Genomic garden: From societal and scientific impacts to biodiversity conservation

Summary

Because of urbanization, deforestation, pollution, climate change, and natural disasters, the loss of biodiversity is a pressing concern globally. As part of our efforts toward biodiversity conservation, we propose the establishment of a genomic garden, where the genome of each plant in the garden is elucidated. Combining science, horticulture, and a digital content hub accessible with any handheld device, the genomic garden serves multiple purposes, from enhancing urban landscapes, facilitating biomedical research, and improving population health to providing entertainment and education for visitors.

Graphical abstract

Lim et al. demonstrate the concept and creation of a genomic garden by integrating plant genome assembly, horticulture, and QR-linked digital interactive elements using the Singapore General Hospital (SGH) Bicentennial Genomic Garden as a showcase. Besides serving as a biophilic environment for patients, staff, and the public, the genomic garden also preserves biodiversity, promotes the advancement of biomedical research, enhances population health, improves urban landscapes, and provides educational opportunities. The concept can be adopted by any public or private gardens and parks globally, contributing to the wealth of plant genomic data.

Introduction

Countries in Southeast Asia have not been spared from the biodiversity loss seen across the globe. This includes Singapore, a developed country among the 10-membered Association of Southeast Asian Nations. Today, Singapore is known as the “Garden City,” but since its founding, the nation has undergone significant ecological transformation, losing much of its primary, swamp, and mangrove forests.^1,2,3 The destruction of Singapore’s natural ecosystems has resulted in a substantial decline in species diversity, including an alarming flora extinction rate of about 34%.⁴ Despite its small size and limited availability of natural resources, Singapore has made tremendous efforts to preserve its local biodiversity. Since 2009, the pragmatic National Biodiversity Strategy and Action Plan has been implemented to find solutions to conserve biodiversity in an urban setting and safeguard the natural heritage of the island country.⁵ In 2015, Singapore Botanic Gardens was recognized as a UNESCO World Heritage Site, becoming the first and only tropical botanic garden on the list.⁶ The biodiversity conservation efforts may be further enhanced by leveraging the latest technological advances. One such avenue is the establishment of a genomic garden, where the genome of each plant grown in the garden is sequenced, assembled, and analyzed. Within this space, each plant presents a botanical beauty for the public and harbors translational value, from bolstering food security to advancing public health initiatives. For developed countries like Singapore, we think that the genomic garden epitomizes one of the practical ways to preserve biodiversity and promote human health while serving the needs of modern nations with forward-looking economies.

Here, we describe the fundamental steps in establishing a genomic garden, including selecting plant species, optimizing sequencing technologies, developing pipelines for genome assembly, and identifying plant species with high potential for further translational studies (Figure 1A). Also, we discuss the potential benefits of a genomic garden, which includes forging international partnerships in academia and industry to maximize its long-term potential and impact (Figure 1B). We elaborate on the considerations we made in this process and share our experience as a guide to others who wish to establish their own genomic garden to catalyze the universal goal of biodiversity conservation while improving global health (Figure 1).

Figure 1.

Guide to establishing a genomic garden

(A) Different integral components to be considered when establishing a genomic garden.

(B) Potential benefits of a genomic garden.

Singapore General Hospital Bicentennial Genomic Garden

In 2021, the SingHealth-Duke-NUS Institute of Biodiversity Medicine (BD-MED) was established in Singapore’s largest academic medical center with the mission of translating biodiversity studies to impact health and medicine. The term “biodiversity medicine” was coined to reflect the rich biodiversity in the region that has yet to be properly and scientifically harnessed for health or medicine, which has tremendous opportunities and room to be developed into a pillar of modern healthcare.⁷ The genomic garden project is an initiative by BD-MED to integrate biodiversity with modern genomics to offer a holistic experience to the public to learn about plants amid nature. Our mission is for the garden to play an essential role in leveraging the multi-faceted translational potential of plants, enhancing biomedical research, improving population health and healing, fostering educational opportunities, and supporting biodiversity conservation efforts. Naturally, the choice of flora selection can be inspired by Southeast Asia’s vast and unique ethnobotanical heritage, encompassing its historical narrative, cultural practices, traditional healing arts, and essential natural assets. Based on these principles and as a pilot study, we created the first genomic garden in our SingHealth Duke-NUS Academic Medical Center, named the Singapore General Hospital Bicentennial Genomic Garden, by curating and sequencing the 100 SEA regional ethnobotanical species planted in the garden (Figures 2A and 2B). The current size of the garden is 3,400 m², with plans to expand the space to 8,500 m² by repurposing adjacent open-air parking spaces.

Figure 2.

The Singapore General Hospital Bicentennial Garden

(A) An aerial view of the Singapore General Hospital Bicentennial Genomic Garden featuring three strategic sections dedicated to local and SEA regional herbal, fruit, and culinary plants spanning 3,400 m².

(C–D) Examples of 9 plants found in Singapore General Hospital Bicentennial Garden across the three categories of (B) regional fruits, (C) culinary plants, and (D) herbal plants.

Choice of plant species for the genomic garden

The genomic garden can be broadly organized into different sections based on the type and function of plants in each section to simplify navigation while enhancing the educational experience. A cross-disciplinary team including botanists, plant molecular biologists, and phytochemists should collaborate in the selection process. Several key considerations can guide the selection process. Priority can be given to species that help fill genomic data gaps in underrepresented taxa, contributing to the conservation of genetic diversity. Equally important are species with unique adaptive traits that can drive agricultural innovation, enhance ecological restoration, and strengthen food security. Ethnobotanical knowledge provides further insight by identifying plants with traditional medicinal uses, which may contain bioactive compounds with nutraceutical potential. Finally, conservation status is a crucial factor, emphasizing endangered or CITES-listed species, especially when space and resources are limited. Indeed, some plants possess both scientific relevance and significant societal value, much like Papilionanthe Miss Joaquim “Agnes”⁸ and Dillenia suffruticosa,⁹ national flowers of Singapore and Brunei Darussalam, with unique phytochemical properties that confer potential health benefits such as antioxidant, anti-inflammatory, and anti-cancer activities. Therefore, visitors to the garden can embark on an educational journey that bridges scientific discovery and public curiosity when they explore plant diversity through a genomic lens. Furthermore, we believe a serene and tranquil garden environment will benefit patients by reducing stress and promoting psychological well-being. Studies^10,11 have shown that exposure to natural settings can decrease recovery times and improve overall mental health, making our garden a potential refuge for healing.

These categories of plants can also be considered when zoning the garden to areas that can tell their own story or convey a concept, like the ecology of local forests. Based on these guidelines, we have organized the SGH Bicentennial Genomic Garden into 4 sections—herbal plants, fruit plants, culinary plants, and orchids. In due course, we will further improve the quality and functions of the garden, for example, by expanding the repertoire of themes or subthemes, such as further sub-diving the “herbal’ section into “anti-cancer,” “anti-diabetics,” etc., as we explore the translational potential of the plants in the garden. In the SGH Bicentennial Genomic Garden, pathways have been carefully designed to lead visitors through the garden, ensuring they encounter diverse plants and educational displays. The meandering paths encourage leisurely exploration, with strategically placed resting spots that provide opportunities for contemplation or highlight points of interest through QR-linked web apps. Additionally, designated spaces have been created to facilitate interaction, such as herbal gardens where visitors can touch and smell the plants or fruit tree areas where they can taste seasonal fruits, enhancing the overall engagement of the experience. Ongoing efforts are also being made to develop areas for classes, workshops, and community events, ensuring that the garden is a versatile resource for the patients, staff, and the community.

Currently, the fruit plant section (Figure 2B) features a diverse range of regional fruits,¹² such as Durio zibethinus (durian, which we have sequenced¹²), known for its distinctive taste and smell, as well as many other fruits, such as Manilkara sapota (sapota), while the culinary plants (Figure 2C) include popular culinary herbs such as Murraya koenigii (curry leaf), Cosmos caudatus (ulam raja), and Piper sarmentosum (kaduk), which are used in culinary cuisines regionally. The herbal plant section (Figure 2D) highlights local medicinal plants such as Strobilanthes crispa (Black Face General), Bidens pilosa (black jack), and Turnera umofolia (West Indian holly). The orchid section showcases orchid hybrids representing the Singapore nation and each institution of SingHealth. Visitors can engage with the plants to learn about their characteristics through an interactive web app that provides information about the plants, their historical and social significance, available scientific findings, and ongoing related research projects (Figure 3). For instance, the garden has a QR code, which enables visitors to learn about the significance of genomic and biological aspects of the national flower of Singapore, Papilionanthe Miss Joaquim “Agnes,”⁸ as well as delve into its history by learning that it was first registered as a hybrid with the Royal Horticultural Society back in 1897 and, in 1981, declared Singapore’s national flower due to its “resilience and year-round blooming.”¹³ In the future, it can also be engineered into a platform for online visitors to explore the garden virtually.

Figure 3.

Interactive web app of the genomic garden

(A) QR codes linking to web apps that could be found in Singapore General Hospital’s Genomic Garden.

(B) A virtual web app that visitors can visit to learn more about plants.

Exploring the translational potential of plants in the genomic garden

The availability and abundance of plants in the genomic garden provide opportunities for translational research to uncover how these plants can benefit health. Alternatively, plant extraction methods can isolate bioactive phytocompounds or essential oils from the plants. These isolated compounds and essential oils can then be applied in biomedical research, using appropriate and relevant in vitro and in vivo models to study their effects on diseases such as cancer, metabolic disorders, skin diseases, neurological disorders, gut microbiome dysbiosis, and infectious diseases. For example, through extensive anti-cancer research using Dillenia suffruticosa, the national flower of Brunei Darussalam, our team has discovered that the plant’s roots are effective against different types of cancers.⁹ Through genomic assembly combined with chemogenomic profiling, we found that triterpenoids are the most abundant constituent within the ethanol-based extract and are likely the reason for conferring the anti-cancer effects from the plant roots. Such studies may accelerate the commercial development of plant extracts as pharmaceuticals, nutraceuticals, or functional foods to enhance human health and well-being, thereby further promoting the value and adoption of genomic gardens.

Plant genome sequencing pipeline

Plants demonstrating significant translational potential will be selected for genomic sequencing to gain deeper insights into the biological functions and mechanisms. We have carefully tested and identified several genome sequencing and analysis pipelines that are optimal for unraveling the genetic blueprints of the plants in the garden. At the core of this scientific venture is applying long-read sequencing and scaffolding techniques, such as chromosomal conformation capture, to generate chromosomal resolution genome assembly. These methods excel at navigating the complex and repetitive nature of plant DNA, which is critical for assembling comprehensive plant genomes (Figure 4). To obtain detailed genome assembly maps, we sequence to a depth of 30–45× genome coverage for each haploid copy of the genome, which can be estimated through various methods such as k-mer spectral^14,15,16 or flow cytometry^17,18 analysis for a novel plant genome. These genomes will complement tissue-specific transcriptomic datasets to enhance understanding of gene structures and functions.

Figure 4.

Plant genome assembly pipeline

HMW, high molecular weight; HiFi, highly accurate long sequencing reads; WGS, whole genome sequencing; Hi-C, high-throughput chromosome conformation capture technique; Omni-C, high-throughput chromosome conformation capture using sequence-independent endonuclease to enable genome wide resolution of chromatin interactions; QC, quality control.

To support these analyses, high-performance computing is invaluable for large-scale plant genome analysis. Recent advancements in long-read sequencing technologies have significantly improved accuracy, making it possible to assemble most plant genomes, which range from 1 to 2 Gb, within hours. For researchers lacking access to high-performance computing facilities, cloud computing services offer the necessary computational resources to conduct their genomic research efficiently. As sequencing technology, pipelines, and tools continue to evolve, periodic evaluation is essential to ensure the efficiency in genome assembly and analysis. Furthermore, the commitment to document and share pipelines in public repositories is crucial to ensure accessibility and reproducibility. This practice not only supports and streamlines plant sequencing initiatives but also strengthens initiatives across biodiversity genomics programs on a global scale. We eagerly welcome collaborations to facilitate emerging genomic gardens.

Technological advancements and bioinformatics have markedly refined the process of decoding a plant’s DNA, making it more accessible to the larger scientific community and the public. This effort elevates the genomic garden beyond mere germplasm; it becomes a dynamic database rich with genomic and biological data. The selection of plants that warrant downstream translational studies will follow with functional annotation, transcriptomic, and metabolomic investigations to explore different aspects of plant biology, obtain additional scientific insight, and develop potential clinical applications. Plants with interesting traits will be accorded additional downstream transcriptomic analysis to shed light on the pathways responsible for these characteristics. For instance, durian, which has a distinctive, pungent aroma during the ripening process, could be sequenced at various stages of maturation or ripening to unveil any relevant biochemical processes contributing to its smell.¹² Our study on Papilionanthe Miss Joaquim “Agnes” also alluded to the high abundance of vandaterosides, which suggests the potential use of Papilionanthe Miss Joaquim “Agnes” as a cosmetic to slow skin aging,⁸ pending future studies. In future studies, we also intend to incorporate epigenetics, single-cell sequencing, and spatial transcriptomics studies of these plants.

Opportunities for international collaborations

We hope the concept of the genomic garden will gain traction, beginning with our neighboring countries and eventually on an international scale. This progression will enhance global participation and collaboration, resulting in greater resource allocation and expanded breadth and depth of biodiversity studies. This new initiative and its implications can be shared with like-minded individuals, institutions, and organizations globally, including public, educational, and commercial institutions. This can be achieved through events such as conferences or organized engagement sessions, fostering collaborative and coordinated efforts to more effectively carry out the functions of genomic gardens, including biodiversity conservation. Significantly, partnerships with other biodiversity conservation programs can be established, not only in Southeast Asia but also in regions such as the US, Europe, and East Asia.^19,20 These partnerships will facilitate cooperation on various processes required to establish and sustain the genomic garden. In addition, to ensure the sustainability and longevity of these efforts, it is naturally important to solicit support and aid, both non-financial and financial (e.g., grants), from international non-profit agencies and foundations that appreciate the efforts’ urgency and impact on humanity and Mother Earth.

For example, we have already kickstarted our international collaboration by establishing a joint biodiversity laboratory at the Universiti Brunei Darussalam, the leading university of the oil-rich country of Brunei on the northeast coast of Borneo, where primary forests are rapidly diminishing due to deforestation and increased land use. However, despite these challenges, Brunei has demonstrated a solid commitment to preserving its rich local biodiversity through impressive efforts and conservation programs. We hope to duplicate this close collaboration with other SEA countries and attract non-profit agencies and foundations to support our programs in biodiversity conservation.

Genomic garden in commercial entities

The genomic garden concept can be easily extended to and adopted by commercial entities. They can play an important role in contributing to biodiversity conservation through financial support, such as providing funding to set up and maintain the genomic garden and public engagement to cultivate a sense of commitment to and ownership of the garden. Their participation can be incentivized by emphasizing the enhancement of their companies’ environmental, social, and governance credentials while reaping potential business benefits, especially for those in the health and medicine sectors. For example, in our collaboration with CapitaLand Group, a real estate group with investment management and development projects spanning 260 cities in over 40 countries, we aim to create a genomic garden in the Geneo building at Singapore Science Park 1 near the National University of Singapore and the biomedical research hub Biopolis to engage the scientific community in the area to understand and preserve local biodiversity. By expanding the repertoire of plant species and making the information public, these projects, driven by commercial entities, will form a distinct channel of efforts to support biodiversity conservation of local and SEA regional plant species.

Conclusions

In conclusion, we have offered guidelines and comprehensive advice for individuals and entities interested in biodiversity conservation and global health to establish their own genomic garden. Our guidelines cover everything from selecting plant species to sequencing pipelines and translational work for population health benefits. Additionally, we have highlighted the significance of international collaborations, whether with academic or commercial institutions, to enhance the depth and breadth of genomic gardens. These collaborations can significantly expand the scope and impact of these gardens.

Unfortunately, it is known that most of the world’s top research institutions, usually with significant financial resources and advanced scientific capabilities, are located outside biodiversity hotspots. Despite its size, Singapore can contribute to regional biodiversity conservation efforts like the genomic garden. At a broader scale, these efforts require collaboration with our neighbors, providing as much tangible and intangible assistance as possible to establish the genomic garden to preserve local biodiversity. Our long-term goal is to collaborate with international communities—academic, commercial, and philanthropic—to safeguard biodiversity while generating greater scientific values, such as understanding the chemogenomic makeup of plants and leveraging this information to benefit human health.

Acknowledgments

The authors would like to thank the Verdant Foundation for their support.

Author contributions

B.T.T. conceived the idea and supervised the project. A.H.L., C.C.Y.N., J.H.H., and E.C.L. carried out different aspects of the project. K.K., P.T., H.K., and I.N. provided expert advice and necessary resources.

Declaration of interests

The authors declare no competing interests.