Open Access Research article

Emergence and evolution of the glycoprotein hormone and neurotrophin gene families in vertebrates

Sandra Dos Santos12, Sylvie Mazan3, Byrappa Venkatesh4, Joëlle Cohen-Tannoudji1 and Bruno Quérat1*

Author Affiliations

1 Univ. Paris Diderot, Sorbonne Paris Cité, Unité Biologie Fonctionnelle et Adaptative (BFA), EAC4413 CNRS, F-75013 Paris, France

2 Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093-0202, USA

3 Développement et évolution des vertébrés, UMR 7150 CNRS - Université Pierre et Marie Curie Paris 6, Université Européenne de Bretagne, Station Biologique, Place Georges Teissier, 29682 Roscoff, France

4 Institute of Molecular and Cell Biology, A*STAR (Agency for Science, Technology and Research), Biopolis, 138673, Singapore

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BMC Evolutionary Biology 2011, 11:332  doi:10.1186/1471-2148-11-332

Published: 15 November 2011

Additional files

Additional file 1:

GPHβ subunit sequences. Amino acid sequences of elephant shark Callorhinchus milii FSHβ, TSHβ and TSHβ2 subunits [GenBank:HQ174783-HQ174785] characterized in this study and of zebrafish Danio rerio TSHβ [GenBank:AY135147] on chr. 6 and TSHβrp [GenBank:XM_001341527.1] on chr. 23. Cysteine residues involved in the cystine knot structure are in red. Potential N-liked glycosylation sites are in bold red.

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Additional file 2:

Neurotrophin sequences. Amino-acid sequence of Callorhinchus milii (references from GeneBank), Scyliorhinus canicula, Petromyzon marinus and Lampetra fluviatilis (references from EMBL) NT encoding sequences characterized in this study aligned with Lampetra NT1 and human NT sequences for comparison (references from GeneBank). Cysteine residues involved in the cystine knot structure are in red. The amino acid sequence of the region of NTF4rp resulting from the shift in the open reading frame (see Additional file 3) is given in italic.

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Additional file 3:

Elephant shark NTF4 and NTF4rp. Comparison of NTF4 [Genebank:HQ174787] and NTF4rp [Genbank:HQ174788] sequences from Callorhinchus milii. Nucleotide deletions causing a shift in the open reading frame are indicated by red dashes and resulting amino acids given in italic. Other differences are highlighted in grey.

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Additional file 4:

Lin7 sequences. Alignment of Lin7-related encoding sequences of Scyliorhinus canicula, Callorhinchus milii (Callo) and Petromyzon marinus characterized in this study with the amphioxus Branchiostoma floridae homologue and sequences from human (Homo), chicken (Gallus) and zebrafish (Danio). Three paralogues are evidenced in Scyliorhinus and two in Petromyzon. References are from GeneBank except for Scyliorhinus sequences that are from EMBL. Positions specific to Lin7b sequences are highlighted in blue, those specific to Lin7a are in red and those to Lin7c are in green. Amino acids identical to Branchiostoma are given by dashes. Gaps are identified by dots. Unknown positions are indicated by interrogation marks. Exon boundaries are indicated in the bottom lines.

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Additional file 5:

Elephant shark KCNA sequences. Callorhinchus milii KCNA sequences. Complete sequences were deposited at GenBank and are given with their accession number. Other, partial sequences are given with their reference from the genome survey sequence at GenBank. Sequences were numbered according to their phylogenetic relationship with other members of the vertebrate KCNA family (see Figure 3).

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Additional file 6:

Lamprey KCNA sequences. Petromyzon marinus KCNA-related sequences extracted from their Contig sequences on the Washington University dedicated server (see Methods) and/or from the Traces archives deposited in GeneBank. The positions in the Contig or trace sequences in the sense or antisense strand (complement) are indicated. The underlined position corresponds to the first nucleotide of the 5' end ATG when appropriate. KCNA sequences were referenced by letters instead of numbers because their relationship with the different known KCNA-types could not be determined.

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Additional file 7:

[GPHβ] tetra-paralogon. Listing of genes identified as constituting the paralogous gene sets comprising GPHβ subunit gene environments ([GPHβ]) in human with some representative orthologues in chicken (Gallus gallus) and lizard (Anolis carolinensis) genomes and the homologous sequences in amphioxus (Branchiostoma floridae). Amphioxus, chicken and lizard gene names are after the human orthologue names as in Ensembl release 62. Genes are given with their approximate location on the chromosome (chromosome number followed by the coordinate rounded up or down to the nearest in megabase pairs) or with their scaffold number (assembly version 2) for amphioxus gene. Each vertebrate gene has hyperlink to its dedicate Ensembl website and amphioxus gene to JGI website (assembly version 1). Genes that have paralogues in all four paralogous gene sets in the human genome are highlighted. nf: genes not found or for which the parental relationships did not appear reliable. Unplaced means that the position in the genome was not given on the Ensembl current release. * indicates chicken genes not found in the available genomic data (NCBI release 2.1) but for which a cDNA is known (see text). Genes may be sorted by columns in order to analyze specific paralogous gene sets.

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Additional file 8:

Human GPH-related gene paralogous gene sets and ancestral chordate and vertebrate proto-chromosome relics. Observed boundaries of the paralogous gene sets comprising the GPH subunit-related genes in human compared to segments (S) or conserved vertebrate linkages (CVL) predicted to derive from the two whole genome duplication events of, respectively, ancestral chordate proto-chromosomes (proto-chr.) G and D, according to [45] and of ancestral vertebrate proto-chromosomes 11 and 13/14 according to [44]. [GPHβ] tetra-paralogon seems to correspond to the sum of the segments derived from proto-chr. 13 (given in red) and 14.

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Additional file 9:

[GPHα-GPA2-GPB5] tetra-paralogon. Listing of genes identified as constituting the paralogous gene sets comprising [GPHα], [GPA2], [GPB5] and [GP-Ghost] environments with their amphioxus homologues. See legend of Additional file 7.

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Additional file 10:

[GPA2] and [GPB5] environments in human and zebrafish. Listing of representative genes in the environment of human and zebrafish gpa2 and gpb5 with their amphioxus homologues. See legend of Additional file 7.

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