How much does the amphioxus genome represent the ancestor of chordates?

Abstract

One of the main motivations to study amphioxus is its potential for understanding the last common ancestor of chordates, which notably gave rise to the vertebrates. An important feature in this respect is the slow evolutionary rate that seems to have characterized the cephalochordate lineage, making amphioxus an interesting proxy for the chordate ancestor, as well as a key lineage to include in comparative studies. Whereas slow evolution was first noticed at the phenotypic level, it has also been described at the genomic level. Here, we examine whether the amphioxus genome is indeed a good proxy for the genome of the chordate ancestor, with a focus on protein-coding genes. We investigate genome features, such as synteny, gene duplication and gene loss, and contrast the amphioxus genome with those of other deuterostomes that are used in comparative studies, such as Ciona, Oikopleura and urchin.

Figure 1:

Phylogenetic relationships between species used in this study. The 11 animals diverged from a common eumetazoan ancestor more than 500 million years ago. Branch lengths are not to scale. Nematostella vectensis: sea anemone; Caenorhabditis elegans: nematode; Drosophila melanogaster: fruit fly; Strongylocentrotus purpuratus: sea urchin; Branchiostoma floridae: amphioxus; Oikopleura dioica: tunicate; Ciona intestinalis and Ciona savignyi: sea squirts; Homo sapiens: human; Gallus gallus: chicken; Danio rerio: zebrafish.

Figure 2:

Venn diagram of gene loss in different chordates. Each of the four species lost the total number of genes indicated in the last column of Table II. The intersections show the number of genes lost in common between any two, three or four species.

Figure 3:

Dot plots of chromosomal homology between animal genomes. Columns represent ancestral chordate linkage groups (CLGs) as defined in [9]. Row represent the 25 longest contigs in the Ciona and amphioxus genome assemblies and individual chromosomes in nematode and chicken. Each dot is a gene that was present in a given CLG, and is present in a given contig or chromosome in a modern species. Gene order was shuffled in chicken chromosomes to erase the biases introduced when inferring the CLG from a vertebrate genome in [9]. A random sample of 10 000 chicken genes was selected for the dot-plot so that the number of genes would be equivalent in each species.