Ku, Chuan (顧銓)

Assistant Research Fellow

  • 2023–present EMBO Global Investigator, European Molecular Biology Organization
  • 2019-present Assistant Research Fellow, Institute of Plant and Microbial Biology, Academia Sinica
  • 2016-2018 Postdoc, Department of Plant and Environmental Sciences, Weizmann Institute of Science, Israel (EMBO Long-Term Fellow)
  • 2013-2016 Dr. rer. nat., Department of Biology, University of Düsseldorf, Germany
  • 2012-2013 RA, Institute of Plant and Microbial Biology, Academia Sinica
  • 2009-2011 M.Sc., Institute of Ecology and Evolutionary Biology, National Taiwan University
  • 2005-2009 B.Sc., Department of Life Science, National Taiwan University
  • +886-2-2787-1147(Lab)
  • +886-2-2787-1059(Office)
  • chuanku@gate.sinica.edu.tw
  • Microbial eukaryote evolution and ecology; algae, protists and giant viruses; omics; single-cell biology; bioinformatics
  • Lab Website
  • Google Scholar
  • ResearchGate

Microbial Eukaryote Evolution and Ecology

Eukaryotes are organisms with complex cells that arose from the fusion of their bacterial and archaeal predecessors. Plants and animals are the most prominent examples to the human eye, but the vast majority of eukaryotes (incl. protists/algae), like their common ancestor, are microscopic unicellular life forms with intriguing evolutionary history and ecological behaviors. It is our broad interest to understand how different microbial eukaryotes came to be what they are today and what roles they play in various environments on Earth.

Our research focuses on two main topics:

Microalgal genomics
Unicellular algae in the ocean are characterized by high growth and turnover rate and account for half of the photosynthetic production on our planet. Currently we are specifically interested in coccolithophores – a group of microalgae capable of converting CO2 and calcium into calcite (chalk) platelets that can be sedimented at the bottom of the ocean. The best known of these armored phytoplankton, Emiliania huxleyi, is a globally distributed species that forms massive annual blooms (dramatic changes in population size) and has diploid and haploid phases with obscure transitions. Using state-of-the-art sequencing technology, omic and bioinformatic methods, and single-cell approaches, our goal is to elucidate the dynamics of coccolithophore genomes across time and space.

Giant viruses and their eukaryotic hosts
Viruses are found in almost all living things and ecosystems. The nucleocytoplasmic large DNA viruses include the largest viruses known today in terms of physical and genome sizes (many even larger than small bacterial genomes) and infect diverse hosts ranging from vertebrates (e.g., African swine fever virus), invertebrates, amoebae, and various algae in both freshwater and seawater. Major themes in our lab include how the large genomes of giant viruses are organized and expressed, as well as how their genome regulation has changed through the long history of coevolution with their eukaryotic hosts.

From time to time we have open positions for postdocs, PhD students, master students and research associates. If you are interested in joining us, please contact Chuan Ku by email.

All publication list

Selected publication list

  • Chia-Chun Tung, Shang-Che Kuo, Chia-Ling Yang, Jhong-He Yu, Chia-En Huang, Pin-Chien Liou, Ying-Hsuan Sun, Peng Shuai, Jung-Chen Su, Chuan Ku#, Ying-Chung Jimmy Lin# (2023): Single-cell transcriptomics unveils xylem cell development and evolution. Genome Biology 24: 3. DOI: 10.1186/s13059-022-02845-1 #Corresponding authors 
  • Tzu-Tong Kao, Tzu-Haw Wang, Chuan Ku# (2022): Rampant nuclear-mitochondrial-plastid phylogenomic discordance in globally distributed calcifying microalgae. New Phytologist 235(4): 1394-1408. DOI: 10.1111/nph.18219 #Corresponding author 
  • Tsu-Wang Sun, Chuan Ku# (2021): Unraveling gene content variation across eukaryotic giant viruses based on network analyses and host associations. Virus Evolution 7(2): veab081. DOI: 10.1093/ve/veab081 #Corresponding author
  • Chuan Ku# (2021): Giant virus-eukaryote interactions as ecological and evolutionary driving forces. mSystems 6(4): e00737-21. DOI: 10.1128/mSystems.00737-21 #Corresponding author
  • Tsu-Wang Sun, Chia-Ling Yang, Tzu-Tong Kao, Tzu-Haw Wang, Ming-Wei Lai, Chuan Ku# (2020): Host range and coding potential of eukaryotic giant viruses. Viruses 12(11): 1337. DOI: 10.3390/v12111337 #Corresponding author
  • Chuan Ku, Uri Sheyn, Arnau Sebé-Pedrós, Shifra Ben-Dor, Daniella Schatz, Amos Tanay, Shilo Rosenwasser, Assaf Vardi (2020): A single-cell view on alga-virus interactions reveals sequential transcriptional programs and infection states. Science Advances 6(21): eaba4137. DOI: 10.1126/sciadv.aba4137
  • Chuan Ku#, Tsu-Wang Sun (2020): Did giant and large dsDNA viruses originate before their eukaryotic hosts? Proceedings of the National Academy of Sciences of the United States of America 117(6): 2747-2748. DOI:10.1073/pnas.1919860117 #Corresponding author
  • Chuan Ku#, Arnau Sebé-Pedrós# (2019): Using single-cell transcriptomics to understand functional states and interactions in microbial eukaryotes. Philosophical Transactions of the Royal Society B 374(1786): 20190098. DOI:10.1098/rstb.2019.0098 #Corresponding authors
  • Chuan Ku, Uri Sheyn, Arnau Sebé-Pedrós, Shifra Ben-Dor, Daniella Schatz, Amos Tanay, Shilo Rosenwasser, Assaf Vardi (2019): Tracking infection dynamics at single-cell level reveals highly-resolved expression programs of a large virus infecting algal blooms. bioRxiv. DOI:10.1101/757542
  • Chuan Ku, Noa Barak-Gavish, Mark Maienschein-Cline, Stefan J. Green, Assaf Vardi (2018): Complete genome sequence of Sulfitobacter sp. strain D7, a virulent bacterium isolated from an Emiliania huxleyi algal bloom in the North Atlantic. Microbiology Resource Announcements 7(19): e01379-18. DOI:10.1128/MRA.01379-18
  • Noa Barak-Gavish, Miguel Frada, Chuan Ku, Peter A. Lee, Giacomo R. DiTullio, Sergey Malitsky, Asaph Aharoni, Stefan J. Green, Ron Rotkopf, Elena Kartvelishvily, Uri Sheyn, Daniella Schatz, Assaf Vardi (2018): Bacterial virulence against an oceanic bloom-forming phytoplankter is mediated by algal DMSP. Science Advances 4(10): eaau5716. DOI: 10.1126/sciadv.aau5716
  • William F. Martin, Mayo Roettger, Chuan Ku, Sriram G. Garg, Shijulal Nelson-Sathi, Giddy Landan (2017): Late mitochondrial origin is an artefact. Genome Biology and Evolution 9(2): 373-379. DOI:10.1093/gbe/evx027
  • Chuan Ku#, William F. Martin# (2016): A natural barrier to lateral gene transfer from prokaryotes to eukaryotes revealed from genomes: the 70% rule. BMC Biology 14:89. DOI:10.1186/s12915-016-0315-9 #Corresponding authors (recommended by Faculty of 1000: http://f1000.com/prime/726862983)
  • Chuan Ku, Shijulal Nelson-Sathi, Mayo Roettger, Filipa L. Sousa, Peter J. Lockhart, David Bryant, Einat Hazkani-Covo, James O. McInerney, Giddy Landan, William F. Martin (2015): Endosymbiotic origin and differential loss of eukaryotic genes. Nature 524:427-432. DOI:10.1038/nature14963 (recommended by Faculty of 1000: http://f1000.com/prime/725729035)
  • Chuan Ku, Shijulal Nelson-Sathi, Mayo Roettger, Sriram Garg, Einat Hazkani-Covo, William F. Martin (2015): Endosymbiotic gene transfer from prokaryotic pangenomes: Inherited chimerism in eukaryotes. Proceedings of the National Academy of Sciences of the United States of America 112(33): 10139-10146. DOI:10.1073/pnas.1421385112
  • Chuan Ku, Mayo Roettger, Verena Zimorski, Shijulal Nelson-Sathi, Filipa L. Sousa, William F. Martin (2014): Plastid origin: Who, when and why? Acta Societatis Botanicorum Poloniae 83(4):281-289 DOI:10.5586/asbp.2014.045
  • Verena Zimorski, Chuan Ku, William F. Martin, Sven B. Gould (2014): Endosymbiotic theory for organelle origins. Current Opinion in Microbiology 22:38-48. DOI:10.1016/j.mib.2014.09.008
  • Chuan Ku, Wen-Sui Lo, Chih-Horng Kuo (2014): Molecular evolution of the actin-like MreB protein gene family in wall-less bacteria. Biochemical and Biophysical Research Communications 446(4):927-932. DOI:10.1016/j.bbrc.2014.03.039
  • Tean-Hsu Chang, Wen-Sui Lo, Chuan Ku, Ling-Ling Chen, Chih-Horng Kuo (2014): Molecular evolution of the substrate utilization strategies and putative virulence factors in mosquito-associated Spiroplasma species. Genome Biology and Evolution 6(3): 500-509. DOI:10.1093/gbe/evu033
  • Chuan Ku, Wen-Sui Lo, Ling-Ling Chen, Chih-Horng Kuo (2014): Complete genome sequence of Spiroplasma apis B31T (ATCC 33834), a bacterium associated with May disease of honeybees (Apis mellifera). Genome Announcements 2(1): e01151-13. DOI:10.1128/genomeA.01151-13
  • Chuan Ku, Jer-Ming Hu (2014): Phylogenetic and cophylogenetic analyses of the leaf-nodule symbiosis in Ardisia subgenus Crispardisia (Myrsinaceae): Evidence from nuclear and chloroplast markers and bacterial rrn operons. International Journal of Plant Sciences 175(1):92-109. DOI:10.1086/673306
  • Chuan Ku, Wen-Sui Lo, Chih-Horng Kuo (2013): Horizontal transfer of potential mobile units in phytoplasmas. Mobile Genetic Elements 3(5):e26145. DOI:10.4161/mge.26145
  • Wen-Sui Lo, Chuan Ku, Ling-Ling Chen, Tean-Hsu Chang, Chih-Horng Kuo (2013): Comparison of metabolic capacities and inference of gene content evolution in mosquito-associated Spiroplasma diminutum and S. taiwanense. Genome Biology and Evolution 5(8):1512-1523. DOI:10.1093/gbe/evt108
  • Chuan Ku, Wan-Chia Chung, Ling-Ling Chen, Chih-Horng Kuo (2013): The complete plastid genome sequence of Madagascar periwinkle Catharanthus roseus (L.) G. Don: Plastid genome evolution, molecular marker identification, and phylogenetic implications in asterids. PLoS ONE 8(6):e68518. DOI:10.1371/journal.pone.0068518
  • Chuan Ku, Wen-Sui Lo, Ling-Ling Chen, Chih-Horng Kuo (2013): Complete genomes of two dipteran-associated spiroplasmas provided insights into the origin, dynamics, and impacts of viral invasion in Spiroplasma. Genome Biology and Evolution 5(6):1151-1164. DOI:10.1093/gbe/evt084
  • Chuan Ku, Jer-Ming Hu, Chih-Horng Kuo (2013): Complete plastid genome sequence of the basal asterid Ardisia polysticta Miq. and comparative analyses of asterid plastid genomes. PLoS ONE 8(4):e62548. DOI:10.1371/journal.pone.0062548
  • Chuan Ku, Liang-Chi Wang, Su-Hwa Chen (2012): Dispersal of airborne pollen in Chatienshan nature reserve, northern Taiwan, with emphasis on Taiwan beech. Taiwania 57(4):331-341.
Postdoctoral researcher
Tzu-Tong Kao
Ph.D. (Biology, Duke University, USA)
+886-2-2787-1147 (R222E)
Research associate
Chia-Ling Yang
M.Sc. (Plant Biology, National Taiwan University)
+886-2-2787-1147 (R222)
Bioinformatician & research associate
Tzu-Haw Wang
M.Sc. (Oceanography, National Taiwan University)
+886-2-2787-1147 (R220)
Undergrad researcher
Tsu-Wang Sun
(Plant Pathology, National Chung Hsing University)
+886-2-2787-1147 (R220)
Research intern
Siwat Chang
B.Sc. (Biochemistry, Imperial College London, UK)
+886-2-2787-1147 (R220C)
Research intern
Vi Le
(Biotechnology, Vietnamese National University, Vietnam)
+886-2-2787-1147 (R222D)