title: Genomic and expression analyses of Tursiops truncatus T cell receptor gamma (TRG) and alpha/delta (TRA/TRD) loci reveal a similar basic public γδ repertoire in dolphin and human.
abstract: The bottlenose dolphin (Tursiops truncatus) is a mammal that belongs to the Cetartiodactyla and have lived in marine ecosystems for nearly 60 millions years. Despite its popularity, our knowledge about its adaptive immunity and evolution is very limited. Furthermore, nothing is known about the genomics and evolution of dolphin antigen receptor immunity.
  
  
  
  Here we report a evolutionary and expression study of Tursiops truncatus T cell receptor gamma (TRG) and alpha/delta (TRA/TRD) genes. We have identified in silico the TRG and TRA/TRD genes and analyzed the relevant mature transcripts in blood and in skin from four subjects. The dolphin TRG locus is the smallest and simplest of all mammalian loci as yet studied. It shows a genomic organization comprising two variable (V1 and V2), three joining (J1, J2 and J3) and a single constant (C), genes. Despite the fragmented nature of the genome assemblies, we deduced the TRA/TRD locus organization, with the recent TRDV1 subgroup genes duplications, as it is expected in artiodactyls. Expression analysis from blood of a subject allowed us to assign unambiguously eight TRAV genes to those annotated in the genomic sequence and to twelve new genes, belonging to five different subgroups. All transcripts were productive and no relevant biases towards TRAV-J rearrangements are observed. Blood and skin from four unrelated subjects expression data provide evidence for an unusual ratio of productive/unproductive transcripts which arise from the TRG V-J gene rearrangement and for a "public" gamma delta TR repertoire. The productive cDNA sequences, shared both in the same and in different individuals, include biases of the TRGV1 and TRGJ2 genes. The high frequency of TRGV1-J2/TRDV1- D1-J4 productive rearrangements in dolphins may represent an interesting oligo-clonal population comparable to that found in human with the TRGV9- JP/TRDV2-D-J T cells and in primates.
  
  
  
  Although the features of the TRG and TRA/TRD loci organization reflect those of the so far examined artiodactyls, genomic results highlight in dolphin an unusually simple TRG locus. The cDNA analysis reveal productive TRA/TRD transcripts and unusual ratios of productive/unproductive TRG transcripts. Comparing multiple different individuals, evidence is found for a "public" gamma delta TCR repertoire thus suggesting that in dolphins as in human the gamma delta TCR repertoire is accompanied by selection for public gamma chain.
authors.affiliation: Department of Biology, University of Bari, via E. Orabona 4, 70125, Bari, Italy.
authors.forename: Giovanna
authors.initials: G
authors.lastname: Linguiti
authors.affiliation: Department of Biology, University of Bari, via E. Orabona 4, 70125, Bari, Italy.
authors.forename: Rachele
authors.initials: R
authors.lastname: Antonacci
authors.affiliation: Biocomputing Group, CIRI-Health Science and Technologies/Department of Biology, University of Bologna, via Selmi 3, 40126, Bologna, Italy.
authors.forename: Gianluca
authors.initials: G
authors.lastname: Tasco
authors.affiliation: Zoomarine Italia SpA, via Casablanca 61, 00071, Pomezia, RM, Italy.
authors.forename: Francesco
authors.initials: F
authors.lastname: Grande
authors.affiliation: Biocomputing Group, CIRI-Health Science and Technologies/Department of Biology, University of Bologna, via Selmi 3, 40126, Bologna, Italy.
authors.forename: Rita
authors.initials: R
authors.lastname: Casadio
authors.affiliation: Department of Biological and Environmental Science e Technologies, University of Salento, via per Monteroni, 73100, Lecce, Italy.
authors.forename: Serafina
authors.initials: S
authors.lastname: Massari
authors.affiliation: Department of Biology, University of Bari, via E. Orabona 4, 70125, Bari, Italy.
authors.forename: Vito
authors.initials: V
authors.lastname: Castelli
authors.affiliation: CNR, Institute for Biomedical Technologies of Bari, via Amendola, 70125, Bari, Italy.
authors.forename: Arianna
authors.initials: A
authors.lastname: Consiglio
authors.affiliation: IMGT®, the international ImMunoGeneTics information system®, Laboratoire d'ImmunoGénétique Moléculaire, Institut de Génétique Humaine, UPR CNRS 1142, University of Montpellier, 34396, Montpellier Cedex 5, France.
authors.forename: Marie-Paule
authors.initials: MP
authors.lastname: Lefranc
authors.affiliation: Department of Biology, University of Bari, via E. Orabona 4, 70125, Bari, Italy. salvatricemaria.ciccarese@uniba.it.
authors.forename: Salvatrice
authors.identifier: 0000-0003-3208-0730
authors.initials: S
authors.lastname: Ciccarese
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D050681:Bottle-Nosed Dolphin / Q000235:genetics* / Q000378:metabolism; D020869:Gene Expression Profiling; D005786:Gene Expression Regulation; D056426:Genetic Loci; D006801:Humans; D008969:Molecular Sequence Data; D010802:Phylogeny; D017433:Protein Structure, Secondary; D012313:RNA / Q000097:blood / Q000302:isolation & purification / Q000378:metabolism; D016693:Receptors, Antigen, T-Cell, alpha-beta / Q000145:classification / Q000235:genetics* / Q000378:metabolism; D016692:Receptors, Antigen, T-Cell, gamma-delta / Q000145:classification / Q000235:genetics* / Q000378:metabolism; D016415:Sequence Alignment; D012867:Skin / Q000378:metabolism
chemical_list: D016693:Receptors, Antigen, T-Cell, alpha-beta; D016692:Receptors, Antigen, T-Cell, gamma-delta; D012313:RNA
keywords: Dolphin genome; Expression analysis; IMGT; T cell receptor; TRA/TRD locus; TRAV and TRDV genes; TRG locus; TRGJ and TRGC genes; TRGV