The spotted gar genome illuminates vertebrate evolution and facilitates human-teleost comparisons
Геном панцирной щуки проливает свет на эволюцию позвоночных и облегчает сопоставление человека и костистых рыб
2016-03-07
SCID: 54.1/5v3kmgm2
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cis-regulatory elementsconserved noncoding elementsspotted gar genometeleost genome duplicationvertebrate evolution
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Abstract (AI)
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.
Key Findings
1
Expression domains and levels of duplicated teleost genes often collectively approximate ancestral gar patterns, supporting subfunctionalization after genome duplication.
2
Gar has a slowly evolving genome that preserves the content and size of many entire ancestral bony-vertebrate chromosomes.
3
The genome illuminates the evolution of immunity, mineralization, and development through conserved Hox, ParaHox, and microRNA genes.
4
The spotted gar genome represents a lineage that diverged from teleosts before teleost genome duplication, providing an intermediate reference between teleosts and tetrapods.
5
Using gar reveals numerous conserved noncoding elements missed by direct human–teleost comparisons; functional studies support conserved regulatory roles relevant to interpreting human GWAS sequences.
Research Object
the spotted gar (Lepisosteus oculatus) genome
Research Subject
the genome’s evolutionary conservation and divergence, including the evolution and function of genes and cis-regulatory elements in immunity, mineralization, development, and human–teleost comparisons
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2016-03-07
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