Fruits, regarded as nature's most prized offerings to humanity (1), hold a significant position in the global agricultural landscape in terms of their nutritional value and availability per person (2). Beyond their edible and nourishing qualities, fruits have also gained immense symbolic and cultural importance (3). The cultivation of horticultural fruit crops has played a pivotal role in recent advancements in health and socioeconomic development (2). With the integration of genomics and fruits, this sector is projected to be the fastest-growing in agriculture. The cultivation of fruit crops not only contributes to the well-being of individuals but also impacts the overall progress of nations (2, 4). The production and per capita consumption of fruits directly influence the standard of living in a country (4). Fruits and vegetables are integral components of a healthy diet and have been linked to a reduced risk of chronic diseases (5). However, despite their numerous health benefits, many individuals fail to incorporate an adequate amount of fruits and vegetables into their daily meals. The World Health Organization recommends a minimum intake of 400 g, or five portions, of fruits and vegetables per day, emphasizing the importance of consuming a diverse range of produce to obtain a variety of essential nutrients (87). To promote fruit and vegetable consumption, strategies aimed at enhancing intake are crucial for overall health. Strategies to promote fruit and vegetable intake are essential for health, and a well-planned and behavior-focused nutrition education can be effective in enhancing fruit and vegetable intake (6).
WHO/FAO plays an important role in identifying health risks and issues through comprehensive surveys and examinations, followed by their efforts in providing valuable guidance on dietary and physical activity guidelines. The WHO report presents an ambitious policy that aims to combat the escalating rates of chronic diseases in less industrialized nations. Consequently, there is a pressing need for further research to determine effective interventions in resource-poor environments (7). In recognition of the nutritional and health benefits of fruits and vegetables, the United Nations General Assembly has designated 2021 as the International Year of Fruits and Vegetables. This initiative aims to raise awareness about the significance of fruits and vegetables in maintaining a balanced and healthy diet, as well as promoting a healthy lifestyle. Additionally, the campaign focuses on reducing losses and waste within the fruit and vegetable sector, while emphasizing the economic, social, and environmental advantages of increasing their production and consumption. The FAO advocates for a comprehensive food systems approach to enhance nutrition and address various challenges, including urbanization, climate change, and food shortages. This approach entails examining agriculture, food supply chains, food environments, and consumer behavior, while integrating sustainable practices throughout the entire production, harvesting, postharvest handling, processing, and consumption processes. By providing a framework and initiating discussions, the FAO highlights the interconnectedness of stakeholders and key issues that should be considered for action during the International Year of Fruits and Vegetables 2021. The primary objective of this initiative is to draw policy attention to the importance of fruits and vegetables in our diets and facilitate the sharing of successful practices (84).
Fruit crops hold substantial economic value and play a pivotal role in contributing to regional and global economies. They are of considerable economic importance across various regions, characterized by high marketable yields and significant contributions to agricultural production. The United Nations' Food and Agriculture Organization (FAO) in its World Programme for the Census of Agriculture 2020 categorizes key fruit and nuts, particularly highlighting tropical and subtropical fruits as Avocado (Persea americana), Fig (Ficus carica), Date Palm (Phoenix dactylifera), Mango (Mangifera indica), Guava (Psidium guajava), Papaya (Carica papaya), Pineapple (Ananas comosus), and Banana (Musa acuminata) (83).
The advent of low-cost sequencing machines in the genomic era has given a tremendous genomic data to the scientific community. The Central Dogma of gene expression involves two main stages: transcription, which converts DNA into RNA, and translation, where RNA is transformed into protein (8). Transcription and translation are key processes in gene expression, with transcripts serving as the intermediary between DNA and protein synthesis (9). Transcription plays a crucial role in regulating gene activity, essentially determining when genes are activated or deactivated, thereby defining the cell's identity and condition (10). Transcripts play a vital role in gene expression, serving as the intermediaries between DNA and protein synthesis (11). The coding region of a transcript, consisting of start and stop codons, known as the coding sequence (CDS), while the untranslated regions (UTRs) play a crucial role in post-transcriptional gene regulation (12). The CDS region is the part of the gene that encodes for the protein, and its length, codon usage, nucleosome positioning, and post-transcriptional modifications can all affect translation initiation, elongation, and overall protein abundance (13, 14). During translation, ribosomes read the sequence of mRNA in the CDS region and use it as a template to assemble the corresponding amino acids into a polypeptide chain, which eventually folds into a functional protein (15). The untranslated regions (UTRs) of mRNA are non-coding regions that flank the coding sequence (CDS) of a gene. There are two UTRs in mRNA: the 5' UTR and the 3' UTR. The 5' UTR is located at the 5' end of the mRNA, while the 3' UTR is located at the 3' end of the mRNA. The 5' UTR is involved in translation initiation, while the 3' UTR is important for the regulation of mRNA stability, localization, and translation efficiency (12, 16, 17). The study of the transcriptome, including mRNA, miRNA, lncRNA, and small RNA, is essential for understanding biological pathways and disease processes (18).
Tissue specificity studies in plants are crucial for understanding the contributions of specific tissues to overall metabolism and gene expression (19). The study of tissue specificity in plants is significant in understanding the molecular basis of plant development, function, and adaptation. Plant tissues consist of many different cell types, each with specific functions, and the identification and characterization of tissue-specific genes can provide valuable insights into the molecular mechanisms that govern these processes. Tissue-specific genes are often associated with specialized cellular functions and can serve as important biomarkers for specific tissues or diseases (20, 21). The development and benchmarking of tissue-specificity metrics, such as the tau, gini and counts are crucial for accurately quantifying the tissue specificity of gene expression. These metrics enable the systematic comparison of different methods for measuring tissue specificity and help identify the most robust and informative approaches for characterizing gene expression patterns across various tissues. Tau stands out as the optimal metric for assessing tissue specificity (22). There are several studies of tissue-specific gene expression studies in agriculture, few of them are- use of tissue-specific promoters in molecular farming to enhance agronomic traits and drive the production of proteins and secondary metabolites in plants (23); improved breeding practices by developing crops with desirable traits (24) and utilization in genome editing (25).
The advancement of genomics and transcriptomic resources has bridged the gap between sequence information obtained from various sequencing projects and functional genomics. The development of next-generation sequencing (NGS) technologies, including second and third-generation sequencing, has significantly improved the genome sequencing of fruits (26). This progress has been instrumental in the development of genomics-assisted breeding programs, facilitated by the enhanced availability of genomic and transcriptomic data for various fruit species (27). RNA sequencing (RNA-Seq) is a powerful technology that enables researchers to study gene expression and transcriptomic data in a high-throughput manner. It has revolutionized the field of genomics by providing a more accurate and comprehensive understanding of gene expression compared to traditional methods. RNA-Seq allows for the detection of differentially expressed genes, alternative splicing events, and gene isoforms, providing valuable insights into gene regulation and function (28, 29). Moreover, RNA-Seq has a wide dynamic range of expression levels, making it suitable for detecting rare and lowly-expressed transcripts (30).
The analysis of gene expression in fruit crops is crucial for a multitude of reasons. Firstly, it enables the elucidation of genetic factors underlying horticultural and agronomic challenges, which are pivotal for enhancing fruit production and crop improvement strategies (31). Secondly, such studies are instrumental in pinpointing key functional and regulatory genes linked to vital traits like disease resistance, stress tolerance, fruit quality, and ripening processes (32). Moreover, comparative analyses of gene expression can shed light on the potential reconfiguration or repurposing of existing genetic pathways, paving the way for the development of novel and varied fruit phenotypes (33). Transcriptome analysis is particularly valuable in identifying genes that exhibit differential expression associated with alternate bearing, a condition in which fruit trees alternate between high and low yield years (34). Gene expression analysis facilitates the identification of genes and genetic markers associated with desirable traits such as fruit quality, nutritional content, disease resistance, and pest control. This, in turn, aids in the development of varieties that can better withstand changing environmental conditions, benefiting farmers, consumers, and the environment (35–37). Lastly, gene expression studies can also be utilized to identify potential markers for assessing the physiological ripeness status of fruits (38).
Despite significant progress in Next-Generation Sequencing (NGS) and the benefits it offers for understanding gene expression, there is a conspicuous gap in research specifically focused on gene expression in fruits. This highlights a critical need for increased research initiatives in this domain. The current landscape of genomic and expression data for various fruit crops such as Avocado, Banana, Guava, Date, Figs, Papaya, and Pineapple lacks a comprehensive and dedicated expression atlas. In contrast, MangoBase has analysed 12 datasets, encompassing 11 BioProjects that extend to 80 samples of Mango Fruit. These studies examine various stages, including changes in pulp firmness and sweetness, peel coloration, and the effects of hot water postharvest treatment and infection with C. gloeosporioides. Dedicated solely to the Mango fruit crop, this database concentrates on fruit tissue and has identified roughly 340 coding sequences from the transcripts (39). This limited focus highlights a significant gap in resources for horticulturists, who need a unified platform that offers access to a wide array of datasets which should encompass various tissues and include data from different treatments and conditions for each cultivar of most fruit crops. Apart from this, tissue specificity metrics calculation needs to be implemented to broaden the area of research for each tissue. Apart from this, there is no dedicated expression atlas for any other tropical or sub-tropical fruit crops.
In our study, we have broadened the existing research in arena of horticulture to include all tropical and subtropical fruit crops identified by the FAO, focusing on those with completely annotated genomes. Our study covers eight such fruit crops, namely, avocados, bananas, guava, dates, figs, mangoes, papayas, and pineapples. This expansion has led to the examination of 177 BioProjects, approximately 15-fold increase, representing 2,060 samples, a 26-fold increase. The extended analysis of this study encompasses every identifiable tissue type within these fruits, including undetermined tissue types categorized as 'unknown.' Regarding genomic data, our study has analysed the expression and provided functional annotations for coding sequences (CDS) and untranslated regions (UTR) of large number of transcripts. As a result, the dataset generated provides extensive biological insights, covering a broad spectrum of transcripts and tissue types across eight tropical and subtropical fruit crops. The study also aims at enriching the database with tissue-specific genes by implementing an analysis of tissue specificity metrics, including the Tau score and Tissue-specificity index (TSI). The proposed Fruit Expression Atlas (FEAtl) stands as a pioneering comprehensive gene expression database, specifically focusing on tropical and subtropical fruit crops such as avocados, bananas, guava, dates, figs, mangoes, papayas, and pineapples, all recognized by the FAO. FEAtl supports several Sustainable Development Goals (SDGs). It enhances food security and sustainable agriculture (SDG 2) by aiding breeding programs for improved yield and resilience, and it contributes to good health (SDG 3) by ensuring the availability of nutritious fruits. The database promotes economic growth (SDG 8) by fostering innovation in agriculture and supports responsible consumption and production (SDG 12) through sustainable practices. Additionally, FEAtl aids climate action (SDG 13) by helping develop climate-resilient crops. This comprehensive resource offers a global perspective on gene expression patterns across all major tissues of these fruit crops. It is an invaluable tool for horticulturists, providing deep insights into the coding and non-coding genes of these fruits, including variations across different cultivars, and under various biotic and abiotic stress conditions. By enhancing the understanding of functional genomics and transcriptomics in these crops, the FEAtl can significantly contribute to the development patterns of these fruits, facilitating international exchange of horticultural commodities and resources, and ultimately benefiting growers worldwide.