Strange IndiaStrange India

As the only surviving lineages of jawless fishes, hagfishes and lampreys provide a critical window into early vertebrate evolution1–3. Here, we investigate the complex history, timing, and functional role of genome-wide duplications4–7 and programmed DNA elimination8,9 in vertebrates in the light of a chromosome-scale genome sequence for the brown hagfish Eptatretus atami. Combining evidence from syntenic and phylogenetic analyses, we establish a comprehensive picture of vertebrate genome evolution including an auto-tetraploidisation (1RV) predating the Early Cambrian cyclostome-gnathostome split, followed by a Mid-Late Cambrian allo-tetraploidisation (2RJV) in gnathostomes and a prolonged Cambrian-Ordovician hexaploidisation (2RCY) in cyclostomes. Subsequently, hagfishes underwent extensive genomic changes with chromosomal fusions accompanied by the loss of genes essential for organ systems (eyes, osteoclasts), accounting in part for the simplification of their body plan1,2. Finally, we characterise programmed DNA elimination in hagfish, identifying protein-coding genes and repetitive elements that are deleted from somatic cell lineages during early development. The elimination of these germline-specific genes provides a mechanism for resolving genetic conflict between soma and germline by repressing germline/pluripotency functions, paralleling findings in lampreys10,11. Reconstruction of the early genomic history of vertebrates provides a valuable framework for further exploration of cyclostome and jawed vertebrate evolution.

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