Fig. 1: Conserved syntenies between amphioxus and various species.

a, Oxford dot plot of orthologous genes between amphioxus and two representative bony vertebrates: spotted gar (Lepisosteus oculatus; top) and chicken (Gallus gallus; bottom). The axes show the index of 6,843 orthologous gene families anchored by mutual best hits from gar, chick, frog and human to amphioxus, with chromosome boundaries indicated. Dashed vertical lines show the location of synteny breakpoints for amphioxus that are consistent in comparisons with other vertebrate (Extended Data Figs. 2 and 3) and invertebrate genomes (see b; Extended Data Fig. 4). Genes are coloured according to this partitioning, defining 17 ancestral CLGs, with labels shown to the right. b, Mutual best-hit dot plot of amphioxus versus scallop, using the same colouring as in a. Syntenic discontinuities in amphioxus (indicated by the dashed lines) are consistent in the scallop. Note that CLGB (dark purple) is distributed across three pairs of homologous chromosomes, implying that this CLG existed as three distinct linkage groups in the scallop–amphioxus common ancestor.