Advances in Vertebrate (Cyto)Genomics Shed New Light on Fish Compositional Genome Evolution

Area of Science:

• Genomics
• Comparative Genomics
• Bioinformatics

Background:

• Previous studies suggested fish genomes have low guanine-cytosine content (GC%) compared to higher vertebrates.
• This view was based on a presumed sharp increase in genic GC% during vertebrate evolution.
• Existing genomic data has not been fully utilized to verify these assumptions.

Purpose of the Study:

• To re-evaluate the guanine-cytosine content (GC%) in animal genomes using public databases.
• To investigate GC% variations across different genomic fractions (DNA, cDNA, CDS) in fish and other chordates.
• To correct misconceptions regarding fish genome composition and vertebrate GC% evolution.

Main Methods:

• Calculation of GC% in DNA (entire genome), cDNA (complementary DNA), and CDS (exons) for various animal genomes.
• Utilizing public genomic databases for data acquisition and analysis.
• Visualization of compositional genome landscape using 2D and 3D representations.

Main Results:

• Fish possess GC-rich genomes, comparable to or richer than higher vertebrates, with GC-enriched exons.
• A general GC-enrichment trend is observed from DNA to cDNA to CDS levels across animal genomes.
• Fish and invertebrates exhibit wider GC% inter-quartile ranges compared to the more constrained avian and mammalian genomes.

Conclusions:

• The study refutes the notion of a sharp increase in gene GC% during the evolution of higher vertebrates.
• Fish genomes are compositionally diverse and often GC-rich, contrary to prior beliefs.
• An online platform was developed to explore AT/GC compositional genome evolution across species.