Fig. 4

Evidence of pericentric inversions between the genomes of channel catfish and blue catfish. Three lines of evidence supported the presence of major pericentric inversions on chromosome 6, chromosome 11, and chromosome 24: (1) long reads mapped at the junctions (left panel); (2) genetic linkage mapping (middle panel); and (3) junction PCR (right panel). With long reads across the inversional junctions, two additional blue catfish and two channel catfish were sequenced in addition to the sequencing templates that were used to generate the reference genomes. Alignments were contiguous when the junctional long reads from blue catfish individuals were mapped against the reference genome sequence of blue catfish, but not against the reference genome sequence of channel catfish and vice versa. This was true for all inverted chromosomes 6, 11, and 24, and for both the left and the right inversion junctions. With genetic mapping, a common set of markers (Additional file 1: Table S17) were identified within the inverted junctions, and the inversion was evident for all inverted chromosomes of 6, 11, and 24. Finally, we designed PCR primers to amplify across the inversion junctions (Additional File 1: Table S17). As expected, the PCR amplicon matched the expectation of inversions, except for the left junction PCR using primers of channel catfish, which generated a band from blue catfish as well, but not of expected size. We believe this band was generated from non-specific primer binding as an artifact