Analysis of the Amphioxus Genome


Amphioxus or cephalochordates are small fish‐like marine invertebrates. The sequenced genome of Branchiostoma floridae is approximately 520 Mb in size and estimated to contain approximately 21 900 protein‐coding loci. Comparison of the amphioxus genome with genomes of other animals made a great impact on the resolution of the long‐standing question of the origin of vertebrates. First, chordates are monophyletic group, in which cephalochordates represent the most basal extant chordate lineage, with urochordates sister to vertebrates. Second, there is highly conserved synteny between the cephalochordate and vertebrate genomes. This allows reconstruction of 17 ancestral chordate linkage groups that are conserved in the modern amphioxus and vertebrate genomes. Third, the two rounds of genome‐wide duplications occurred in the vertebrate lineage after their divergence from cephalochordates and urochordates. Fourth, whereas most duplicate genes have been lost, a disproportionate number of genes are retained and involved in developmental processes to produce novel features and complexity of vertebrate biology.

Key concepts

  • The phylum Chordata consists of the subphyla Cephalochordata (amphioxus), Urochordata (ascidians) and Vertebrata, and these three groups are characterized by possession of a notochord, a hollow dorsal neural tube, a perforated pharyngeal region and a post‐anal tail.

  • Chordates are monophyletic group in which cephalochordates represent the most basal extant lineage, suggesting a free‐living ancestor of chordates.

  • Seventeen ancestral chordate linkage groups that are conserved in the modern amphioxus and vertebrate genomes are revealed by highly conserved synteny between the two genomes.

  • The two rounds of genome‐wide gene duplications occurred in the vertebrate lineage after their divergence from cephalochordates and urochordates.

  • A disproportionate number of genes which were produced by the genome‐wide duplication are retained and involved in developmental processes to produce novel features and complexity of vertebrate biology.

Keywords: amphioxus genome; evolution of chordates; origin of vertebrates; ancestral chordate linkage groups; two rounds of genome‐wide gene duplications

Figure 1.

(a) Adult amphioxus Branchiostoma floridae, about 3 cm in length. Animals with yellowish gonad are females, while white ones are males. (Photo courtesy of Dr. Eiichi Shoguchi.) (b) The structure of the adult amphioxus body. a, cerebral vesicle; b, mouth; c, gill slit; d, neural tube; e, endostyle; f, notochord; g, coelom; h, gonad; i, myotome; j, alimentary canal; k, dorsal fin; l, atrium; m, atriopore; n, anus; o, caudal fin. (Sketch courtesy of Dr. Teruaki Nishikawa.)

Figure 2.

Phylogenic relationship of amphioxus. (a) Bayesian phylogenetic tree of deuterostome relationships, using amino acid substitutions in 1090 genes. Long branches for sea squirt (Ciona) and larvacean (Oikopleura) indicate high levels of amino acid substitution. This tree topology was observed in 100% of sampled trees, after discarding the first 25% of samples as ‘burn‐in’. (From Putnam et al. . Reproduced by permission of Nature Publishing Group.) (b) A novel and likely scenario for the origin and evolution of chordates. The deuterostome ancestor was a motile and free‐living ancestor. The motile hemichordate acorn‐worm‐like ancestor evolved to cephalochordates, and then to vertebrates in a straight lineage, while urochordates were derived to evolve a sessile adult form. (From Satoh . Modified from Lacalli .)

Figure 3.

Macrosynteny between four amphioxus scaffolds (18, 149, 162 and 207) to human chromosome 17. Note that orthologous genes from these scaffolds are concentrated in specific regions of the chromosome, and that several scaffolds, for example, 18 and 162, or 149 and 207, have a high density of hits to the segments of the chromosome. (From Putnam et al. . Reproduced by permission of Nature Publishing Group.)

Figure 4.

Partitioning of the human chromosomes into segments with defined patterns of conserved synteny to amphioxus (Branchiostoma floridae) scaffolds. Numbers 1–17 at the top represent the 17 reconstructed ancestral CLGs, and letters a–d represent the four products resulting from two rounds of genome duplication. Coloured bars are segments of the human genome, shown grouped by ancestral linkage group (above), and in context of the human chromosomes (below). (From Putnam et al. . Reproduced by permission of Nature Publishing Group.)



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Satoh, Noriyuki(Sep 2009) Analysis of the Amphioxus Genome. In: eLS. John Wiley & Sons Ltd, Chichester. [doi: 10.1002/9780470015902.a0021556]