Fig. 2

Chromosomal rearrangements inferred from a conserved synteny comparison. a Pipefish and platyfish chromosomes are broadly congruent. Strings connecting orthologous genes between the species’ genomes are colored by pipefish chromosome. b Pipefish LG 1 and 14 are each orthologous to two platyfish chromosomes, likely because chromosome fusions occurred in the syngnathid lineage. Several scaffolds from fused chromosomes 1 and from 14, including those shown in the insets, show blocks of conserved synteny to both “ancestral” chromosomes in platyfish (LG 1 and 24 or LG 14 and 23). This pattern indicates that some number of intra-chromosomal rearrangements blended segments across the chromosomal junction after the chromosomes fused. Strings connecting orthologs are color-coded by platyfish chromosome. Pipefish scaffolds are shown in alternately shaded rectangles along the chromosome. c On LG 16, differences in the orientation and location of orthologous gene blocks suggest inversions and transpositions have occurred since the last common ancestor of pipefish and platyfish. Strings connecting orthologous genes are colored according to the pipefish scaffold each gene resides on. Support for scaffold order and orientation can be seen in the linkage map for pipefish LG 16, shown above