Comparing the Human and Sea Urchin Genomes

Abstract

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.
close

References

Burke RD (2011) Deuterostome neuroanatomy and the body plan paradox. Evolution and Development 13: 110–115.

Burke RD, Angerer LM, Thorndyke MC et al. (2006) A genomic view of the sea urchin nervous system. Developmental Biology 300: 434–460.

Cameron RA, Rowen L, Nesbitt R et al. (2006) Unusual gene order and organization of the sea urchin Hox cluster. Journal of Experimental Zoology Part B Molecular and Developmental Evolution 304B: 1–14.

Davidson EH (2006) The Regulatory Genome. Gene Regulatory Networks in Development and Evolution. San Diego: Academic Press/Elsevier.

Fugmann SD (2010) The origins of the Rag genes – From transposition to V(D)J recombination. Seminars in Immunology 22: 10–16.

Fugmann SD, Messier C, Novack LA, Cameron RA and Rast JP (2006) An ancient evolutionary origin of the Rag1_2 gene locus. Proceedings of the National Academy of Sciences of the USA 103: 3728–3733.

Howard‐Ashby M, Materna SC and Brown CT (2006) High regulatory gene use in sea urchin embryogenesis: implications for bilaterian development and evolution. Developmental Biology 300: 27–34.

Hynes RO (2012) The evolution of metazoan extracellular matrix. Journal of Cell Biology 196: 671–679.

Livingston BA, Killian C and Wilt F (2006) A genome‐wide analysis of biomineralization‐related genes in the sea urchin, Strongylocentrotus purpuratus. Developmental Biology 300: 335–348.

Materna SC, Berney K and Cameron RA (2006) The S. purpuratus genome: a comparative perspective. Developmental Biology 300: 485–495.

Oliveri P, Qiang T and Davidson EH (2008) Global regulatory logic for specification of an embryonic cell lineage. Proceedings of the National Academy of Sciences of the USA 105: 5955–5962.

Pertea M and Salzberg SL (2010) Between a chicken and a grape: estimating the number of human genes. Genome Biology 11: 206.

Peter IS and Davidson EH (2009) Network topologies controlling the progressive process of endoderm, specification in sea urchin embryos. Developmental Biology 331: 515.

Peter IS, Faure E and Davidson EH (2012) Predictive computation of genomic logic processing functions in embryonic development. Proceedings of the National Academy of Sciences of the USA 109: 16434–16442.

Qiang T, Cameron RA, Worley KC, Gibbs RA and Davidson EH (2012) Gene structure in the sea urchin Strongylocentrotus purpuratus based on transcriptome analysis. Genome Research 22: 2079–2087.

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

Rast JP, Smith LC, Litman G and Coll ML (2006) The sea urchin genome sequence provides a new perspective on animal immunity. Science 314: 952–956.

Samanta MP, Tongprasit W and Istrail S (2006) A high‐resolution transcriptome map of the sea urchin embryo. Science 314: 960–962.

The Sea Urchin Sequencing Consortium (2006) The purple sea urchin genome. Science 314: 941–952.

Ullrich‐Luter EM, Dupont S, Arboleda E, Hausen H and Arnone MI (2011) Unique system of photoreceptors in sea urchin tube feet. Proceedings of the National Academy of Sciences of the USA 108: 8367–8372.

Whittaker CA, Bergeron K and Whittle J (2006) The echinoderm adhesome. Developmental Biology 300: 252–266.

Further Reading

Arnone MI, Rizzo F and Annunciata R (2006) Genetic organization and embryonic expression of the ParaHox genes in the sea urchin S. purpuratus: insights into the relationship between clustering and colinearity. Developmental Biology 300: 63–73.

Bourlat SJ, Juliusdottir T and Lowe CJ (2006) Deuterostome phylogeny reveals monophyletic chordates and the new phylum Xenoturbellida. Nature 444: 85–88.

Bradham CA, Foltz KR, McClay DR et al. (2006) The sea urchin kinome: a first look. Developmental Biology 300: 180–193.

Ebert TA and Southon JR (2003) Red sea urchins (Strongylocentrotus franciscanus) can live over 100 years: confirmation with A‐bomb 14‐carbon. Fishery Bulletin 101: 915–922.

Messier‐Solek C, Buckley KM and Rast JP (2010) Highly diversified innate receptor systems and new forms of animal immunity. Seminars in Immunology 22: 39–47.

Meyer A and Schartl M (1999) Gene and genome duplications in vertebrates: the one‐to‐four(‐to‐eight in fish) rule and the evolution of novel gene functions. Current Opinion in Cell Biology 11: 699–704.

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.

Contact Editor close
Submit a note to the editor about this article by filling in the form below.

* Required Field

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