The spotted gar genome illuminates vertebrate evolution and facilitates human-teleost comparisons

TLDR

The spotted gar genome, diverging before teleost genome duplication, is a slowly evolving, chromosome‑conserved resource that preserves many ancestral bony vertebrate chromosomes. The study aims to connect human biology to fish biomedical models by sequencing the spotted gar genome, which diverged before teleost genome duplication. The authors sequenced the spotted gar genome to create a comparative resource linking human and teleost biology. The gar genome illuminates evolution of immunity, mineralization, and development, reveals conserved cis‑regulatory elements and noncoding sequences, and shows that teleost duplicated genes subfunctionalize to match gar expression patterns, providing a resource for understanding post‑duplication evolution and human regulatory sequences.

Abstract

Ingo Braasch, John Postlethwait and colleagues report the genome of the spotted gar (Lepisosteus oculatus), whose lineage diverged from teleosts before genome duplication. Their data provide insights into the evolution of genes involved in immunity, mineralization and development and facilitate the comparison of cis-regulatory elements between teleosts and humans. To connect human biology to fish biomedical models, we sequenced the genome of spotted gar (Lepisosteus oculatus), whose lineage diverged from teleosts before teleost genome duplication (TGD). The slowly evolving gar genome has conserved in content and size many entire chromosomes from bony vertebrate ancestors. Gar bridges teleosts to tetrapods by illuminating the evolution of immunity, mineralization and development (mediated, for example, by Hox, ParaHox and microRNA genes). Numerous conserved noncoding elements (CNEs; often cis regulatory) undetectable in direct human-teleost comparisons become apparent using gar: functional studies uncovered conserved roles for such cryptic CNEs, facilitating annotation of sequences identified in human genome-wide association studies. Transcriptomic analyses showed that the sums of expression domains and expression levels for duplicated teleost genes often approximate the patterns and levels of expression for gar genes, consistent with subfunctionalization. The gar genome provides a resource for understanding evolution after genome duplication, the origin of vertebrate genomes and the function of human regulatory sequences.