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

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Jr-Kai Yu's Lab

  • Jr-Kai Yu
    Associate Research Fellow & MRS Chief
    • SpecialtyDevelopmental Biology, Evolution of Development
    • E-mailjkyu@gate.sinica.edu.tw
    • Tel02-2787-1516, 03-9880544 ext 17
    • LabR403/ICOB
Lab IntroductionOpenClose

My research is focused on developmental mechanisms of the cephalochordate amphioxus. Amphioxus is a basal chordate and is the best available stand-in for the proximate invertebrate ancestor of the vertebrates. The body plans of amphioxus and vertebrates share chordate key features (e.g. dorsal nerve cord, notochord, segmented somites, and pharyngeal gill slits). However, vertebrates have additional characters not present in amphioxus- namely, a more elaborate head and forebrain, migratory neural crest, and neurogenic placodes. My goal in studying the developmental genetics of amphioxus is to elucidate the basic patterning mechanisms for the chordate body plan. Because of its important evolutionary position, comparative studies of amphioxus with vertebrates will also provide important insights to understand the origin of the patterning mechanisms that lead to the vertebrate body plan.

One of the specific questions I would like to address with amphioxus as a model system is the origin of neural crest. Arising at the neural plate border, vertebrate neural crest cells undergo an epithelial to mesenchymal transition (EMT) to become a migratory cell population that forms numerous differentiated cell types, including the craniofacial skeleton, much of the peripheral nervous system, and pigment cells of the skin. Evolution of the neural crest is a hallmark of vertebrates, responsible for many complex structures of the vertebrate head that are lacking in invertebrate chordates, like amphioxus. By comparing the genetic controls operating during development at the edges of the neural plate in embryos of amphioxus and traditional vertebrate models, we can start to pin-point which part of the gene regulatory network might have been changed over time.

cDNA database for the cephalochordate amphioxus Branchiostoma floridae

Lab MemberOpenClose
Name Job Title Telephone Email Remark
Jr-Kai Yu Assistant Research Fellow 02-2787-1516 jkyu@gate.sinica.edu.tw
PublicationOpenClose
  1. Ching‐Yi Lin, (Jr‐Kai Yu*), Yi‐Hsien Su*. Evidence for BMP‐mediated specification of primordial germ cells in an indirect‐developing hemichordate. Evolution & Development. e12361, 2020-12.

  2. Che-Yi Lin, Mei-Yeh Jade Lu, Jia-Xing Yue, Kun-Lung Li, Yann Le Pétillon, Luok Wen Yong, Yi-Hua Chen, Fu-Yu Tsai, Yu-Feng Lyu, Cheng-Yi Chen, Sheng-Ping L. Hwang, Yi-Hsien Su*, (Jr-Kai Yu*). Molecular asymmetry in the cephalochordate embryo revealed by single-blastomere transcriptome profiling. PLOS Genetics. 16(12) e1009294, 2020-12.

  3. 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*. Deeply conserved synteny resolves early events in vertebrate evolution.. NATURE ECOLOGY & EVOLUTION. 4(6), 820-830, 2020-06.

  4. Wang YT, Tseng TL, Kuo YC, (Yu JK), Su YH, Poss KD, Chen CH*. Genetic Reprogramming of Positional Memory in a Regenerating Appendage.. CURRENT BIOLOGY. 29(24), 4193-4207.e4, 2019-12.

  5. Su YH*, Chen YC, Ting HC, Fan TP, Lin CY, Wang KT, (Yu JK*). BMP controls dorsoventral and neural patterning in indirect-developing hemichordates providing insight into a possible origin of chordates.. Proceedings of the National Academy of Sciences of the United States of America. 116(26), 12925-12932, 2019-06.

  6. Kawaguchi M, Sugiyama K, Matsubara K, Lin CY, Kuraku S, Hashimoto S, Suwa Y, Yong LW, Takino K, Higashida S, Kawamura D, (Yu JK), Seki Y*. Co-option of the PRDM14-CBFA2T complex from motor neurons to pluripotent cells during vertebrate evolution.. Development (Cambridge, England). 146(2), dev168633, 2019-01.

  7. Yong LW, Kozmikova I, (Yu JK*). Using Amphioxus as a Basal Chordate Model to Study BMP Signaling Pathway.. Methods in Molecular Biology. 1891, 91-114, 2019.

  8. Marletaz, F., Firbas, P.N., Maeso, I. #, Tena, J.J., Bogdanovic, O., Perry, M., Wyatt, C.D.R., de la Calle-Mustienes, E., Bertrand, S., Burguera, D., Acemel, R.D., van Heeringen, S.J., Naranjo, S., Herrera-Ubeda, C., Skvortsova, K., Jimenez-Gancedo, S., Aldea, D., Marquez, Y., Buono, L., Kozmikova, I., Permanyer, J., Louis, A., Albuixech-Crespo, B., Le Petillon, Y., Leon, A., Subirana, L., Balwierz, P.J., Duckett, P.E., Farahani, E., Aury, J.M., Mangenot, S., Wincker, P., Albalat, R., Benito-Gutierrez, E., Canestro, C., Castro, F., D'Aniello, S., Ferrier, D.E.K., Huang, S., Laudet, V., Marais, G.A.B., Pontarotti, P., Schubert, M., Seitz, H., Somorjai, I., Takahashi, T., Mirabeau, O., Xu, A., Yu, J.K., Carninci, P., Martinez-Morales, J.R., Crollius, H.R., Kozmik, Z., Weirauch, M.T., Garcia-Fernandez, J., Lister, R., Lenhard, B., Holland, P.W.H., Escriva, H. #, Gomez-Skarmeta, J.L. # and Irimia, M. # (2018). Amphioxus functional genomics and the origins of vertebrate gene regulation. Nature 564, 64-70.

  9. Nakashima, K.#, Kimura, S., Ogawa, Y., Watanabe, S., Soma, S., Kaneko, T., Yamada, L., Sawada, H., Tung, C.H., Lu, T.M., Yu, J.K., Villar-Briones, A., Kikuchi, S. and Satoh, N. (2018). Chitin-based barrier immunity and its loss predated mucus-colonization by indigenous gut microbiota. Nature Communications 9, 3402.

  10. Fan, T.P., Ting, H.C., Yu, J.K. and Su, Y.H.# (2018). Reiterative use of FGF signaling in mesoderm development during embryogenesis and metamorphosis in the hemichordate Ptychodera flava. BMC Evolutionary Biology 18, 120.

  11. Zieger, E., Garbarino, G., Robert, N.S.M., Yu, J.K., Croce, J.C., Candiani, S. and Schubert, M.# (2018). Retinoic acid signaling and neurogenic niche regulation in the developing peripheral nervous system of the cephalochordate amphioxus. Cell Mol Life Sci, 75, 2407-2429.

  12. Kozmikova, I.# and Yu, J.K.# (2017). Dorsal-ventral patterning in amphioxus: current understanding, unresolved issues, and future directions. Int J Dev Biol 61, 601-610.

  13. Yong, L.W., Bertrand, S., Yu, J.K., Escriva, H. and Holland, N.D.# (2017). Conservation of BMP2/4 expression patterns within the clade Branchiostoma (amphioxus): Resolving interspecific discrepancies. Gene Expr Patterns 25-26, 71-75.

  14. Su, Y.H.# and Yu, J.K.# (2017). EvoDevo: Changes in developmental controls underlying the evolution of animal body plans. Dev Biol 427, 177-178. (Editorial for the special issue).

  15. Hu, H., Uesaka, M., Guo, S., Shimai, K., Lu, T.M., Li, F., Fujimoto, S., Ishikawa, M., Liu, S., Sasagawa, Y., Zhang, G., Kuratani, S., Yu, J.K., Kusakabe, T.G., Khaitovich, P., Irie, N.# and the EXPANDE Consortium (2017). Constrained vertebrate evolution by pleiotropic genes. Nat Ecol Evol 1, 1722-1730.

  16. Yue, J.X., Kozmikova, I., Ono, H., Nossa, C.W., Kozmik, Z., Putnam, N.H., Yu, J.K. and Holland, L.Z.# (2016). Conserved noncoding elements in the most distant genera of Cephalochordates: the goldilocks principle. Genome Biol Evol 8, 2387-405.

  17. Yong, L.W. and Yu, J.K.# (2016). Tracing the evolutionary origin of vertebrate skeletal tissues: insights from cephalochordate amphioxus. Curr Opin Genet Dev 39, 55-62.

  18. Lin, C.Y., Tung, C.H., Yu, J.K.# and Su, Y.H.# (2016). Reproductive periodicity, spawning induction, and larval metamorphosis of the hemichordate acorn worm Ptychodera flava. J Exp Zool B Mol Dev Evol 326, 47-60.

  19. Chang, Y.C., Pai, C.Y., Chen, Y.C., Ting, H.C., Martinez, P., Telford, M.J., Yu, J.K. and Su, Y.H.# (2016). Regulatory circuit rewiring and functional divergence of the duplicate admp genes in dorsoventral axial patterning. Dev Biol 410, 108-18.

  20. Yue, J.X., Li, K.L. and Yu, J.K.# (2015). Discovery of germline-related genes in Cephalochordate amphioxus: A genome wide survey using genome annotation and transcriptome data. Mar Genomics 24 Pt 2, 147-57.

  21. Stumpp, M., Hu, M.Y., Tseng, Y.C., Guh, Y.J., Chen, Y.C., Yu, J.K., Su, Y.H. and Hwang, P.P.# (2015). Evolution of extreme stomach pH in bilateria inferred from gastric alkalization mechanisms in basal deuterostomes. Sci Rep 5, 10421.

  22. Soukup, V., Yong, L.W., Lu, T.M., Huang, S.W., Kozmik, Z.# and Yu, J.K.# (2015). The Nodal signaling pathway controls left-right asymmetric development in amphioxus. EvoDevo 6, 5.

  23. Simakov, O.#, Kawashima, T., Marletaz, F., Jenkins, J., Koyanagi, R., Mitros, T., Hisata, K., Bredeson, J., Shoguchi, E., Gyoja, F., Yue, J.X., Chen, Y.C., Freeman, R.M., Jr., Sasaki, A., Hikosaka-Katayama, T., Sato, A., Fujie, M., Baughman, K.W., Levine, J., Gonzalez, P., Cameron, C., Fritzenwanker, J.H., Pani, A.M., Goto, H., Kanda, M., Arakaki, N., Yamasaki, S., Qu, J., Cree, A., Ding, Y., Dinh, H.H., Dugan, S., Holder, M., Jhangiani, S.N., Kovar, C.L., Lee, S.L., Lewis, L.R., Morton, D., Nazareth, L.V., Okwuonu, G., Santibanez, J., Chen, R., Richards, S., Muzny, D.M., Gillis, A., Peshkin, L., Wu, M., Humphreys, T., Su, Y.H., Putnam, N.H., Schmutz, J., Fujiyama, A., Yu, J.K., Tagawa, K., Worley, K.C., Gibbs, R.A., Kirschner, M.W., Lowe, C.J., Satoh, N.#, Rokhsar, D.S.# and Gerhart, J.# (2015). Hemichordate genomes and deuterostome origins. Nature 527, 459-65.

  24. Jandzik, D., Garnett, A.T., Square, T.A., Cattell, M.V., Yu, J.K. and Medeiros, D.M.# (2015). Evolution of the new vertebrate head by co-option of an ancient chordate skeletal tissue. Nature 518, 534-537.

  25. Yue, J.X., Yu, J.K., Putnam, N.H. and Holland, L.Z.# (2014). The transcriptome of an amphioxus, Asymmetron lucayanum, from the Bahamas: a window into chordate evolution. Genome Biol Evol 6, 2681-96.

  26. Tung, C.H., Cheng, Y.R., Lin, C.Y., Ho, J.S., Kuo, C.H., Yu, J.K.# and Su, Y.H.# (2014). A new copepod with transformed body plan and unique phylogenetic position parasitic in the acorn worm Ptychodera flava. Biol Bull 226, 69-80.

  27. Satoh, N.#, Tagawa, K., Lowe, C.J., Yu, J.K., Kawashima, T., Takahashi, H., Ogasawara, M., Kirschner, M., Hisata, K., Su, Y.H. and Gerhart, J. (2014). On a possible evolutionary link of the stomochord of hemichordates to pharyngeal organs of chordates. Genesis 52, 925-34.

  28. Ono, H., Kozmik, Z., Yu, J.K. and Wada, H.# (2014). A novel N-terminal motif is responsible for the evolution of neural crest-specific gene-regulatory activity in vertebrate FoxD3. Dev Biol 385, 396-404.

  29. Li, K.L., Lu, T.M. and Yu, J.K.# (2014). Genome-wide survey and expression analysis of the bHLH-PAS genes in the amphioxus Branchiostoma floridae reveal both conserved and diverged expression patterns between cephalochordates and vertebrates. EvoDevo 5, 20.

  30. Chen, S.H., Li, K.L., Lu, I.H., Wang, Y.B., Tung, C.H., Ting, H.C., Lin, C.Y.#, Su, Y.H.# and Yu, J.K.# (2014). Sequencing and analysis of the transcriptome of the acorn worm Ptychodera flava, an indirect developing hemichordate. Mar Genomics 15, 35-43.