(1) Evolutionary Genomics of Coccolithophores

Coccolithophores are essential primary producers in the global ocean, converting dissolved inorganic carbon into intricate calcium carbonate scales known as coccoliths. These structures facilitate carbon sequestration to deeper waters by acting as ballast. Despite their ecological importance, the origin and evolutionary history of these striking algae remain inadequately resolved.

Our research focuses on unraveling the evolutionary history and genomic diversity of coccolithophores. We employ advanced genomic sequencing techniques to assemble high-quality genomes from different Haptophyta lineages, encompassing both calcifying coccolithophores and their non-calcifying relatives. This genomic work is complemented by transcriptomics analysis and detailed microscopic observations that examine coccolith morphology and the intracellular structures involved in their formation.

By integrating these methodologies, we aim to construct a robust phylogeny that elucidates the diversification and evolutionary trajectories of coccolithophores. Our comparative genomic analyses seek to uncover the underlying factors contributing to the observed variability in genome size, gene composition, the discordance between nuclear and organellar phylogenies within these species, and the origins and evolution of the key calcification genes.

Through this comprehensive approach, we aim to deepen our understanding of the genetic and morphological evolution of coccolithophores, shedding light on their reproductive biology and the origin of calcification mechanisms—crucial knowledge in an era of changing ocean chemistry and climate.

(1) 鈣板藻 (coccolithophores) 的演化基因體學

鈣板藻是全球海洋中重要的初級生產者，能將溶解的無機碳轉化為稱為鈣板的複雜碳酸鈣結構。這些鈣板透過壓艙石效應促進碳向深海的封存。儘管它們在生態系統中具有重要地位，但關於這些引人注目的藻類的起源和演化歷史仍未得到充分解答。

我們的研究專注於揭示鈣板藻的演化歷史和基因體多樣性。我們運用先進的基因體定序技術，組裝來自不同定鞭藻類群的高品質基因體，包括鈣化的鈣板藻及其非鈣化的近緣種。此基因體研究輔以轉錄體分析和詳細的顯微觀察，檢視鈣板的形態及其形成過程中涉及的細胞內結構。

透過整合這些方法，我們旨在重建定鞭藻的系統發生樹，闡明鈣板藻的多樣化和演化軌跡。並且利用比較基因體分析尋求導致這些物種中基因體大小、基因組成、核基因體與胞器基因體系統發生不一致性的潛在因素，以及關鍵鈣化基因的起源和演化。

透過這種全面的方法，我們希望加深對鈣板藻的遺傳、形態演化與生殖生物學的理解，探索其鈣化機制的起源——這些知識在當前海洋化學和氣候變遷的時代至關重要。

(3) Adaptation and evolution of cheilanthoid ferns in xeric habitats

Not all ferns live in shaded and moist environments. Cheilanthoids, an ecologically unique group of ferns comprising over 20 genera and approximately 500 species, have adapted to and diversified within high-light and xeric habitats, primarily in deserts. Furthermore, a derived lineage of the group has migrated back to seasonally drought regions in monsoon Asia.

Adapting to xeric or seasonally drought habitats, cheilanthoids have developed various strategies, including drought tolerance (utilizing specialized structures to reduce water loss), drought deciduousness, and desiccation tolerance (resurrective ferns!). Our research encompasses the study of their evolutionary history and drought-related morphological structures and functions (Kao et al., 2019), modes of reproduction and speciation in deserts (Kao et al., 2020), as well as the analysis of the contributions of different drought adaptation strategies to their macroevolution.

(3) 碎米蕨 (cheilanthoids) 對乾旱環境的適應與演化

在許多蕨類選擇在陰暗潮濕的環境中生活的同時，也有部分的蕨類選擇在高光與乾燥的環境中生活。鳳尾蕨科（Pteridaceae）的碎米蕨支是其中的佼佼者，它們起源於沙漠並分化出 20 多個屬與近 500 個物種，並且藉由對乾旱環境的適應，散播回到了潮濕但有季節性乾旱的季風亞洲。

面對季節性乾旱的挑戰，碎米蕨支的物種多次演化出各種耐受或逃避乾旱的策略，例如生成減少水分散失的構造、在乾季落葉，或者產生能夠忍受脫水的葉片，因而能在雨季復活。我們對該群植物的研究涵蓋它們的演化歷史（Kao et al., 2019）、在沙漠中的種化機制（Kao et al., 2020），同時深入探討耐旱相關的形態構造與功能，以及這些構造策略對於它們巨觀演化的影響。