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Jr-Kai Yu|Institute of Cellular and Organismic Biology, Academia Sinica

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  • Jr-Kai Yu Professor Jr-Kai Yu Research ID Professor Jr-Kai Yu ORCID
    Research Fellow & MRS Chief
    • SpecialtyDevelopmental Biology, Evolution of Development
    • E-mailjkyu@gate.sinica.edu.tw
    • Tel02-2787-1516, 03-9880544 ext 17
    • Website Jr-Kai Yu's Lab
    • LabR403/ICOB
Professional ExperienceOpenClose
2022
Research Fellow, Institute of Cellular and Organismic Biology, Academia Sinica
2016-2022
Associate Research Fellow, Institute of Cellular and Organismic Biology, Academia Sinica
2007-2016
Assistant Research Fellow, Institute of Cellular and Organismic Biology, Academia Sinica
2005-2007
Postdoctoral Scholar, Division of Biology, California Institute of Technology, USA.
2005
Postdoctoral research fellow, Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, USA.
2005
Ph.D., Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, USA
Research InterestOpenClose

My research is focused on the evolution of developmental mechanisms. I am interested in the origins of chordate and vertebrate novel characters, particularly in understanding the developmental and genomic changes that may have led to the emergence of these innovations. My research team mainly uses cephalochordates (Amphioxus) as our model organism. Amphioxus represent an early-branching chordate group and thus occupy a key phylogenetic position for understanding the possible characters in the proximate invertebrate ancestor of the vertebrates. We apply comparative genomics/transcriptomics and molecular developmental analyses to investigate the key evolutionary changes during the invertebrate-to-vertebrate transition. This transition represents one of the most significant events in the history of life; however, many questions surrounding how vertebrate innovations may have emerged remain unanswered. In collaboration with other researchers, I also extend my research program to other invertebrate deuterostome animals, including hemichordates and echinoderms. The long-term goal of my research program is to understand the genomic and developmental basis underlying the evolution of the distinct body plans of major deuterostome phyla.

Selected PublicationOpenClose
  1. Tsai FY, Lin CY, Su YH, Yu JK*, Kuo DH* (2025) Evolutionary history of bilaterian FoxP genes: complex ancestral functions and evolutionary changes spanning 2R-WGD in the vertebrate lineage. Mol Biol Evol. 42(4):msaf072.
  2. Leong WI, Yu JK, Tsai IJ, Kaczmarek Ł, Lee YC, Lin CP* (2024) Echiniscus gemmatus sp. nov. (Heterotardigrada: Echiniscidae; the spinulosus morphogroup) from Macau, China. Zootaxa 5551(2): 333–352.
  3. Yu JK*, Peng LY, Chen CY, Lu TM, Holland ND, & Holland LZ (2024) Asymmetric segregation of maternal mRNAs and germline-related determinants in Cephalochordate embryos: implications for the evolution of early patterning events in chordates. Integrative & Comparative Biology 64(5): 1243–1254.
  4. Chou C, Lin CY, Lin CY, Wang A, Fan TP, Wang KT, Yu JK, Su YH* (2024) Tracing the evolutionary origin of chordate somites in the hemichordate Ptychodera flava. Integrative & Comparative Biology 64(5): 1226–1242.
  5. Pérez-Posada A*, Lin CY, Fan TP, Lin CY, Chen YC, Gómez-Skarmeta JL, Yu JK, Su YH*, Tena JJ* (2024) Hemichordate regulatory genomics and the gene expression dynamics of deuterostomes. Nat Ecol Evol 8: 2213–2227.
  6. Lin CY, Marlétaz F, Pérez-Posada A, Martínez García PM, Schloissnig S, Peluso P, Conception GT, Bump P, Chen YC, Chou C, Lin CY, Fan TP, Tsai CT, Gómez Skarmeta JL, Tena JJ, Lowe CJ, Rank DR, Rokhsar DS*, Yu JK*, Su YH* (2024) Chromosome-level genome assemblies of two hemichordates provide new insights into deuterostome origin and chromosome evolution, PLOS Biology, 22(6): e3002661.
  7. Huang Z, Xu L*, Cai C, Zhou Y, Liu J, Xu Z, Zhu Z, Kang W, Cen W, Pei S, Chen D, Shi C, Wu X, Huang Y, Xu C, Yan Y, Yang Y, Xue T, He W, Hu X, Zhang Y, Chen Y, Bi C, He C, Xue L, Xiao S, Yue Z, Jiang Y, Yu JK, Jarvis ED, Li G, Lin G*, Zhang Q*, Zhou Q* (2023) Three amphioxus reference genomes reveal gene and chromosome evolution of chordates. Proc Natl Acad Sci USA 120 (10) e2201504120.
  8. Cheng YR*, Lin CY, Yu JK* (2023) Embryonic and post-embryonic development in the parasitic copepod Ive ptychoderae (Copepoda: Iviidae): Insights into its phylogenetic position. PLOS One 18:e0281013.
  9. Gil-Gálvez A, Jiménez-Gancedo S, Pérez-Posada A, Franke M, Acemel RD, Lin CY, Chou C, Su YH, Yu JK, Bertrand S, Schubert M, Escrivá H, Tena JJ*, Gómez-Skarmeta JL (2022) Gain of gene regulatory network interconnectivity at the origin of vertebrates. Proc Natl Acad Sci USA 119 (11) e2114802119.
  10. Yong LW, Lu TM, Tung CH, Chiou RJ, Li KL & Yu JK* (2021) Somite compartments in amphioxus and its implications on the evolution of the vertebrate skeletal tissues. Front Cell Dev Biol 9:607057.
  11. Lin CY, Yu JK* & Su YH* (2021) Evidence for BMP-mediated specification of primordial germ cells in an indirect-developing hemichordate. Evol & Dev 2021 23:28-45.
  12. Lin CY, Lu MYJ, Yue JX, Li KL. Le Pétillon Y, Yong LW, Chen YH, Tsai FU, Lyu YF, Chen CY, Hwang SPL, Su YH* & Yu JK* (2020) Molecular asymmetry in the cephalochordate embryo revealed by single-blastomere transcriptome profiling. PLOS Genetics 16:e1009294.
  13. Simakov O*, Marletaz F, Yue JX, O'Connell B, Jenkins J, Brandt A, Calef R, Tung CH, Huang TK, Schmutz J, Satoh N, Yu JK, Putnam NH, Green RE & Rokhsar DS* (2020). Deeply conserved synteny resolves early events in vertebrate evolution. Nat Ecol Evol 4:820-830.
  14. 1Su YH*, Chen YC, Ting HC, Fan TP, Lin CY, Wang KT & Yu JK* (2019). BMP controls dorsoventral and neural patterning in indirect-developing hemichordates providing insight into a possible origin of chordates. Proc Natl Acad Sci USA 116:12925-12932.