Identical Genomic Organization of Two Hemichordate Hox Clusters

Abstract

Summary Genomic comparisons of chordates, hemichordates, and echinoderms can inform hypotheses for the evolution of these strikingly different phyla from the last common deuterostome ancestor [1–5]. Since hox genes play pivotal developmental roles in bilaterian animals [6–8], we analyzed the Hox complexes of two hemichordate genomes. We find that Saccoglossus kowalevskii and Ptychodera flava both possess 12-gene clusters, with mir10 between hox4 and hox5, in 550kb and 452kb intervals, respectively. Genes hox1-9 of the clusters are in the same genomic order and transcriptional orientation as their orthologs in chordates, with hox1 at the 3′ end of the cluster. At the 5′ end, each cluster contains three posterior genes specific to Ambulacraria (the hemichordate-echinoderm clade), two forming an inverted terminal pair. In contrast, the echinoderm Strongylocentrotus purpuratus contains a 588kb cluster [9] of 11 orthologs of the hemichordate genes, ordered differently, plausibly reflecting rearrangements of an ancestral hemichordate-like ambulacrarian cluster. Hox clusters of vertebrates and the basal chordate amphioxus [10] have similar organization to the hemichordate cluster, but with different posterior genes. These results provide genomic evidence for a well-ordered complex in the deuterostome ancestor for the hox1-9/10 region, with the number and kind of posterior genes still to be elucidated.

Hemichordate genomes and deuterostome origins

“…On a more local scale, we find hundreds of tightly linked conserved gene clusters of three or more genes (‘micro-synteny’; Methods; Supplementary Note 7) including Hox 30 and ParaHox 31 clusters in both acorn worms (Extended Data Fig. 4), as also found in echinoderms 32,33 .…”

Hemichordata

“…The recent sequencing and comparison of the S. kowalevskii and P. fl ava genomes has revealed the identical genomic organisation of their 12-gene Hox clusters (Freeman et al 2012 ), which is reminiscent of the Hox cluster organisation of B. simodensis (Ikuta et al 2009 ). With the exception of differences at the posterior end of these clusters, the hemichordate organisation is strikingly similar to that of chordates, supporting the idea that the ambulacrarian ancestor possessed minimally a 12-gene Hox cluster with at least nine genes organised and oriented the same as their chordate orthologs (Freeman et al 2012 ).…”

“…Lately, the genomes of Ptychodera fl ava and Saccoglossus kowalevskii have been sequenced and used for genome comparisons between these two species (Freeman et al 2012 ). This will provide an important resource to identify the genetic toolkit and regulatory elements of acorn worms.…”

Sea Lily Muscle Lacks a Troponin-Regulatory System, While it Contains Paramyosin

“…Troponin gene might have lost or suppressed during evolution from deuterostomes ancestor to echinoderms. A matter of particular interest is that whether troponin is present in the thin filaments of the muscle of hemichordates that are classed as members of Ambulacraria together with echinoderms (Freeman et al, 2012), but currently, no information is available as to muscle proteins of hemichordates.…”