Number of chemokine and chemokine receptor genes identified in vertebrate genomes. We had previously identified chemokine genes from 10 mammalian genomes (Nomiyama et al. 2010). Here, we have omitted five genomes from the survey list but added two genomes to cover a wide range of mammals. In total, we searched seven mammalian genomes (human, mouse, cow, elephant, opossum, wallaby, and platypus) for the analyses. In addition, three birds (chicken, zebra finch, and duck), a reptile (anole lizard), an amphibian (Xenopus), four teleost fish (medaka, stickleback, zebrafish, and Tetraodon), a cartilaginous fish (elephant shark) and a jawless fish (sea lamprey) were included in the survey. Phylogenetic relationships of these organisms among chordates are shown. More detailed taxonomic classifications are shown in Fig. S1 in Supporting Information. The first split in vertebrates occurred between jawed and jawless vertebrates (gnathostomes and agnathans), followed by the divergence of jawed vertebrates into cartilaginous and bony fish (chondrichthyes and osteichthyes). Divergence times (Mya, million years ago) (Hedges & Kumar 2003) are not to scale. A hypothetical origin time for the adaptive immune system is indicated. The timings of the two successive rounds of WGD (1R and 2R) and the teleost-specific WGD (3R) are also shown. Although the timing of the 2R has long been in dispute, Kuraku et al. (2009) recently showed that both 1R and 2R occurred before the split between jawed and jawless vertebrates. Recent studies indicate that tunicates (previously known as urochordates) are the invertebrates most closely related to vertebrates (Delsuc et al. 2006). The amino acid sequences of the chemokines and their database accession numbers are shown in Fig. S1A in Supporting Information. The chemokine receptor sequences and their accession numbers (Nomiyama et al. 2011) have been updated and are shown in Fig. S1B in Supporting Information. Phylogenetic trees of vertebrate chemokines and chemokine receptors are shown in Fig. S4 in Supporting Information.
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