我們的研究聚焦於利用基因體學的工具，探索微生物在自然界中演化與適應的奧秘。實驗室長期關注的對象包括真菌、酵母菌（特別是Saccharomyces屬）、食蟲植物與其共生微生物，以及其他與亞洲環境（從森林到海底到人體）息息相關的真核微生物。我們特別擅長運用Oxford Nanopore Technologies（ONT）等第三代定序技術，透過長讀序列的優勢解析複雜基因體與遺傳調控機制，致力於回答基因組層面的生態與演化問題。

Our research focuses on utilising omic tools to explore the microognism evolution and adaptation in nature. We have long-standing interests in fungi, yeast (particularly the genus Saccharomyces), carnivorous plants and their symbiotic microorganisms, as well as other eukaryotic microbes closely related to Asia’s environment. We are particularly interested in applying third-generation sequencing technologies, such as Oxford Nanopore Technologies (ONT), to leverage the advantages of long-read sequencing for quantifying diversity at various timescales (comparative, population and communities), aiming to address ecological and evolutionary questions at the genomic level.

主要研究方向如下：

• 自然環境中的微生物族群基因體學與生物地理學
• 真菌與酵母菌的基因體演化
• 食蟲植物與微生物之間的互動與共演化
• 寄生生物的基因組演化與致病機制
• 第三代定序技術的開發與應用

自然環境中的微生物族群基因體學與生物地理學 Genomics and Biogeography of Microbial Populations in Natural Environments

微生物族群在自然界的遷移與散布涉及複雜的生物地理過程。我們以真菌與線蟲等重要生態角色為研究對象，透過基因體比較與族群分析，探索微生物如何透過宿主（如植物、昆蟲）或環境因素（如風、水流）進行遷移與散布，並分析這些過程如何影響微生物的遺傳多樣性及族群結構。透過ONT長讀技術，我們成功組裝了多個微生物物種的染色體級基因組，揭示其與宿主共遷或環境散布的遺傳標誌，進一步闡明微生物族群演化的生物地理學基礎。

Microbial migration and dispersal in nature involve complex biogeographic processes. Focusing on ecologically significant microbes such as fungi and nematodes, we use genomic comparisons and population analyses to investigate how microbes migrate and disperse via hosts (e.g., plants, insects) or environmental vectors (e.g., wind, water currents), and how these processes shape their genetic diversity and population structure. Utilizing ONT long-read sequencing technology, we have successfully assembled chromosome-level genomes of various microbial species, revealing genetic signatures related to host-mediated migration or environmental dispersal, thereby enhancing our understanding of the biogeographic basis of microbial population evolution.

真菌與酵母菌的基因體演化 Genomic Evolution of Fungi and Yeast

真菌與酵母菌在各種環境中展現了豐富的生活史策略，例如有性與無性繁殖、孢子化及菌絲生長等。我們透過比較基因體學及族群基因體學方法，研究這些生命策略如何影響真菌基因體的變化、維持與適應。例如，透過分析野外及發酵環境中的Saccharomyces酵母菌菌株，我們發現有性生殖頻率的改變會明顯影響基因組內雜合性的維持與喪失。此外，我們亦研究染色體重組及雜合性喪失如何影響酵母菌的演化適應，進一步理解真菌生活史演化背後的基因調控機制。

Fungi in particular and yeast exhibit diverse life-history strategies in various environments, such as sexual and asexual reproduction, sporulation, and filamentous growth. We employ comparative genomics and population genomic approaches to study how these life-history strategies influence genomic changes, maintenance, and adaptation. For instance, by analyzing wild and fermentative Saccharomyces strains, we discovered that variations in sexual reproduction frequency significantly affect genomic heterozygosity maintenance and loss. Additionally, we investigate how chromosomal recombination and loss of heterozygosity shape yeast evolutionary adaptation, thereby advancing our understanding of the genetic mechanisms behind fungal life-history evolution.

食蟲植物與微生物之間的互動與共演化 Interactions and Co-evolution between Carnivorous Plants and Microbes

食蟲植物為適應養分貧乏的環境，演化出捕食動物並與微生物共生的獨特策略。我們的研究首次揭示了毛氈苔（Drosera spatulata）與其共生的嗜酸性真菌（Acrodontium crateriforme）在捕食與消化昆蟲過程中密切合作，雙方形成緊密的共生關係。我們透過基因體、轉錄體及代謝體等多重組學的分析，釐清這種獨特互動的遺傳基礎與生理機制。未來我們也計畫進一步探索其他食蟲植物的共生微生物組成及其生態功能，從而更全面地理解植物與微生物共演化的多樣性。

Carnivorous plants have evolved unique strategies involving animal prey capture and microbial symbiosis to survive in nutrient-poor environments. Our studies have revealed, for the first time, a close cooperative interaction between the sundew (Drosera spatulata) and its symbiotic acidophilic fungus (Acrodontium crateriforme) during insect capture and digestion, forming a tightly integrated symbiotic relationship. Using genomic, transcriptomic, and metabolomic analyses, we elucidate the genetic basis and physiological mechanisms underlying this unique interaction. In the future, we plan to further explore the microbial symbionts and their ecological roles in other carnivorous plants to comprehensively understand plant-microbe co-evolutionary diversity.

寄生生物的基因組演化與致病機制 Genomic Evolution and Pathogenic Mechanisms of Parasites

寄生是一種普遍的生命策略，寄生生物往往經歷基因組簡化、基因家族擴張或收縮、甚至水平基因轉移等演化過程。我們透過比較病原微生物與其近緣自由生活物種的基因組，找出寄生適應的遺傳跡象與致病相關基因。此外，藉由宿主與病原體的共培養實驗，我們探索這些致病基因在感染過程中的動態調控，以期深入理解寄生生物如何操控宿主代謝及免疫反應。

Parasitism is a prevalent life strategy characterized by genomic simplification, gene family expansions or contractions, and even horizontal gene transfer. By comparing the genomes of pathogenic microbes with their free-living relatives, we identify genetic signatures of parasitic adaptation and disease-related genes. Furthermore, through host-pathogen co-culture experiments, we explore dynamic gene regulation during infection to better understand how parasites manipulate host metabolism and immune responses.

第三代定序技術的開發與應用 Development and Application of Long-read Sequencing

為了有效解決複雜基因組解析的挑戰，本實驗室積極發展並優化ONT長讀定序的實驗與分析流程，包括全基因組組裝、變異偵測、表觀遺傳修飾分析等技術。我們持續改進生物資訊分析管線，提升定序資料的準確性與應用範圍。ONT技術不僅支持我們對微生物及其共生體的研究，更為現場即時監測微生物族群提供了新的可能性。

To effectively resolve complex genomic challenges, our lab actively develops and optimizes experimental and analytical pipelines for ONT long-read sequencing, including genome assembly, variant detection, and epigenetic modifications analysis. We continuously refine bioinformatics pipelines to improve sequencing accuracy and broaden application capabilities. ONT technology not only supports our studies on microbes and their symbionts but also provides novel possibilities for real-time microbial population monitoring in field conditions.

The species that we studied - can you guess which is which?

From left to right:

1. Saccharomyces cerevisiae
2. Fusarium keratoplasticum and Fusarium falciforme
3. Acrodontium crateriforme
4. Tropical broadleaf forests
5. Human gut
6. Bursaphelenchus xylophilus
7. Aphelenchoides besseyi species complex
8. Free-living marine nematodes
9. Us.