The complete sequences of Takifugu Toll-like receptor (TLR) loci and gene predictions from many draft genomes enable comprehensive molecular phylogenetic analysis. Strong selective pressure for recognition of and response to pathogen-associated molecular patterns has maintained a largely unchanging TLR recognition in all vertebrates. There are six major families of vertebrate TLRs. This repertoire is distinct from that of invertebrates. TLRs within a family recognize a general class of pathogen-associated molecular patterns. Most vertebrates have exactly one gene ortholog for each TLR family. The family including TLR1 has more speciesspecific adaptations than other families. A major family including TLR11 is represented in humans only by a pseudogene. Coincidental evolution plays a minor role in TLR evolution. The sequencing phase of this study produced finished genomic sequences for the 12 Takifugu rubripes TLRs. In addition, we have produced >70 gene models, including sequences from the opossum, chicken, frog, dog, sea urchin, and sea squirt. coincidental evolution ͉ multigene family ͉ concerted evolution T he Toll-like receptor (TLR) multigene family encodes important recognition receptors of the innate immune system that have been conserved in both the invertebrate and vertebrate lineages (1, 2). TLRs recognize a variety of endogenous and exogenous ligands; many of the latter are conserved molecules essential for pathogen survival. TLR genes have been recognized in a number of vertebrate genomes, and many partial and full-length sequences are available. Recent additions include draft predictions from the Japanese pufferfish Takifugu rubripes (3), the zebrafish Danio rerio (4-6), and the chicken Gallus gallus (7), and partially or fully sequenced mRNAs, including one from the goldfish Carassius auratus (8), several from the Japanese flounder Paralichthys olivaceus (9), and several from the rainbow trout Oncorhynchus mykiss (10). These papers provide incremental molecular phylogenetic analyses, and several reviews are available (11-13). Additionally, the draft genomes of the frog Xenopus tropicalis, chicken G. gallus, and opossum Monodelphis domesticus are now available. We present a complete molecular phylogenetic analysis of the known vertebrate TLR genes in the context of the complete genomic sequences of the T. rubripes TLRs.
MethodsSequencing and Assembly. A draft genome sequence of T. rubripes was obtained by pairwise shotgun sequencing (14) through the efforts of an international collaboration (15). Sequence finishing was performed in part as described (16), with additional details provided in Supporting Text, which is published as supporting information on the PNAS web site.Bioinformatics. TLRs were identified as genes coding for both an N-terminal leucine-rich repeat (LRR) domain and a C-terminal Toll-IL-resistance (TIR) domain. To form the basis of our study, vertebrate sequences from the nonredundant DDBJ͞EMBL͞ NCBI database (GenBank) were identified by similarity to known TLRs (Data Set 1, which is...