceae family, is native to the Brazilian Atlantic Forest and distributed across various ecological environments, including regions with contrasting edaphoclimatic conditions. Known for its production of secondary metabolites with significant biological activity, pitanga holds considerable pharmacological potential. Genomic and transcriptomic resources for this species are therefore valuable for understanding the genetic mechanisms that enable its adaptation to diverse ecosystems and for identifying candidate genes relevant for crop improvement and bioprospection. To explore whether genetic diversity is associated with population adaptation to environmental conditions, we first generated a draft genome of E. uniflora, totaling 385.1 Mbp with an N50 value of 26,199 bp, assembled de novo from Illumina-sequence reads. Likewise, gene prediction, based on Viridiplantae protein references, identified 30,663 protein-coding genes. Comparative genomics revealed 2,219 orthologous clusters, 40% of which were functionally annotated and encompassing 1,772 gene ontology terms. This draft genome also facilitated the identification of microsatellite markers, whose variation was analyzed across pitanga samples from two contrasting natural environments: Restinga and Riparian forest. The microsatellite profile showed a natural bias towards monomeric repeats, with genetic diversity differences across both populations that could be used as molecular markers for phenotype selection and plant breeding. Furthermore, RNA sequencing coupled with a Transcriptogram approach revealed significant differences in gene expression between the two populations. Pitangas from the Restinga ecosystem exhibited a stronger stress response, with distinct gene expression patterns associated with osmoprotection, cell wall modification, detoxification, nutrient balance, and epigenetic regulation. These patterns are likely linked to enhanced adaptation to the water and osmotic stress conditions, characteristic of this environment. Together, these findings enhance our knowledge of genetic diversity within E. uniflora populations and the molecular basis of their environmental adaptability. Such insights are critical for understanding how plants rapidly adapt to climate change and how these adaptations affect population dynamics, important for conservation strategies, population management, and the development of resilient cultivars.

红果仔（Pitanga，学名Eugenia uniflora L.）隶属于桃金娘科（Myrtaceae），原生分布于巴西大西洋森林，可在多种生态环境中存活，涵盖土壤气候条件迥异的区域。该物种因能够合成具有显著生物活性的次生代谢产物（secondary metabolites）而广受关注，具备可观的药理学开发潜力。因此，针对该物种的基因组与转录组资源，对于解析其适应多样生态系统的遗传机制，以及鉴定作物改良与生物勘探相关的候选基因具有重要价值。为探究遗传多样性是否与种群对环境条件的适应相关，研究团队首先基于Illumina测序读长，从头组装了红果仔的草图基因组（draft genome），其总长度为385.1 Mbp，N50值为26199 bp。同时，基于绿色植物（Viridiplantae）的蛋白参考序列进行基因预测，共鉴定出30663个蛋白编码基因。比较基因组学分析揭示了2219个直系同源簇（orthologous clusters），其中40%获得了功能注释，涵盖1772个基因本体（Gene Ontology，GO）条目。该草图基因组还助力鉴定了微卫星标记（microsatellite markers），研究人员对来自两种截然不同的自然生境——海滨沙生林（Restinga）与河岸林（Riparian forest）的红果仔样本的微卫星变异开展了分析。结果显示，微卫星图谱呈现出对单核苷酸重复的天然偏好，两个种群间存在遗传多样性差异，这些差异可作为表型选择与植物育种的分子标记。此外，结合转录组图谱（Transcriptogram）分析方法的RNA测序结果显示，两个种群的基因表达存在显著差异。来自海滨沙生林生态系统的红果仔表现出更强的胁迫响应，其独特的基因表达模式与渗透保护、细胞壁修饰、解毒作用、营养平衡及表观遗传调控（epigenetic regulation）相关。此类模式可能与该生境特有的水分与渗透胁迫（osmotic stress）适应性增强有关。综上，这些研究结果增进了我们对红果仔种群内遗传多样性及其环境适应性分子基础的认知。此类见解对于理解植物如何快速适应气候变化，以及这些适应性如何影响种群动态至关重要，这对于保护策略制定、种群管理以及抗逆品种培育均具有重要意义。