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Remove FREE. SEQtools was used to visualize the predicted transcripts and their three-frame translations [ 25 ]. Orthologous genes and their genomic positions were identified in medaka, zebrafish, stickleback, Xenopus tropicalis , chicken, mouse and human genomes using ContigView software within the Ensembl genome browser [ 28 ]. NITR sequences described from medaka, zebrafish, Southern pufferfish, channel catfish, rainbow trout, Japanese flounder and Tetraodon Additional file 3 were included in alignments [ 2 , 3 , 4 , 10 , 11 , 12 , 13 , 14 ].
Primer sequences are listed in Additional File 4. We thank Chris Amemiya for very helpful discussions and advice on phylogenetic relationships, Jacques Robert and Alexander Taranin for sharing the chromosomal location of Xenopus tropicalis CD8B and Barbara Pryor for editorial assistance. This article is published under license to BioMed Central Ltd. Skip to main content Skip to sections. Advertisement Hide. Download PDF.
The medaka novel immune-type receptor NITR gene clusters reveal an extraordinary degree of divergence in variable domains. Open Access. First Online: 19 June Background Novel immune-type receptor NITR genes are members of diversified multigene families that are found in bony fish and encode type I transmembrane proteins containing one or two extracellular immunoglobulin Ig domains.
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Results Forty-four NITR genes in medaka Oryzias latipes are located in three gene clusters on chromosomes 10, 18 and 21 and can be organized into 24 families including inhibitory and activating forms. Conclusion Comprehensive phylogenetic analyses between the complete datasets of NITRs from medaka and zebrafish indicate multiple species-specific expansions of different families of NITRs.
This process is experimental and the keywords may be updated as the learning algorithm improves. Background The two major forms of novel immune-type receptors NITRs possess either one N-terminal ectodomain of the Ig variable V type, which may contain a joining J or J-like sequence or an N-terminal V domain plus a second C-terminal Ig domain of the intermediate I type. Medaka encode 44 NITRs on three chromosomes The reduced levels of protein sequence identity between NITRs found in different species make it difficult to identify genetic orthologs between fish species outside of conserved core residues.
In order to identify NITR genes from medaka, we data mined the recently released medaka genome database [ 16 , 17 ]. By using zebrafish NITR sequences as queries, it was possible to identify a number of candidate genes that encode Ig domains. By then restricting the queries only to genes that encode an authentic NITR I-type domain [ 14 ], NITR gene clusters were identified on medaka chromosomes 10, 18 and The search was then directed to include all genes predicted to encode V domains in these genomic regions.
It is possible that certain genes described here may represent allelic variants and that additional NITR genes may be identified in future releases of the medaka genome. Open image in new window. Twelve families consist of multiple up to five members and the remaining families are singletons. Each NITR family was assigned a number and for families with multiple members, each member was assigned a letter e. With the exception of the NITR9 family see below in which activating potential rather than V structure served as the basis for assignment to a specific gene family, unequivocal orthologs between the NITRs of medaka and any other species were not identified and the numbering of these genes was arbitrary.
The initial search criteria for identifying medaka NITRs was directed to the I domain, which possesses six highly conserved cysteines. The majority of NITRs in medaka and other species can be classified as inhibitory based on the presence of one or two cytoplasmic ITIM or itim sequences Figure 4 and Additional File 8 as well as by the absence of a charged transmembrane residue, a conserved feature of activating receptors.
The complete annotation of NITRs in zebrafish and medaka permits the investigation of potential shared synteny. The larger zebrafish NITR gene cluster on chromosome 7 is adjacent to the map4k2l , men1 and rtn3 genes [ 2 ] and the larger medaka NITR gene cluster is linked to these genes on chromosome 18 Table 1. Medaka and zebrafish possess two FGFRL1 orthologs referred to as fgfrl1a and fgfrl1b in zebrafish and fgfrl1 1of2 and fgfrl1 2of2 in medaka.
Medaka orthologs of additional genes adjacent to the NITR gene cluster on zebrafish chromosome 14 are also encoded on medaka chromosome 10 Table 1. These observations indicate that the NITR gene clusters on medaka chromosome 18 and zebrafish chromosome 7 share conserved synteny whereas the NITR gene cluster on medaka chromosome 10 and zebrafish chromosome 14 share conserved synteny. Three NITRs are encoded by the zebrafish NITR gene cluster on chromosome 14 whereas 10 NITRs are encoded by the corresponding gene cluster in medaka suggesting either gene loss in zebrafish or gene duplications in medaka.
Figure 6 NITR gene clusters independently evolved in medaka and zebrafish.
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Data mining Using zebrafish nitr1c and nitr3a as queries, putative medaka NITR genes were identified by searching version 1. DOC 76 KB. DOC 55 KB.
PDF 89 KB. Predicted translational start sites are underlined. PDF KB. The number assigned to each interior branch corresponds to the bootstrap value. Branch lengths correspond to the number of amino acid substitutions estimated by Poisson correction, scale indicated below. PDF 23 KB. The sequences shown include a portion of the transmembrane domain exon and the two cytoplasmic domain exons.
Dashes indicate gaps in the nucleotide alignment. Asterisks indicate nucleotide identity. Stop codons are indicated by red highlighting in the nucleotide sequence and by dashes in the protein sequence. Downward arrowheads define predicted RNA splice sites.
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The differences in predicted protein sequence likely reflect allelic variations between the out-bred, orange-red transcripts and Hd-rR genomic sequence. Sequences were compiled from version 1. An ITIM-like sequence lacks a consensus residue in either the first or last position.
Charged residues are white text on black. Zebrafish Nitr9 has been shown to partner with and signal via Dap12 [ 15 ]. PDF 8 KB.
Although the CD8A and CD8B genes are tightly linked in a medaka, b zebrafish, c stickleback and d human, flanking genes are not well conserved between fish and human. Data were acquired using release NCBI 36 of the human genome, release 1. Gene names and chromosomal order were identified via Contig View within the Ensembl Genome Browser [ 28 ]. Three predicted olfactory receptor OR genes are indicated on medaka chromosome 21, although the exact number of OR genes has not been determined.
Data were acquired using release NCBI 36 of the human genome and release 1. Predicted protein structures are shown and structural features are as in Figure 4 plus cytoplasmic activating motifs YxxM ; and a functionally unresolved motif YxxH. PDF 44 KB. Ol, medaka Oryzias latipes ; Dr, zebrafish Danio rerio ; Ip, channel catfish Ictalurus punctatus ; Om, rainbow trout Oncorhynchus mykiss ; Sn, Southern pufferfish Spheroides nephelus ; Po Japanese flounder Paralichthys olivaceus and Tn, pufferfish Tetraodon nigroviridis. Specific NITR gene numbers are indicated e. Only one NITR gene family member is incorporated; additional family members are indicated in parenthesis.
These labels are presented in parentheses for NITR families, which do not consistently conform to these definitions.