Elephant shark sequence reveals unique insights into the evolutionary history of vertebrate genes: A comparative analysis of the protocadherin cluster

Abstract

Cartilaginous fishes are the oldest living phylogenetic group of jawed vertebrates. Here, we demonstrate the value of cartilaginous fish sequences in reconstructing the evolutionary history of vertebrate genomes by sequencing the protocadherin cluster in the relatively small genome (910 Mb) of the elephant shark (Callorhinchus milii). Human and coelacanth contain a single protocadherin cluster with 53 and 49 genes, respectively, that are organized in three subclusters, Pcdhalpha, Pcdhbeta, and Pcdhgamma, whereas the duplicated protocadherin clusters in fugu and zebrafish contain >77 and 107 genes, respectively, that are organized in Pcdhalpha and Pcdhgamma subclusters. By contrast, the elephant shark contains a single protocadherin cluster with 47 genes organized in four subclusters (Pcdhdelta, Pcdhepsilon, Pcdhmu, and Pcdhnu). By comparison with elephant shark sequences, we discovered a Pcdhdelta subcluster in teleost fishes, coelacanth, Xenopus, and chicken. Our results suggest that the protocadherin cluster in the ancestral jawed vertebrate contained more subclusters than modern vertebrates, and the evolution of the protocadherin cluster is characterized by lineage-specific differential loss of entire subclusters of genes. In contrast to teleost fish and mammalian protocadherin genes that have undergone gene conversion events, elephant shark protocadherin genes have experienced very little gene conversion. The syntenic block of genes in the elephant shark protocadherin locus is well conserved in human but disrupted in fugu. Thus, the elephant shark genome appears to be less prone to rearrangements compared with teleost fish genomes. The small and "stable" genome of the elephant shark is a valuable reference for understanding the evolution of vertebrate genomes.

Fig. 1.

Genomic organization of the elephant shark protocadherin cluster. Constant exons at the end of each subcluster are shown in red color. Variable exons in the same paralog subgroup or intersubcluster subgroup are shown in the same color. Only a single pseudogene (ψ1) was identified. νCX2b is an alternatively spliced “constant” exon. The positions and identification numbers of BAC clones sequenced are shown below.

Fig. 2.

Phylogenetic analysis of protocadherin constant region exons. The tree was generated from alignment of protein sequences of the protocadherin constant regions by Neighbor-joining method based on sequence distance matrix. The tree is unrooted. Bootstrap values (%) of only the major nodes are shown. Cm, Callorhinchus milii; Hs, Homo sapiens; Mm, Mus musculus; Lm, Latimeria menadoensis; Dr, Danio rerio; Fr, Fugu rubripes; Xt, X. tropicalis; Gg, Gallus gallus.

Fig. 3.

Comparison of the promoter elements of protocadherin genes. The core promoter elements of elephant shark Pcdhε (A), Pcdhμ (B), and Pcdhν (C); human Pcdhα (D), Pcdhβ (H), and Pcdhγ (F); coelacanth Pcdhα (E) and Pcdhγ (G); and fugu Pcdhα (I) and Pcdhγ (J) were identified by MEME (http://meme.sdsc.edu/meme/intro.html) and displayed as WebLogo plots.

Fig. 4.

A model to explain the evolutionary history of the protocadherin cluster in jawed vertebrates. Variable exons are indicated by boxes and constant exons by red bars. Intersubcluster paralogs or orthologs between species are shown in the same color. White boxes represent protocadherin genes or paralog subgroups with no apparent intersubcluster paralogs or orthologs. Encircled “D” denotes whole-genome duplication in the ray-finned fish lineage.