Pigmentation pathway evolution after whole-genome duplication in fish

Abstract

Whole-genome duplications (WGDs) have occurred repeatedly in the vertebrate lineage, but their evolutionary significance for phenotypic evolution remains elusive. Here, we have investigated the impact of the fish-specific genome duplication (FSGD) on the evolution of pigmentation pathways in teleost fishes. Pigmentation and color patterning are among the most diverse traits in teleosts, and their pigmentary system is the most complex of all vertebrate groups. Using a comparative genomic approach including phylogenetic and synteny analyses, the evolution of 128 vertebrate pigmentation genes in five teleost genomes following the FSGD has been reconstructed. We show that pigmentation genes have been preferentially retained in duplicate after the FSGD, so that teleosts have 30% more pigmentation genes compared with tetrapods. This is significantly higher than genome-wide estimates of FSGD gene duplicate retention in teleosts. Large parts of the melanocyte regulatory network have been retained in two copies after the FSGD. Duplicated pigmentation genes follow general evolutionary patterns such as the preservation of protein complex stoichiometries and the overrepresentation of developmental genes among retained duplicates. These results suggest that the FSGD has made an important contribution to the evolution of teleost-specific features of pigmentation, which include novel pigment cell types or the division of existing pigment cell types into distinct subtypes. Furthermore, we have observed species-specific differences in duplicate retention and evolution that might contribute to pigmentary diversity among teleosts.Our study therefore strongly supports the hypothesis that WGDs have promoted the increase of complexity and diversity during vertebrate phenotypic evolution.

Keywords: conserved synteny; fish; functional module; genome duplication; melanocyte; pigment cell.

FIG. 1.—

Evolution of the Sox10 transcription factor gene. (A) Maximum likelihood (ML) phylogeny of vertebrate Sox10 proteins based on 563 AA positions. The tree is rooted with human SOX9. Bootstrap values (ML/Neighbor-Joining [NJ]) above 50% are shown. The FSGD generated two Sox10 in teleosts, Sox10a (blue), and Sox10b (green). Sox10a is missing in zebrafish. (B) The microsynteny pattern of Sox10 regions in vertebrate genome shows double conserved synteny between the two teleost sox10 paralogons and human chr22q13. A sox10a paralogon could not be identified in zebrafish, and the zebrafish sox10b (dashed red bar) is not included in the Zv7 genome assembly but has been mapped to chr3 (Dutton et al. 2001). Numbered bars represent genes contributing to conserved synteny, and genes that do not contribute to conserved synteny are not shown. Dotted lines connect orthologous genes.

FIG. 2.—

Macrosynteny of FSGD-duplicated pigmentation genes. Blue lines connect paralogous genes on the 21 chromosomes in the Tetraodon genome (Tni1–Tni21). Red lines connect paralogous pigmentation gene duplicates, showing that they mostly follow the major routes of FSGD duplication. A highly similar pattern is also observed for stickleback, medaka, and zebrafish (not shown).

FIG. 3.—

Evolution of teleost pigmentation gene repertoires following the FSGD. (A) In the five extant teleost genomes, around 30% of FSGD-duplicated pigmentation genes (P; n = 128) have been retained. Duplicated liver genes (L; n = 187) have been retained by only 14% in extant teleosts. In the hypothetical euteleost ancestor, almost twice as many duplicates had been retained for pigmentation genes compared with liver genes (39.1% vs. 21.4%). For all five teleost genomes as well as for the reconstructed euteleost ancestor, the retention rates of pigmentation versus liver genes are significantly different (χ² tests; **P < 0.01, ***P < 0.001). (B) Losses of pigmentation gene duplicates mapped onto the teleost phylogeny (Setiamarga et al. 2008). Numbers of pigmentation genes retained in duplicate are given in boxes. Gene loss rates in percent are based on the number of retained duplicates at the previous node in the phylogeny. The majority of duplicate losses have occurred before the divergence of the five euteleost species (60.9%). Within acanthomorphs (medaka, stickleback, pufferfishes), further losses have occurred shortly after the split from the zebrafish lineage (18.0%) and lineage-specific gene losses are relatively rare. Gene loss rates of pigmentation genes are generally lower than of liver genes (L; see also supplementary fig. S25, Supplementary Material online).

FIG. 4.—

Impact of the FSGD on the melanocyte/-phore signaling network. Many components have been identified by pigmentation mutants in both, mammals and teleosts. Diverse external signals are integrated on the promoter of the Mitf transcription factor gene, the master regulator of melanophore development (Béjar et al. 2003; Levy et al. 2006). Mitf regulates the expression of melanogenic enzymes, which catalyze the biosynthesis of melanin from tyrosine in melanosomes. The αMSH peptide is encoded by the Pomc gene. Lef1 is a downstream target of the Wnt signaling pathway. Red indicates duplications as result of the FSGD present in all five teleost genomes analyzed and gray indicates singleton genes. Molecules with divided red/gray shading indicate genes retained in duplicate in some teleost lineages but singleton in others (see table 1). Most of the key regulators of the melanophore signaling network have been retained in two copies in teleosts. The signaling network is adapted from Tachibana et al. (2003), Levy et al. (2006), and Lin and Fisher (2007).