• E-mailDaniel.Chourrout@uib.no
  • Phone+47 55 58 43 13+47 908 91 044
  • Visitor Address
    Thormøhlens gt. 55
  • Postal Address
    Postboks 7800
    5020 Bergen

The evolution of Chordates and how they diversified into three main subphyla (vertebrates, cephalochordates, tunicates) remains enigmatic, partly because of comparatively scarce information from fossil records. Together with Eric Thompson’s group, we have established a new model system of non-vertebrate chordates with Oikopleura dioica, a tunicate larvacean which in contrast to ascidians keeps tail and general chordate body plan during all its life. This species is also appealing for genetic analysis due to a very short life cycle (6 days at 15˚C). Its female fecundity is fairly high (several hundred eggs) and its culture in the lab over many generations has become well controlled.  During the last decade, our group has been particularly active in genomic studies, with the following key findings:

  •  The Oikopleura genome organization and gene complement are very divergent from the expected chordate ancestor (Seo et al, Science 2001). This divergence results from a particularly high mutation rate in the history of larvaceans. We recently demonstrated with in silico and experimental approaches the loss of a most conserved DNA repair mechanism in the larvacean lineage (unpublished).
  • The extremely rapid evolution of larvacean genomes proved instrumental to capture transient features characteristic of genomic changes, such as intron gains (Denoeud et al, 2010). To study the history of genome changes, we considerably extended our panel of larvacean genomes during the last few years (unpublished).
  • Incorporating Oikopleura coding sequences in phylogenetic studies led to revise the whole chordate tree, with tunicates and not cephalochordates now considered to be the sister group of vertebrates (Delsuc et al, Nature 2006).

With the new evolutive scenario emerging from our genomic studies, we redefined our research objectives and now put the emphasis on how larvaceans may have been simplified from anatomically more complex chordate ancestors. This type of studies became possible only when we recently succeeded to genetically manipulate its development, through  gene expression knock downs (RNAi) and now with gene knock outs (CRISPR). We are now able to implement functional studies of transcription factors and their targets to characterize the destiny of:

  • Nine Hox genes, whose expression patterns were described earlier and suggested important changes of function compared to other chordates. These genes are no longer clustered in  the genome (Seo et al, Nature 2004).
  • Multiple genes suspected to govern the formation of the Oikopleura house, a large and complex extracellular structure representing  a spectacular innovation of larvaceans for filter feeding and other life cycle features (unpublished and see Eric Thompson’s page).

Finally, our group has been involved in other genome studies, contributing to elucidate the evolutionary pathways leading to the current diversity of metazoans (Chourrout et al, Nature 2006; Schuettengruber et al, Cell 2007; Wang et al, Nature Ecology and Evolution 2017).

  • Wang S, Zhang J, Jiao W, Li J, Xun X, Sun Y, Guo X, Huan P, Dong B, Zhang J, Hu X, Sun X, Wang J, Zhao C, Wang Y, Wang D, Huang X, Wang R, Lv J, Li Y, Zhang Z, Liu B, Lu W, Hui Y, Liang J, Zhou Z, Hou R, Li X, Liu Y, Li H, Ning X, Lin Y, Zhao L, Xing Q, Dou J, Li Y, Mao J, Guo H, Dou H, Li T, Mu C, Jiang W, Fu Q, Fu X, Miao Y, Liu J, Yu Q, Li R, Liao H, Li X, Kong Y, Jiang Z, Chourrout D,*, Li R* & Bao Z* (2017). The scallop genome provides insights into evolution of bilaterian karyotype and developmental control. Nat Ecol Evol 1,0120
  • Henriet S, Sumic S, Doufoundou-Guilengu C1, Flo Jensen M, Grandmougin C, Fal K, Thompson E, Volf JN and Chourrout D (2015).  Embryonic expression of endogenous retroviral RNAs in somatic tissues adjacent to the Oikopleura germline  Nucleic Acids Res doi:10.1093/nar/gkv169 
  • Martí-Solans J, Ferrández-Roldán A, Godoy-Marín H, Badia-Ramentol J, Torres-Aguila NP, Rodríguez-Marí A, Bouquet JM, Chourrout D, Thompson EM, Albalat R, Cañestro C (2015).  Oikopleura dioica culturing made easy: a low-cost facility for an emerging animal model in EvoDevo.  Genesis 53:183-193.
  • Mikhaleva Y, Kreneisz O, Olsen LC, Glover JC, Chourrout D (2015).  Modification of the larval swimming behavior in Oikopleura dioica, a chordate with a miniaturized central nervous system by dsRNA injection into fertilized eggs.  J Exp Zool Part B 324:114-127.
  • Danks G, Campsteijn C, Parida M, Butcher S, Doddapaneni H, Fu B, Petrin R, Metpally R, Lenhard B, Wincker P, Chourrout D, Thompson EM and JR Manak (2013). OikoBase: A genomics and developmental transcriptomics resource for the urochordate Oikopleura dioica.  Nucleic Acids Res 41: 845-853.
  • Yadetie F, Butcher S, Forde HE, Campsteijn C, Bouquet JM, Karlsen OA, Denoeud F, Metpally R, Thompson EM, Manak JR, Goksoyr A, and D Chourrout (2012). Conservation and divergence of chemical defence system in the tunicate Oikopleura dioica revealed by genome wide response to two xenobiotics.  BMC Genomics 13, 55.
  • Angotzi A, Mungpakdee S, Stefansson S, Male R, Chourrout D (2011).  Involvement of Prop1 homeobox gene in the early development of fish pituitary gland.  Gen Comp Endocrinol Volum 171.(3) s. 332-340.
  • Denoeud F, Henriet S, Mungpakdee S, Aury JM, Da Silva C, Brinkmann H, Mikhaleva J, Olsen LC, Jubin C, Cañestro C, Bouquet JM, Danks G, Poulain J, Campsteijn C, Adamski M, Cross I, Yadetie F, Muffato M, Louis A, Butcher S, Tsagkogeorga G, Konrad A. Singh S, Jensen MF, Cong EH, Eikeseth-Otteraa H, Anthouard V, Kachouri-Lafond R, Nishino A, Ugolini M, Chourrout P, Nishida H, Aasland R, Huzurbazar S, Westhof E, Delsuc F, Lehrach H, Reinhardt R, Weissenbach J, Roy SW, Artiguenave F, Postlethwait JH, Manak JR, Thompson EM, Jaillon O, Du Pasquier L, Boudinot P, Liberles DA, Volff JN, Philippe H, Lenhard B, Crollius HR, Wincker P and D Chourrout (2010). Plasticity of animal genome architecture unmasked by rapid evolution of a pelagic tunicate.  Science, 330:1381-1385.
  • Bouquet JM, Spriet E, Troedsson C, Ottera H, Chourrout D, Thompson EM (2009).  Culture optimization for the emergent zooplanktonic model organism Oikopleura dioica.  J Plankton Res, 31, 359–370.
  • Angotzi AR, Ersland KM, Mungpakdee S, Stefansson S, Chourrout D (2008).  Independent and dynamic reallocation of pitx gene expression during vertebrate evolution, with emphasis on fish pituitary development.  Gene, 417, 19-26.
  • Mungpakdee S, Seo HC, Angotzi AR, Dong X, Akalin A, Chourrout D (2008).  Differential Evolution of the Thirteen Atlantic Salmon Hox Clusters.  Mol Biol Evol, 25, 1333-1343.
  • Mungpakdee S, Seo HC, Chourrout D (2008).  Spatio-temporal expression patterns of anterior Hox genes in Atlantic salmon (Salmo salar).  Gene Expr Patterns, 8, 508-514.
  • Stach T, Winter J, Bouquet JM, Chourrout D, Schnabel R (2008). Embryology of a planktonic tunicate reveals traces of sessility.  Proc Natl Acad Sci USA, 105, 7229-7234.
  • Schuettengruber B, Chourrout D, Vervoort M, Leblanc B, Cavalli G (2007).  Genome regulation by polycomb and trithorax proteins. Cell 23;128(4):735-45.
  • Søviknes AM, Chourrout D, Glover JC (2007).  Development of the caudal nerve cord, motoneurons, and muscle innervation in the appendicularian urochordate Oikopleura dioica.  J Comp Neurol Jul 10;503(2):224-43.
  • Chourrout D, Delsuc F, Chourrout P, Edvardsen RB, Rentzsch F, Renfer E, Jensen MF, Zhu B, de Jong P, Steeele RE, Technau U (2006). Minimal ProtoHox cluster inferred from bilaterian and cnidarian Hox complements. Nature, 442(7103):684-7.
  • Delsuc F, Brinkmann H, Chourrout D and Philippe H (2006). Tunicates and not cephalochordates are the closest living relatives of vertebrates. Nature, 439:965-968
  • Edvardsen RB, Seo HC, Jensen MF, Mialon A, Mikhaleva J, Bjordal M, Cartry J, Reinhardt R, Weissenbach J, Wincker P and Chourrout D (2005). Remodelling of the homeobox gene complement in the tunicate Oikopleura dioica. Current Biology, 15:R12-13. 
  • Søviknes AM, Chourrout D and Glover JC (2005). Development of putative GABAergic neurons in the appendicularian urochordate Oikoleura dioica. J Comp Neurol, 490:12-28.
  • Weill M, Philips A, Chourrout D and Fort P (2005). The caspase family in urochordates: distinct evolutionary fates in ascidians and larvaceans. Biology of the Cell, 97(11):857-66.
  • Edvardsen RB, Lerat E, Maeland AD, Flaat M, Tewari R, Jensen MF, Lehrach H, Reinhardt R, Seo HC and Chourrout D (2004). Hypervariable and Highly Divergent Intron/Exon Organizations in The Chordate Oikopleura dioica. Journal of Molecular Evolution, 59:448-457.
  • Ganot P, Kallesøe T, Reinhardt R, Chourrout D and Thompson EM (2004). Spliced-leader RNA trans splicing in a chordate, Oikopleura dioica, with a compact genome. Molecular and Cellular Biology, 24:7795-7805.
  • Seo HC, Edvardsen RB, Maeland AD, Bjordal M, Jensen MF, Hansen A, Flaat M, Weissenbach J, Lehrach H, Wincker P, Reinhardt R and Chourrout D (2004). Hox cluster disintegration with persistent anteroposterior order of expression in Oikopleura dioica. Nature, 431:67-71.
  • Volff JN, Lehrach H, Reinhardt R and Chourrout D (2004). Retroelement dynamics and a novel type of chordate retrovirus-like elements in the miniature genome of the tunicate Oikopleura dioica. Molecular Biology and Evolution, 21:2022-2033.
  • Nilsen IW, Myrnes B, Edvardsen RB and Chourrout D (2003). Urochordates carry multiple genes for goose-type lysozyme and no genes for chicken- or invertebrate-type lysozymes. Cellular and Molecular Life Sciences, 60:2210-2218.
  • Uzbekova S, Amoros C, Cauty C, Mambrini M, Perrot E, Hew CL, Chourrout D and Prunet P (2003). Analysis of cell-specificity and variegation of transgene expression driven by salmon prolactin promoter in stable lines of transgenic rainbow trout. Transgenic Res, 12:213-227.
  • Seo HC, Kube M, Edvardsen RB, Jensen MF, Beck A, Spriet E, Gorsky G, Thompson EM, Lehrach H, Reinhardt R and Chourrout D (2001). Miniature genome in the marine chordate Oikopleura dioica. Science, 294:2506.
  • Fu L, Mambrini M, Perrot E and Chourrout D (2000). Stable and full rescue of the pigmentation in a medaka albino mutant by transfer of a 17 kb genomic clone containing the medaka tyrosinase gene. Gene, 241:205-211.
  • Deschet K, Bourrat F, Ristoratore F, Chourrout D and Joly JS (1999). Expression of the medaka (Oryzias latipes) Ol-Rx3 paired-like gene in two diencephalic derivatives, the eye and the hypothalamus. Mechanims of Development, 83:179-182.
  • Joly JS, Kress C, Vandeputte M, Bourrat F and Chourrout D (1999). Irradiation of Fish Embryos Prior to Blastomere Transfer Boosts the Colonisation of their Gonads by Donor-Derived Gametes. Molecular Reproduction Development, 53:394-397.
  • Nguyen V, Deschet K, Loosli F, Godet F, Joly JS, Wittbrodt J, Chourrout D and Bourrat F (1999). Morphogenesis of the optic tectum in the medaka (Oryzias latipes): a morphological and molecular study, with special emphasis on cell proliferation. Journal of Comparative Neurology, 413:385-404.
  • Ristoratore F, Carl M, Deschet K, Richard-Parpaillon L, Boujard D, Wittbrodt J, Chourrout D, Bourrat F and Joly JS (1999). The midbrain-hindbrain boundary genetic cascade is activated ectopically in the diencephalon in response to the widespread expression of one of its components, the medaka gene Ol-eng2. Development, 126:3769-3779.
  • Joly JS, Bourrat F, Nguyen V and Chourrout D (1997). Ol-Prx 3, a member of a new class of homeobox genes, is unimodally expressed in several domains of the developing and adult CNS of the medakafish (Oryzias latipes). Proc Natl Acad Sci USA, 94:12987-12992.
  • Baroiller JF, Chourrout D, Fostier A and Jalabert B (1995). Temperature and sex chromosomes govern sex-ratios of the mouthbrooding cichlid fish Oreochromis niloticus.Journal of Experimental Zoology 273:216-223.
  • Michard-Vanhée C, Chourrout D, Stromberg S, Thuvander A and Pilström L (1994). Lymphocyte expression in transgenic trout by mouse immunoglobulin promoter/enhancer.Immunogenetics 40:1-8.
  • Nakayama I, Foresti F, Tewari R, Schartl M and Chourrout D (1994). Sex chromosome polymorphism and heterogametic males revealed by two cloned DNA probes in the ZW/ZZ fish Leporinus elongatus. Chromosoma 103:31-39.
Academic article
  • 2009. Culture optimization for the emergent zooplanktonic model organism Oikopleura dioica. Journal of Plankton Research. 359-370.
  • 2008. Spatio-temporal expression patterns of anterior Hox genes in Atlantic salmon (Salmo salar). Gene Expression Patterns. 508-514.
  • 2008. Independent and dynamic reallocation of pitx gene expression during vertebrate evolution, with emphasis on fish pituitary development. Gene. 19-26.
  • 2008. Differential evolution of the 13 Atlantic salmon Hox clusters. Molecular biology and evolution. 1333-1343.
  • 2007. Development of the caudal nerve cord, motoneurons, and muscle innervation in the appendicularian urochordate Oikopleura dioica. Journal of Comparative Neurology. 224-243.
  • 2006. Tunicates and not cephalochordates are the closest living relatives of vertebrates. Nature. 965-968.
  • 2006. Minimal ProtoHox cluster inferred from bilaterian and cnidarian Hox complements. Nature. 684-687.
  • 2005. The caspase family in urochordates: distinct evolutionary fates in ascidians and larvaceans. Biology of the Cell. 857-866.
  • 2003. Urochordates carry multiple genes for goose-type lysozyme and no genes for chicken- or invertebrate-type lysozymes. Cellular and Molecular Life Sciences (CMLS). 2210-2218.
Academic literature review
  • 2007. Genome regulation by polycomb and trithorax proteins. 735-745.

More information in national current research information system (CRIStin)

Daniel Chourrout is Director of the Sars Centre since it was established in 1997. His research is focused on the evolution of chordate development, using Oikopleura and other tunicate larvaceans as model systems. The activity of his group includes comparative genome and development studies. Before moving to Norway, Daniel Chourrout was heading the Laboratory of Fish Genetics at INRA (French Institute of Research for Agriculture), with his own research on rainbow trout genetics and later on medaka development. His training is in Genetics (PhD from the University Pierre et Marie Curie in Paris).