Lukacs et al. BMC Genomics 2010, 11:154 http://www.biomedcentral.com/1471-2164/11/154 Page 8 of 17 Figure 3 Unrooted Phylogenetic tree of teleost MHC class I sequences. Phylogenetic tree analysis performed using PhyML 3.0 based on JTT model of evolution for full-length amino acid sequences. Consensus trees were based on 100 bootstrap replications and reported with the bootstrap support values (in percent) indicated at the respective nodes. Sequence references are as follows:Auha-UA [Genbank: AAD37813], Dare- UBA*01 [Genbank: CAA86732], Dare-UAA*01 [Genbank: CAA86731], Dare-UDA*01 [Genbank: AAF20178], Dare-UEA [Genbank: AAH53140], Dare- ZE*0201 [Genbank: CAD12790], Dare-L [Genbank: CAD56801], Furu-UBA [Genbank: AAC41236], Gaac-UAA*01 [Genbank: ABN14358], Gaac-UBA*01, Genbank: ABN14357], Icpu-SAA [Genbank: CK423282], Icpu-UAA [Genbank: AAD08650], Icpu-UBA [Genbank: AAD08648], Icpu-UCA [Genbank: AAD08647], Onmy-SAA [Genbank: AF091779], Onmy-UBA [Genbank: AF287483], Onmy-UCA [Genbank: BAD89552], Onmy-UDA [Genbank: AY523666], Onmy-UEA [Genbank: BAD89553], Onmy-UGA [Genbank: AAP04358 ], Onmy-LAA [Genbank: ABI21842 ], Onmy-LBA [Genbank: ABI21844], Orla-UAA*0101 [Genbank: BAD93265], Orla-UBA*0201 [Genbank: BAB83850], Orla-UCA*0101 [Genbank: BAB63957], Orla-UDA*0201 [Genbank: BAB83843], Orla-UEA*0201 [Genbank: BAB83837], Paol-UA1 [Genbank: BAD13367], Paol-ZE [Genbank: BAD13366], Pore-UA [Genbank: CAA90791], Sasa-LBA [Genbank: DY733800 and GO062643], Sasa-UBA*0301 [Genbank: AAN75116], Sasa-UBA*1001 [Genbank: AAN75118 ], [Genbank: ABQ59666], Sasa-ZAA*0101 [Genbank: DQ099914], Teni-UA [Genbank: CR724171], Teni-ZE [Genbank: CAF90807], HLA-A2 [Genbank: AAA76608]. Sasa-UDA, Sasa-UGA, Sasa-UHA1, Sasa-UHA2, Sasa-ULA, Sasa-SAA, Sasa-ZAA*0201, Sasa-ZBA, Sasa-ZCA are described in this paper. separate nodes together with their rainbow trout homo- logs. Overall, the U-lineage sequences from all teleosts cluster together with their taxonomic superorder families, that is; acanthopterygii, protacanthopterygii and ostariophysi. One exception is the Sasa-UHA1 and Sasa-UHA2 that branch off early on a separate node from all other U-lineage sequences, showing a more dis- tant phylogenetic relationship. Whether the UHA sequences diverged this early as the phylogenetic tree indicates stands as an open debate as the UHA genes are located on a separate linkage group (LG14), suggest- ing a separate evolutionary origin from the other U-line- age located on linkage group 3 and 15. Interestingly, the a3 domain (exon 4) of the UHA molecules shows very low amino acid conservation in comparison to other U-lineage genes. Likewise, the human nonclassical gene MR1 [23], show a similar identity in the a1 and a2 domains towards the classical counterparts (HLA-A, HLA-B and HLA-C) while the a3 domain is more diver- gent. The functional relevance of this lack of conserva- tion remains unknown. The Z-lineage molecules also cluster together with their taxonomic superorder families, although including fewer sequences than the U-lineage sequences. So far the Atlantic salmon is the only teleost species reported, with 3 different expressed Z-lineage genes.