Comparing the Human and Sea Urchin Genomes


To compare the genomes of humans and sea urchins seems, at first glance, awkward. The human body is bilaterally symmetrical with a complex head containing many sensory structures, whereas the sea urchin has radial symmetry and a globose form with no suggestion of a head. However, sea urchins belong to a group of animals (the echinoderms) that lies on the same major branch of the tree of life (the deuterostomes) to which humans belong. As echinoderms diverged very early from the major lineage of the deuterostomes, their genomes reflect the basic qualities of this lineage and inform to a deep reach of time the evolutionary changes leading to the human genome. Even though the sea urchin form differs radically from that of vertebrates, they share many of the same gene families. Indeed, the invention of new genes in this evolutionary path is subordinate to the diverse changes in the abundance of genes in existing families.

Key Concepts:

  • The relative proximity of sea urchins to humans on the deuterostome branch of the evolutionary tree renders them a good comparison to humans for gene and genome evolution.

  • The sea urchin genome is one‚Äźquarter the size of the human but has about the same number of genes.

  • Gene comparisons between these distantly related species show that differences in body plans result from spatial and temporal differences in gene activity rather than the possession of different genes.

  • The sea urchin HOX gene cluster is modified from the linear arrangement found in humans.

  • Without an adaptive immune system, the sea urchin appears to use a huge expansion in innate immune genes.

Keywords: deuterostomes; echinoderms; phylogeny; protein family evolution; biomineralisation; innate immunity

Figure 1.

An abbreviated tree of the bilaterian phyla showing the deuterostome groups in more detail.

Figure 2.

A diagram of multiple reciprocal BLAST comparisons among selected metazoan gene sets. The number of matches is indicated in the boxes over arrows and the number of gene predictions is shown under each species name. Abbreviations: Hs, Homo sapiens; Mm, Mus musculus; Ci, Ciona intestinalis; Sp, Strongylocentrotus purpuratus; Nv, Nematostella vectensis; Dm, Drosophila melanogaster and Ce, Caenorhabditis elegans.

Adapted from Materna et al.2006. © Elsevier.
Figure 3.

A diagram of the Hox cluster gene order including the nearby gene positions. The Hox genes are indicated by their paralogue group numbers and the direction of transcription is shown by the grey arrows. The BAC clone ID numbers included in the sequence segment from each haplotype is indicated above the arrow for that haplotype. There is a 50 kb overlap between the two haplotypes in the sequence.

Adapted from Cameron et al.2006.


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Further Reading

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Raible F, Tessmar‐Raible K and Arboleda E (2006) Opsins and clusters of sensory G‐protein coupled receptors in the sea urchin genome. Developmental Biology 300: 461–475.

Rizzo F, Fernandez‐Serra M, Squarzoni P, Archimandritis A and Arnone MI (2006) Identification and developmental expression of the ets family in the sea urchin (Strongylocentrotus purpuratus). Developmental Biology 300: 35–48.

Tu Q, Brown CT, Davidson EH and Oliveri P (2006) Sea urchin Forkhead gene family: phylogeny and embryonic expression. Developmental Biology 300: 49–62.

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Cameron, R Andrew(Oct 2013) Comparing the Human and Sea Urchin Genomes. In: eLS. John Wiley & Sons Ltd, Chichester. [doi: 10.1002/9780470015902.a0020745.pub2]