A large new subset of TRIM genes highly diversified by duplication and positive selection in teleost fish

doi:10.1186/1741-7007-7-7

BMC Biology

Volume 7

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Levraud JP
Yahmi M
Lauret E
Briolat V
Herbomel P
Benmansour A
Boudinot P

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Levraud JP
Yahmi M
Lauret E
Briolat V
Herbomel P
Benmansour A
Boudinot P
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Research article

A large new subset of TRIM genes highly diversified by duplication and positive selection in teleost fish

Lieke M van der Aa¹^,2 , Jean-Pierre Levraud³ , Malika Yahmi¹ , Emilie Lauret¹ , Valérie Briolat³ , Philippe Herbomel³ , Abdenour Benmansour¹ and Pierre Boudinot¹

¹Virologie et Immunologie Moléculaires, Institut National de la Recherche Agronomique, Jouy-en-Josas, France

²Cell Biology and Immunology Group, Wageningen University, Marijkeweg 40, 6709 PG, Wageningen, The Netherlands

³Unité Macrophages et Développement de l'Immunité, URA 2578 du Centre National de la Recherche Scientifique, Institut Pasteur, 25, rue du Docteur Roux, 75015 Paris, France

author email corresponding author email

BMC Biology 2009, 7:7doi:10.1186/1741-7007-7-7


Published:	5 February 2009

Additional files

Additional file 1:

Figure S1 – Distance trees of RBB (A) or B30.2 (B) domains from zebrafish ftrs. Sequences have been aligned using Clustalw, and the distance tree built using a NJ algorithm.

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Additional file 2:

Table S1. Details about zebrafish finTRIM-related genes: nomenclature, location, accession numbers.

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Additional file 3:

Table S2.ftr-like genes in other teleosts: genes corresponding to significant blastp hits on Ensembl ab initio databases for medaka, stickleback and tetraodon are reported: Ensembl name, location, number of exons.

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Additional file 4:

Figure S2.ftr sequences used for PAML analysis. The alignments of nucleotide and protein sequences used for the positive selection analysis are reported for RBB (A) and B30.2 (B) domains.

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Additional file 5:

Table S3. Results of GARD analysis.

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Additional file 6:

Table S4. PAML results of zebrafish finTRIM groupA sequences: detected sites under positive selection by BEB analysis. Section B30.2: PAML analysis was carried out with both the complete B30.2 domain and the segmented alignments before (1 to 285 nt) or after (286 to 485 nt) the detected breakage point by GARD. Section RBB : PAML analysis was carried out with both the complete RBB domain and the segmented alignments before (1 to234 nt) or after (238 to 465 nt) the detected breakage point by GARD (section1). The numbering of amino acids corresponds with the sequence of zebrafish finTRIM 13.

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