Phylogenetic analysis of cnidarian TIR sequences in comparison to a selection of TIR domains from other species

<p><b>Copyright information:</b></p><p>Taken from "The innate immune repertoire in Cnidaria - ancestral complexity and stochastic gene loss"</p><p>Genome Biology 2007;8(4):R59-R59.</p><p>Published online 16 Apr 2007</p><p>PMCID:PMC1896004.</p><p></p> The maximum likelihood (ML) tree shown is the result of analysis of an HMM-based alignment of TIR domains. A number of the TIR sequences identified and discussed in the text are incomplete due to the presence of introns of unknown size, and hence were not included in the phylogenetic analyses. Three clades are resolved by these analyses, corresponding to the TIR domains characteristic of the 'MyD88-type', 'Toll/TLR-type' and 'IL-1R-type'. In addition to the TIR domain, the first of these types contains a death domain and the second contains multiple LRRs. Like the mammalian receptors for interleukin 1, the three proteins falling into the third clade each also contain multiple immunoglobulin domains. Note that HyTRR1 does not contain such domains and that it is not yet clear whether either of the proteins does. The sequences included in the analysis were predicted from genomic clones (ApGenomic) and from an cDNA clone (AmTIR-1). lacks a canonical Toll/TLR, having only two MyD88 genes and the two sequences known as TRR-1 and TRR-2; and sequences are indicated by the prefixes Hy and Nv, respectively. Reference sequences: HsMyD88, human MyD88 (SwissProt:Q99836); DmMyD88, fly MyD88 (GenBank:); SdMyD88, MyD88 (EMBL:CAI68016); Dmtoll, fly Toll (SwissProt:P08953); HsTLR4, human TLR4 (EMBL:CAD99157); (GenBank:)