Ancient Duplications and Expression Divergence in the Globin Gene Superfamily of Vertebrates: Insights from the Elephant Shark Genome and Transcriptome

Abstract

Comparative analyses of vertebrate genomes continue to uncover a surprising diversity of genes in the globin gene superfamily, some of which have very restricted phyletic distributions despite their antiquity. Genomic analysis of the globin gene repertoire of cartilaginous fish (Chondrichthyes) should be especially informative about the duplicative origins and ancestral functions of vertebrate globins, as divergence between Chondrichthyes and bony vertebrates represents the most basal split within the jawed vertebrates. Here, we report a comparative genomic analysis of the vertebrate globin gene family that includes the complete globin gene repertoire of the elephant shark (Callorhinchus milii). Using genomic sequence data from representatives of all major vertebrate classes, integrated analyses of conserved synteny and phylogenetic relationships revealed that the last common ancestor of vertebrates possessed a repertoire of at least seven globin genes: single copies of androglobin and neuroglobin, four paralogous copies of globin X, and the single-copy progenitor of the entire set of vertebrate-specific globins. Combined with expression data, the genomic inventory of elephant shark globins yielded four especially surprising findings: 1) there is no trace of the neuroglobin gene (a highly conserved gene that is present in all other jawed vertebrates that have been examined to date), 2) myoglobin is highly expressed in heart, but not in skeletal muscle (reflecting a possible ancestral condition in vertebrates with single-circuit circulatory systems), 3) elephant shark possesses two highly divergent globin X paralogs, one of which is preferentially expressed in gonads, and 4) elephant shark possesses two structurally distinct α-globin paralogs, one of which is preferentially expressed in the brain. Expression profiles of elephant shark globin genes reveal distinct specializations of function relative to orthologs in bony vertebrates and suggest hypotheses about ancestral functions of vertebrate globins.

Keywords: Chondrichthyes; gene duplication; gene family evolution; globin; myoglobin; neuroglobin.

Fig. 1.

Bayesian phylogram depicting relationships among globin genes from representative deuterostome taxa. Numbers next to the nodes are Bayesian posterior probabilities. Terminal branches leading to elephant shark globins are shown in red. The tree was rooted by using plant globins as outgroup sequences (see Materials and Methods). The inset on top shows the organismal phylogeny for the representative deuterostome taxa included in the analysis.

Fig. 2.

Bayesian phylogram depicting relationships among GbX genes from representative vertebrate taxa. Numbers next to the nodes are Bayesian posterior probabilities. Patterns of conserved synteny are depicted for GbX paralogs in each of three clades.

Fig. 3.

Patterns of conserved synteny in genomic regions that harbor paralogous GbX genes in representative vertebrate taxa.

Fig. 4.

Phyletic distribution of paralogous globin genes in the genomes of vertebrates.

Fig. 5.

Expression profiles of elephant shark globin genes in ten tissues. Gene-specific mRNA levels were quantified using RNA-seq. Transcript abundances are measured in transcripts per million (TPM).