Chromosome‐level bichir genomes reveal ancestral bony vertebrate architecture and regulatory innovations underlying lung origin

We present the first genomes-scale analysis of two bichir species, revealing an exceptionally conserved karyotype that recapitulates the ancestral bony vertebrate architecture. Massive DNA transposon expansions, rather than LINEs, may drive their large genomes. Crucially, we identify lung-vertebrate-specific conserved non-coding element insertions near key developmental genes (ZFPM2 and FOXP2), with enhancer signatures and expression support, providing comparative genomic evidence that local regulatory innovations may have contributed to the evolutionary origin of lungs.