, Volume 55, Issue 7, pp 480–490 | Cite as

Initial characterization of a protochordate histocompatibility locus

  • Anthony W. De TomasoEmail author
  • Irving L. Weissman
Original Paper


The colonial protochordate, Botryllus schlosseri, undergoes a natural transplantation reaction which is controlled by a single, highly polymorphic locus called the Fu/HC. We are using map-based cloning to identify Fu/HC gene(s), and have currently delineated their location to an approximately 1-cM region of the B. schlosseri genome. The Fu/HC physical map currently consists of 85 sequence-tagged sites mapped on a minimum tiling path of 800 kb which consists of five contigs, with four gaps remaining to be crossed, and is estimated to be 75% completed. Approximately half this region has been sequenced throughout the locus, allowing the first analysis of a metazoan histocompatibility locus outside of vertebrates. This has resulted in the identification of 18 predicted genes, a number of which have been found to be expressed. Several of these genes are well conserved among the chordates; however, none of the predicted or expressed genes are linked within the genome of any organism in the databases. In addition, the Fu/HC is one of the most polymorphic loci ever described, and physical mapping has revealed that the locus is quite dynamic, and includes features such as hotspots of recombination.


Allorecognition Botryllus schlosseri Genomics Physical mapping Positional cloning 



We are indebted to Ron Davis, Audrey Southwick and Molly Miranda at the Stanford Genome and Technology Center for their generosity in the sequencing of large-insert clones. Fosmid sequencing is also being done at the University of Oklahoma Genome Center, under the auspices of the NIH-funded Genome Sequencing Network. We also thank David Ransom for tips and protocols on AFLP cloning. Kathi Ishizuka, Karla Palmeri and Vicki Tacaks have been responsible for B. schlosseri mariculture and breeding, and K. Palmeri has assisted in library screening. This work was supported by the NIH (RO1AI41588) to I.L.W. A.W.D. was an NIH postdoctoral scholar. Accession numbers for genomic sequence are: AC135107, AC139528, AC138022, AC140855, AC140856, AC139257, AC138953, AC139529 AC142501, AC136512, AC140854.


  1. Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search Programs. Nucleic Acids Res 25:3389–3402PubMedGoogle Scholar
  2. Azumi K, De Santis R, De Tomaso AW, Rigoutsos I, Yoshizaki F, Pinto MR, Marino R, Shida K, Ikeda M, Ikeda M, Arai M, Inoue Y, Shimizu Y, Satoh N, Rokhsar DS, DuPasquier L, Kasahara M, Satake M, Nonaka M (2003) Genomic analysis of immunity in a basal chordate and the emergence of the vertebrate immune system: waiting for Godot. Immunogenetics (in press)Google Scholar
  3. Boyd HC, Brown SK, Harp JA, Weissman IL (1986) Growth and sexual maturation of laboratory-cultured Monterey Botryllus schlosseri. Biol Bull 170:91–109Google Scholar
  4. Burge CB, Karlin S (1998) Finding the genes in genomic DNA. Curr Opin Struct Biol 8:346–354Google Scholar
  5. Burnet FM (1971) Self-recognition in colonial marine forms and flowering plants in relation to the evolution of immunity. Nature 232:123–126Google Scholar
  6. Cannon JP, Haire RN, Litman GW (2002) Identification of diversified genes that contain immunoglobulin-like variable regions in a protochordate. Nature Immunology 3:1200–1207Google Scholar
  7. De Tomaso AW, Weissman IL (2003) Construction and characterization of large insert libraries (BAC and Fosmid) from the colonial protochordate Botryllus schlosseri. Marine Biotechnol 5:103–115Google Scholar
  8. De Tomaso AW, Saito Y, Ishizuka KJ, Palmeri KJ, Weissman IL (1998) Mapping the genome of a model protochordate. I. A low resolution genetic map encompassing the fusion/histocompatibility (Fu/HC) locus of Botryllus schlosseri. Genetics 149:277–287PubMedGoogle Scholar
  9. Dehal P et al (2002) The draft genome of Ciona intestinalis: insights into chordate and vertebrate origins. Science 298:2157–2167CrossRefPubMedGoogle Scholar
  10. DuPasquier L, Flajnik M (1999) Origin and evolution of the vertebrate immune system. In: Paul WE (ed) Fundamental immunology. Lippincott-Raven, PhiladelphiaGoogle Scholar
  11. Flajnik MF, Kasahara M (2001) Comparative genomics of the MHC: glimpses into the evolution of the adaptive immune system. Immunity 15:351–62PubMedGoogle Scholar
  12. Flajnik MF, Ohta Y, Namikawa-Yamada C, Nonaka M (1999) Insight into the primordial MHC from studies in ecothermal vertebrates. Immunol Rev 167:59–68PubMedGoogle Scholar
  13. Frohman MA, Dush MK, Martin GR (1987) Rapid production of full-length cDNAs from rare transcripts; amplification using a single gene-specific oligonucleotide primer. Proc Natl Acad Sci USA 85:8998–9002Google Scholar
  14. Karre K (1997) How to recognize a foreign submarine. Immunol Rev 155:5–9PubMedGoogle Scholar
  15. Kasahara M (1998) What do the paralogous regions in the genome tell us about the origin of the adaptive immune system? Immunol Rev 166:159–175Google Scholar
  16. Kaufman J, Milne S, Gobel TW, Walker BA, Jacob JP, Auffray C, Zoorob R, Beck S (1999) The chicken B locus is a minimal essential major histocompatibility complex. Nature 1999 401:923–925CrossRefGoogle Scholar
  17. Michelmore RW, Paran I, Kesseli RV (1991) Identification of markers lined to disease-resistance genes by bulked segregant analysis: a rapid method to detect markers in specific genomic regions by using segregating populations. Proc Natl Acad Sci USA 88:9828–9832PubMedGoogle Scholar
  18. Oka H, Watanabe H (1960) Problems of colony specificity in compound ascidians. Bull Biol Stn Asamushi 10:153–155Google Scholar
  19. Olson M, Hood L, Cantor C, Botstein D (1989) A common language for physical mapping of the human genome. Science 245:1434–1435PubMedGoogle Scholar
  20. Orita M, Iwahana H, Kanazawa H, Hayashi K, Sikeya T (1989) Detection of polymorphisms of human DNA by gel electrophoresis as single strand conformation polymorphisms. Proc Natl Acad Sci USA 86:2766–2770PubMedGoogle Scholar
  21. Rosati F, De Santis R (1978) Studies on fertilization in the ascidians 1. Self-sterility and specific recognition between gametes of Ciona intestinalis. Exp Cell Res 121:111–119Google Scholar
  22. Ross MT, LaBrie S, McPherson J, Stanton VP Jr (1999) Screening large-insert libraries by hybridization. In In: Boyl A (ed) Current protocols in human genetics. Wiley, New York, pp 5.6.1–5.6.52Google Scholar
  23. Sabbadin A (1962) Le basi genetiche dell capacita di fusione fra colonie in Botryllus schlosseri (Ascidiacea). Atti Accad Na Lincei Rend 32:1031–1035Google Scholar
  24. Scofield VL, Schlumpberger JM, West LA, Weissman IL (1982) Protochordate allorecognition is controlled by an MHC-like gene system. Nature 295:499–502PubMedGoogle Scholar
  25. Sorrentino R, Iannicola C, Costanzi S, Chersi A, Tosi R (1991) Detection of complex alleles by direct analysis of DNA heteroduplexes. Immunogenetics 33:118–123PubMedGoogle Scholar
  26. Stone SL, Anderson EM, Mullen RT, Goring DR (2003) ARC1 is an E3 Ubiquitin ligase and promotes the ubiquitination of proteins during the rejection of self-incompatible Brassica pollen. Plant Cell 15:885–898CrossRefPubMedGoogle Scholar
  27. Vos P, Rogers R, Bleeker M, Reijans M, van de Lee T, Hornes M, Frijters A, Pot J, Peleman J, Kuiper M, Zabeau M (1995) AFLP: a new technique for DNA fingerprinting. Nucleic Acids Res 23:4407–4414PubMedGoogle Scholar

Copyright information

© Springer-Verlag 2003

Authors and Affiliations

  1. 1.Hopkins Marine StationPacific GroveUSA
  2. 2.Department of PathologyStanford University School of MedicineStanfordUSA

Personalised recommendations