From bud to brew: Multi-omics study decodes tea leaf development

Nanjing Agricultural University The Academy of Science

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Model for the coordinated regulation of bud-to-leaf development and metabolism in tea plant. 

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Credit: Horticulture Research

Tea quality depends on coordinated leaf growth and metabolite accumulation, yet the cellular mechanisms underlying this process remain unclear. In a new multi-omics study, researchers combined single-nucleus RNA sequencing, bulk transcriptomics, and metabolomics to map the developmental transition from bud to mature leaf. They identified distinct cell types and uncovered dynamic shifts in phytohormones, flavonoids, and amino acids during development. Crucially, the study reveals how key genes—including CsmiRNA396b, CsUGT94P1, CsTCP3, and CsTCP14—coordinate leaf expansion and flavonoid glycoside biosynthesis, offering a cellular-level framework for understanding how tea flavor and quality are formed.

Tea leaves contain abundant flavonoids, amino acids, and phytohormones that shape flavor, aroma, and nutritional value. Although individual metabolic pathways and regulatory genes have been characterized, how leaf development and metabolite synthesis are integrated remains poorly understood. The bud-to-leaf transition involves coordinated cell proliferation, differentiation, and metabolic reprogramming. However, most previous studies relied on bulk tissue analyses, masking cell-type-specific regulation. In addition, interactions among microRNAs, transcription factors, and hormone pathways during this transition have not been systematically resolved. Due to these limitations, there is an urgent need for in-depth, cell-resolution investigations into the coordinated regulation of leaf development and metabolism in tea plants.

In a study published (DOI: 10.1093/hr/uhaf281) on January 1, 2026, in Horticulture Research, scientists from the Tea Research Institute of the Chinese Academy of Agricultural Sciences and collaborating institutions applied single-nucleus RNA sequencing to tea buds and successive leaves. By integrating transcriptomic and metabolomic profiling, the team constructed a high-resolution atlas of eight major cell types and 17 cell clusters. Their analyses identified developmental-stage-specific hormone patterns and revealed that genes such as CsmiRNA396b, CsUGT94P1, CsTCP3, and CsTCP14 play central roles in coordinating leaf growth and flavonoid biosynthesis.

The researchers profiled nuclei from buds and the first three leaves, identifying eight major cell types, including palisade mesophyll and proliferating cells. As leaves matured, the proportion of palisade mesophyll cells increased, while proliferating cells decreased. Pseudo-time trajectory analysis revealed branching developmental paths accompanied by activation of genes associated with chloroplast biogenesis and phenylpropanoid metabolism.

Metabolomic profiling uncovered stage-specific hormonal shifts. Auxin, cytokinin, abscisic acid, and jasmonic acid levels declined during maturation, whereas GA8 increased. In contrast, flavonoids—particularly flavonol glycosides and catechins—accumulated progressively, while amino acids such as L-theanine were most abundant in buds and declined in later stages.

Spatial transcriptomic analysis showed that flavonoid biosynthetic genes were predominantly expressed in palisade mesophyll cells. Enzyme assays confirmed that CsUGT94P1 catalyzes the glycosylation of flavonols, explaining the increase in flavonoid glycosides during development. Meanwhile, CsmiRNA396b regulated leaf size by repressing CsGRF1, CsGRF2, and CsGRF3. Two transcription factors encoded by CsTCP3 and CsTCP14 acted antagonistically: CsTCP3 promoted flavonoid accumulation but restricted leaf expansion, whereas CsTCP14 enhanced leaf growth while suppressing flavonoid biosynthesis.

“Our study shows that bud-to-leaf development represents coordinated cellular and metabolic reprogramming rather than simple growth,” the authors explain. “By linking cell-type-specific gene expression to metabolite dynamics, we demonstrate how regulatory networks involving CsmiRNA396b, CsTCP3, CsTCP14, and CsUGT94P1 integrate developmental control with flavor-related metabolism.” The researchers note that resolving these mechanisms at single-cell resolution provides a molecular foundation for improving both tea yield and quality.

The findings offer practical implications for tea breeding and quality optimization. By identifying genes such as CsUGT94P1 and CsTCP3 that influence flavonoid glycoside accumulation, breeders may be able to modulate bitterness and astringency without compromising leaf growth. The discovery that CsmiRNA396b regulates leaf size also opens avenues for improving shoot architecture and harvest efficiency. Beyond tea, the study establishes a framework for dissecting developmental–metabolic coordination in other perennial crops. As single-cell technologies continue to advance, integrated multi-omics strategies are expected to transform our understanding of crop quality formation at cellular resolution.

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References

DOI

10.1093/hr/uhaf281

Original Source URL

https://doi.org/10.1093/hr/uhaf281

Funding information

This work was supported by Central Public-interest Scientific Institution Basal Research Fund (No. 1610212024002), the China Agricultural Research System of MOF and MARA (CARS-019), and the Chinese Academy of Agricultural Sciences through the Agricultural Science and Technology Innovation Program (CAAS-ASTIP-2021-TRICAAS), Zhejiang Provincial Natural Science Foundation of China, under Grant No. LZ22C160008, and Jiangxi Province Talent Plan (jxsq2023102020) to L.C.

About Horticulture Research

Horticulture Research is an open access journal of Nanjing Agricultural University and ranked number one in the Horticulture category of the Journal Citation Reports ™ from Clarivate, 2023. The journal is committed to publishing original research articles, reviews, perspectives, comments, correspondence articles and letters to the editor related to all major horticultural plants and disciplines, including biotechnology, breeding, cellular and molecular biology, evolution, genetics, inter-species interactions, physiology, and the origination and domestication of crops.

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Journal

Horticulture Research

DOI

10.1093/hr/uhaf281 

Subject of Research

Not applicable

Article Title

Integrated single-nucleus transcriptomic and metabolomic insights into bud-to-leaf development and metabolite synthesis in tea plant

 

Over 70% of global ecosystems remain unsampled for critical underground fungi

Society for the Protection of Underground Networks

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Drylands including deserts, steppe regions, and grasslands, are often overlooked in ecology. This is surprising as they cover roughly 45% of the Earth’s terrestrial surface. Examples include the Kazakh steppe, the Chihuahuan Desert, and the Sahelian Acacia savanna. They may be underrepresented or biased in ecological sampling because vegetation cover is typically sparse.

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Credit: Yevgeniy Lechshenko / SPUN

Underground, intricate networks of soil fungi underpin the functioning of terrestrial ecosystems. Yet despite their global importance, only 30% of global ecosystems have been sampled for these fungal partners.

Arbuscular mycorrhizal fungi form important resource trade partnerships with plants. The fungi grow complex networks to help plants acquire nutrients, such as phosphorus and nitrogen. In exchange, plants provide carbon to the fungi, with roughly one billion tons of carbon transferred annually from plants to mycorrhizal fungal partners. Because these networks move massive amounts of carbon, nutrients, and water, they are often referred to as one of Earth’s circulatory systems.

In a study published in FEMS Microbiology Letters, researchers analyzed environmental DNA from the largest global dataset of arbuscular mycorrhizal fungi compiled to date. Their findings reveal a striking gap: More than 70% of the world’s ecoregions have no sequencing data for AM fungi. By mapping these gaps, the researchers highlight how data collection has been heavily skewed toward just a few regions. This month, the study was awarded “Best Study of 2025” in FEMS Microbiology Letters by the journal’s Senior Editors. 

“Arbuscular mycorrhizal fungi underpin the functioning of most terrestrial ecosystems, but our data are heavily skewed toward a limited set of regions,” Dr. Justin Stewart the lead author and evolutionary biologist notes. “If we want robust predictions about biodiversity, carbon cycling, and ecosystem resilience, we need far more representative global sampling.”

Large areas of Africa, parts of Asia, boreal systems, and drylands remain severely underrepresented. The consequences extend beyond biodiversity surveys. Arbuscular mycorrhizal fungi influence plant productivity, soil aggregation, and carbon stabilization. Without more representative sampling, projections of fungal distributions and their contributions to climate mitigation and restoration targets carry substantial uncertainty. Drawing attention to these severe data gaps can encourage researchers to focus future sampling efforts in key habitats.

The study is part of an ongoing global effort led by the Society for the Protection of Underground Networks. Their mission is to map and advocate for the protection of Earth’s mycorrhizal networks. Last year, collaborators published global maps of mycorrhizal fungal diversity in Nature. These maps integrated nearly three billion DNA sequences, satellite imagery, and approximately 25,000 soil samples to generate predictive models of mycorrhizal fungal biodiversity and endemism globally. 

While these models can predict biodiversity patterns globally – including in ecosystems without samples – they require validation. Uncertainty increases in areas with little or no empirical data. Underground arbuscular mycorrhizal fungal DNA data is still missing or not publicly available for more than 600 terrestrial ecosystems. Reducing this uncertainty will require targeted sampling and ground truthing campaigns across underrepresented regions.

To address this, SPUN launched the Underground Explorers Program, a decentralized and community-led initiative in which researchers and local communities collect soil samples in underrepresented ecosystems. By expanding sampling into overlooked habitats, the program aims to reduce uncertainty in global maps and generate open access data that improve predictions and forecasts of fungal biodiversity. 

“Environmental DNA allows us to identify fungal species from even a teaspoon of soil,” Dr. Bethan Manley, the Lead Computational Biologist at SPUN and an author on this study. “It is one of the most reliable tools we have for documenting biodiversity belowground because it captures species of fungi that spend their whole lives out of sight in the soil, many of which are impossible to cultivate in the lab. But these environmental DNA sequencing surveys can only work once the soil is collected in the first place. Expanding sampling on the ground remains essential.” 

By identifying where information is missing, the new analysis provides a roadmap for future research. Filling these gaps will clarify the biogeographic distributions of AM fungal species and strengthen their integration into environmental policy, restoration planning, and global carbon models.

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Advancing knowledge on the biogeography of arbuscular mycorrhizal fungi to support Sustainable Development Goal 15: Life on Land. FEMS Microbiology Letters

https://doi.org/10.1093/femsle/fnaf055

This work was supported by grants from the Jeremy and Hannelore Grantham Environmental Trust, Paul Allen Family Foundation, the Schmidt Family Foundation, NWO Gravity Grant MICROP (024.004.014), the European Union (ERC, Programme—HORIZON, acronym—NUCLEAR MIX, Project–101076062), and an Ammodo grant. GlobalAMFungi was supported by the Ministry of Education, Youth and Sports of the Czech Republic grant Talking microbes—understanding microbial interactions within One Health framework (CZ.02.01.01/00/22_008/0004597).

The Society for the Protection of Underground Networks (SPUN) is a science-based initiative launched in 2021 to map and advocate for the protection of the mycorrhizal communities that regulate Earth’s climate and ecosystems. 
 

 

These fungi form extensive networks of mycelium in soils, where they establish intimate associations with plant roots. The fungal threads forage for nutrients in the soil and trade them with plants in exchange for carbon, with global transfers estimated to reach roughly one billion tons of carbon per year.

Credit

Loreto Oyarte Gálvez - VU Amsterdam, AMOLF, SPUN

 

Colored areas on the map indicate ecoregions without publicly available AM fungal sequencing data. More than 70% of terrestrial ecoregions remain unsampled for AM fungi. Across those ecoregions where sampling has occurred, the mean number of samples per ecoregion is only four, highlighting limited replication even in represented regions. These colored regions represent priority targets for future field expeditions and coordinated sampling efforts.

Credit

SPUN

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Journal

FEMS Microbiology Letters

DOI

10.1093/femsle/fnaf055 

Method of Research

Data/statistical analysis

Subject of Research

Not applicable

Article Title

Advancing knowledge on the biogeography of arbuscular mycorrhizal fungi to support Sustainable Development Goal 15: Life on Land

 

People’s gut bacteria worse in areas with higher social deprivation

King's College London

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Living in a poorer neighbourhood in the UK could impact the make-up of your gut microbiome, potentially leading to worse health. 

New research, led by King’s College London and the University of Nottingham, found that people living in areas of higher social deprivation have a less diverse range of bacteria in their gut. 

The study, published in npj biofilms and microbiomes, also found people in these areas have less short-chain fatty acid-producing bacteria – which are vital for reducing inflammation and regulating energy metabolism.  

These differences in gut bacteria could lead to worse health outcomes including mental health and metabolic health (which helps manage people’s energy levels), immune system function, and mood stability. 

In particular, the research found a link between those in areas of higher deprivation who had worse gut microbiomes and mental health conditions such as anxiety. 

In the study, the researchers analysed the gut bacteria of 1,390 female twin individuals from TwinsUK along with their residential postcodes to identify the participants’ area level socioeconomic status.  

To measure the deprivation of an area they primarily used the well-established Townsend Deprivation Index. The Townsend Deprivation Index measures deprivation using practical indicators like unemployment, overcrowding, and home or car ownership to measure material deprivation of different areas.  

The researchers identified 12 bacterial species linked to living in more deprived areas. Two of these, Lawsonibacter and Intestinimonas massiliensis, were negatively associated not only with deprivation, but also with higher rates of anxiety and diabetes. These two bacteria normally produce butyrate, a helpful substance in the gut that supports blood sugar control, energy balance, and communication between the gut and the brain. Changes in these bacteria may help explain how social disadvantage could affect both mental and physical health. 

The findings suggest the gut microbiome may play a role in the connections between social deprivation and adverse health outcomes. Researchers hope that interventions such as fibre-rich diets that support butyrate-producing bacteria, and targeted probiotic approaches to improve gut health, could help counter some of the harmful effects that socioeconomic stress has on a person’s mental and physical wellbeing. 

Dr Cristina Menni, Senior author of the study and a Senior Lecturer in Molecular Epidemiology at King’s College London, said: “Although this is still an emerging area of research, we know that the diversity of bacteria in the gut plays an important role on overall health. Our findings suggests that people who live in more socially deprived areas of the UK may have less diverse gut microbiomes, which could affect other aspects of their health. We hope that this might lead to interventions that support gut health and help improve overall wellbeing.” 

Dr Yu Lin, first author of the study and a Research Associate at King’s College London, said: “The gut microbiome might be one of the ways our environment and social circumstances, such as chronic stress, financial strain, access to healthy food, affect both our mental health and our metabolic health. These microbes, in turn, influence how the body process energy and communicate with the brain. In other words, the bacteria in our gut could help explain how where we live and the stresses we face shape our overall wellbeing. We hope that our findings will contribute to new strategies for supporting health in disadvantaged communities.”  

Dr Ana Valdes, Professor of Molecular Epidemiology at the University of Nottingham, said: "By uncovering how social deprivation translates into biological changes – fundamentally altering our gut microbiome composition – we can now design targeted interventions to reverse some of these health inequalities. Understanding these pathways gives us actionable targets, whether through dietary fibre, probiotics, or other gut-focused strategies, to break the cycle linking poverty to poor health outcomes." 

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Journal

npj Biofilms and Microbiomes

Subject of Research

People