Jr_Kai_Yu
  • Jr-Kai Yu

    Associate Professor

  • Tel 1: +886-2-27871516
  • Tel 2: +886-2-27899517
  • Fax:
  • E-mail 1: jkyu@gate.sinica.edu.tw
  • E-mail 2:
  • Website:
  • Research Room: Institute of Cellular and Organismic Biology, Academia Sinica
  • Field: Developmental Biology, Evolution of Development
  • Academic Background:
  • Research Achievements/Publications:
      Journal Papers:
    • Yong LW, Lu TM, Tung CH, Chiou RJ, Li KL, & Yu JK* (2021) Somite compartments in amphioxus & its implications on the evolution of the vertebrate skeletal tissues. Front Cell Dev Biol, 9:607057.
    • Lin CY, Yu JK*, & Su YH* (2021) Evidence for BMP-mediated specification of primordial germ cells in an indirect-developing hemichordate. Evol & Dev, 23:28-45.
    • 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.
    • Simakov O*, Marletaz F, Yue JX, O'Connell B, Jenkins J, Br&t 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.
    • Su YH*, Chen YC, Ting HC, Fan TP, Lin CY, Wang KT, & Yu JK* (2019) BMP controls dorsoventral & neural patterning in indirect-developing hemichordates providing insight into a possible origin of chordates. Proc Natl Acad Sci USA, 116(26):12925-12932.
    • 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*(2019) Co-option of the PRDM14–CBFA2T complex from motor neurons to pluripotent cells during vertebrate evolution. Development, 146: dev168633.
    • Marletaz F, Firbas PN, Maeso I*, Tena JJ, Bogdanovic O, Perry M, Wyatt CDR, de la Calle-Mustienes E, Bertr& S, Burguera D, Acemel RD, van Heeringen SJ, 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 PJ, Duckett PE, Farahani E, Aury JM, Mangenot S, Wincker P, Albalat R, Benito-Gutierrez E, Canestro C, Castro F, D'Aniello S, Ferrier DEK, Huang S, Laudet V, Marais GAB, Pontarotti P, Schubert M, Seitz H, Somorjai I, Takahashi T, Mirabeau O, Xu A, Yu JK, Carninci P, Martinez-Morales JR, Crollius HR, Kozmik Z, Weirauch MT, Garcia-Fern&ez J, Lister R, Lenhard B, Holland PWH, Escriva H*, Gomez-Skarmeta JL*, & Irimia M* (2018) Amphioxus functional genomics & the origins of vertebrate gene regulation. Nature. 564:64-70.
    • Nakashima K*, Kimura S, Ogawa Y, Watanabe S, Soma S, Kaneko T, Yamada L, Sawada H, Tung CH, Lu TM, Yu JK, Villar-Briones A, Kikuchi S, & Satoh N (2018) Chitin-based barrier immunity & its loss predated mucus-colonization by indigenous gut microbiota. Nat Commun, 9(1):3402.
    • Zieger E, Garbarino G, Robert NSM, Yu JK, Croce JC, C&iani S, & Schubert M* (2018) Retinoic acid signaling & neurogenic niche regulation in the developing peripheral nervous system of the cephalochordate amphioxus. Cellular & Molecular Life Sciences, 75(13):2407-2429.
    • Hu H, Uesaka M, Guo S, Shimai K, Lu TM, Li F, Fujimoto S, Ishikawa M, Liu S, Sasagawa Y, Zhang G, Kuratani S, Yu JK, Kusakabe TG, Khaitovich P, Irie N*, & the EXP&E Consortium (2017) Constrained vertebrate evolution by pleiotropic genes. Nat Ecol Evol, 1(11):1722-1730.
    • Yong LW, Bertr& S, Yu JK, Escriva H, & Holland ND* (2017) Conservation of BMP2/4 expression patterns within the Glade Branchiostoma (amphioxus): Resolving interspecific discrepancies. Gene Expression Patterns, 25-26:71-75.
    • Su YH* & Yu JK (2017) EvoDevo: Changes in developmental controls underlying the evolution of animal body plans. Developmental Biology, 427(2):177-178. SI.
    • Kozmikova I* & Yu JK* (2017) Dorsal-ventral patterning in amphioxus: current underst&ing, unresolved issues, & future directions. International Journal of Developmental Biology, 61(10-12):601-610.
    • Yong LW & Yu JK* (2016) Tracing the evolutionary origin of vertebrate skeletal tissues: insights from cephalochordate amphioxus. Curr Opin Genet Dev, 39:55-62.
    • Yue JX, Kozmikova I, Ono H, Nossa CW, Kozmik Z, Putnam NH, Yu JK, & Holland LZ* (2016) Conserved Noncoding Elements in the Most Distant Genera of Cephalochordates: The Goldilocks Principle. Genome Biology & Evolution, 8(8): 2387-2405.
    • Chang YC, Pai CY, Chen YC, Ting HC, Martinez P, Telford MJ, Yu JK, & Su YH* (2016) Regulatory circuit rewiring & functional divergence of the duplicate admp genes in dorsoventral axial patterning. Developmental Biology, 410(1):108-118.
    • Lin CY, Tung CH, Yu JK*, & Su YH (2016) Reproductive periodicity, spawning induction, & larval metamorphosis of the hemichordate acorn worm Ptychoderaflava, Journal of Experimental Zoology Part B-Molecular & Developmental Evolution, 326(1):47-60.
    • Yue JX, Li KL, & Yu JK* (2015) Discovery of germline-related genes in Cephalochordate amphioxus: A genome wide survey using genome annotation & transcriptome data, Marine Genomics, 24(2) SI:147-157.
    • Soukup V, Yong LW, Lu TM, Huang SW, Kozmik Z, & Yu JK* (2015) The Nodal signaling pathway controls left-right asymmetric development in amphioxus. EvoDevo, 6:5.
    • Stumpp M, Hu MY, Tseng YC, Guh YJ, Chen YC, Yu JK, Su YH, & Hwang PP* (2015) Evolution of extreme stomach pH in bilateria inferred from gastric alkalization mechanisms in basal deuterostomes. Scientific Reports, 5:10421.
    • J&zik D, Garnett AT, Square TA, Cattell MV, Yu JK, & Medeiros DM* (2015) Evolution of the new vertebrate head by co-option of an ancient chordate skeletal tissue. Nature, 518:534-537.
    • Satoh N*, Tagawa K, Lowe C, Yu JK, Kawashima T, Takahashi H, Ogasawara M, Kirschner M, Hisata K, Su YH, & Gerhart J (2014) On a possible evolutionary link of the stomochord of hemichordates to pharyngeal organs of chordates. Genesis, 52(12):925-934.
    • Yue JX, Yu JK. Putnam N, & Holland LZ* (2014) The transcriptome of an amphioxus, Asymmetronlucayanum, from the Bahamas: A window into chordate evolution. Genome Biology & Evolution, 6, 2681-2696.
    • Chen, SH, Li KL, Lu IH, Wang YB, Tung CH, Ting HC, Lin CY, Lin CY*, Su YH*, & Yu JK* (2014) Sequencing & analysis of the transcriptome of the acorn worm Ptychodera flava, an indirect developing hemichordate. Marine Genomics, 15:35-43.
    • Tung CH#, Cheng YR #, Lin CY, Ho JS, Kuo CH, Yu JK*, & Su YH* (2014) A new copepod with transformed body plan & unique phylogenetic position parasitic in the acorn worm Ptychodera flava. Biological Bulletin, (#contributed equally) 226: 69-80.
    • Ikuta T#, Chen YC#, Annunziata R, Ting HC, Tung CH, Koyanagi R, Tagawa K, Humphreys T, Fujiyama A, Saiga H, Satoh N, Yu JK, Arnone MI, & Su YH* (2013) Identification of an intact ParaHox cluster with temporal colinearity but residual spatial colinearity in the hemichordate Ptychodera flava. BMC Evolutionary Biology, 13:129 (#contributed equally). Introduced by a commentary article in BMC Biology.
    • Wu HR, Chen YT, Su YH, Luo YJ, Holland LZ, & Yu JK* (2011) Asymmetric localization of germline markers Vasa & Nanos during early development in the amphioxus Branchiostoma floridae. Developmental Biology, 353:147-159.
    • Yu JK, Meulemans D, McKeown SJ, & Bronner-Fraser M* (2008) Insights from the amphioxus genome on the origin of vertebrate neural crest. Genome Research, 18:1127-1132.
    • Putnam NH, Butts T, Ferrier DEK, Furlong RF, Hellsten U, Kawashim T, Robinson-Rechavi M, Shoguchi E, Terry A, Yu JK, Benito-Gutiérrez È, Dubchak I, Garcia-Fernàndez J, Grigoriev IV, Horton AC, Jong PJd, Jurka J, Kapitonov V, Kohara Y, Kuroki Y, Lindquist E, Lucas S, Osoegawa K, Pennacchio LA, Salamov AA, Satou Y, Sauka-Spengler T, Schmutz J, Shin-I T, Toyoda A, Gibson-Brown JJ, Bronner-Fraser M, Fujiyama A, Holland LZ Holland PWH, Satoh N, & Rokhsar DS* (2008) The amphioxus genome & the evolution of the chordate karyotype. Nature, 453: 1064-1071.
    • Holland LZ*, Albalat R, Azumi K, Benito-Gutiérrez È, Blow MJ, Bronner-Fraser M, Brunet F, Butts T, C&iani S, Dishaw LJ, Ferrier DEK, Garcia-Fernàndez J, Gibson-Brown JJ, Gissi C, Godzi, A, Hallböök F, Hirose D, Hosomichi K, Ikuta T, Inoko, H, Kasahara M, Kasamatsu J, Kawashima T, Kimura A, Kobayashi M, Kozmik Z, Kubokawa K, Laudet V, Litman GW, McHardy AC, Meulemans D, Nonaka M, Olinski RP, Pancer Z, Pennacchio LA, Pestarino M, Rast JP, Rigoutsos I, Robinson-Rechavi M, Roch G, Saiga H, Sasakura Y, Satake M, Satou Y, Schubert M, Sherwood N, Shiina T, Takatori N, Tello J, Vopalensky P, Wada S, Xu A, Ye Y, Yoshida K, Yoshizaki F, Yu JK, Zhang Q, Zmasek CM, Putnam NH, Rokhsar DS, Satoh N, & Holland PWH (2008) The amphioxus genome illuminates vertebrate origins & cephalochordate biology. Genome Research, 18(7): 1100-1111.
    • Yu JK, Mazet F, Chen YT, Huang SW, Jung KC & Shimeld SM* (2008) The Fox genes of Branchiostoma floridae. Development Genes & Evolution, 218(11-12): 629-638.
    • Yu JK*, Wang MC, Shin-i T, Kohara Y, Holland LZ, Satoh N, & Satou Y (2008) A cDNA resource for the cephalochordate amphioxus Branchiostoma floridae. Development Genes & Evolution, 218(11-12):723-727.
    • Yu JK, Satou Y, Holland ND, Shin IT, Kohara Y, Satoh N, Bronner-Fraser M, & Holland LZ* (2007) Axial patterning in cephalochordates & the evolution of the organizer. Nature, 445(7128):613-617.
    • Schubert M, Yu JK, Holland ND, Escriva H, Laudet V, & Holland LZ* (2005) Retinoic acid signaling acts via Hox1 to establish the posterior limit of the pharynx in the chordate amphioxus. Development, 132(1):61-73.
    • Yu JK, Holland ND, & Holland LZ* (2004) Tissue-specific expression of FoxD reporter constructs in amphioxus embryos. Developmental Biology, 274(2):452-461.
    • Holland LZ* & Yu JK (2004) Cephalochordate (amphioxus) embryos: procurement, culture, & basic methods. Methods in Cell Biology, 74:195-215.
    • Yu JK*, Holland ND, & Holland LZ (2003) AmphiFoxQ2, a novel winged helix/forkhead gene, exclusively marks the anterior end of the amphioxus embryo. Development Genes & Evolution, 213(2):102-105.
    • Mazet F, Yu JK, Liberles DA, Holland LZ, & Shimeld SM* (2003) Phylogenetic relationships of the Fox (Forkhead) gene family in the Bilateria. Gene, 316:79-89.
    • Yu JK*, Holland LZ, & Holland ND (2002) An amphioxus nodal gene (AmphiNodal) with early symmetrical expression in the organizer & mesoderm & later asymmetrical expression associated with left-right axis formation. Evolution & Development, 4(6):418-425.
    • Yu JK, Holland LZ, Jamrich M, Blitz IL, & Hollan ND* (2002) AmphiFoxE4, an amphioxus winged helix/forkhead gene encoding a protein closely related to vertebrate thyroid transcription factor-2: expression during pharyngeal development. Evolution & Development, 4(1):9-15.
    • Yu JK*, Holland ND, & Holland LZ (2002) An amphioxus winged helix/forkhead gene, AmphiFoxD: insights into vertebrate neural crest evolution. Developmental Dynamics, 225(3):289-297.
    • Holland ND*, & Yu JK (2002) Epidermal receptor development & sensory pathways in vitally stained amphioxus (Branchiostoma floridae). Acta Zoologica, 83(4):309-319.
    • Chen CA, Chen CP, Fan TY, Yu JK, & Hsieh HL* (2002) Nucleotide sequences of ribosomal internal transcribed spacers & their utility in distinguishing closely related Perinereis polychaets (Annelida; Polychaeta; Nereididae). Marine Biotechnology, 4(1):17-29.
    • Yu JK, Liao TH, Chen CA*, Liao TH, Fang LS, & Tsai WS (2000) Do color patterns of Pocillopora damicornis reflect Zooxanthellae diversity? Coral Reefs, 19(1):98-99.
    • Dai CF*, Fan TY, & Yu JK (2000) Reproductive isolation & genetic differentiation of a scleractinian coral Mycedium elephantotus. Marine Ecology Progress Series, 201: 179-187.
    • Chen CA*, Wallace GC, Yu JK, & Wei NV (2000) Strategies for amplification by polymerase chain reaction of the complete sequence of the gene encoding nuclear large subunit ribosomal RNA in corals. Marine Biotechnology, 2(6):558-570.
    • Chen CA* & Yu JK (2000) Universal primers for amplification of mitochondrial small subunit ribosomal RNA-encoding gene in scleractinian corals. Marine Biotechnology, 2(2):146-153.
    • Yu JK, Wang HY, Lee SC, & Dai CF* (1999) Genetic structure of a scleractinian coral, Mycedium elephantotus, in Taiwan. Marine Biology, 133(1): 21-28.
    • Book Chapter
    • Yu JK. & Holland LZ (2010) Cephalochordates (Amphioxus, or Lancelets): A Model for Underst&ing the Evolution of Chordate Characters, pp. 335-363. In: “Emerging Model Organisms, A Laboratory Manual, Volume 2”. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York.