Evolution of isochores in rodents

Area of Science:

• Genomics
• Evolutionary Biology
• Mammalian Genetics

Background:

• Mammalian genomes exhibit diverse isochore patterns, with rats and mice showing a unique GC content organization.
• The isochore patterns in most rodent species beyond mice and rats are largely uncharacterized.
• Understanding these patterns is crucial for evolutionary insights into rodent diversification.

Purpose of the Study:

• To investigate the taxonomic distribution of isochore patterns across various rodent species.
• To compare GC content variations in the LCAT gene and associated sequences among rodents.
• To identify novel modes of isochore evolution within the rodent lineage.

Main Methods:

• Sequencing of the nuclear gene LCAT (lecithin:cholesterol acyltransferase) from 17 rodent species.
• Comparative analysis of GC content at third codon positions and in introns of the LCAT gene.
• Bioinformatic analysis of extensive sequence databases from diverse rodent groups.

Main Results:

• All murid rodents exhibit significantly lower GC content in LCAT sequences, indicating a shared "GC homogenization" pattern.
• Hamster sequence data reveals an isochore pattern identical to rats and mice.
• Hystricomorphs, like guinea pigs, show GC-poor LCAT sequences with "GC reordering"—significant GC changes without altering the overall isochore pattern.
• Sciurids and glirids display nonconservative isochore evolution compared to nonrodents.

Conclusions:

• Rodents possess distinct isochore patterns, including GC homogenization and GC reordering, differing from the general mammalian pattern.
• At least two novel isochore evolution patterns were identified in rodents.
• No investigated rodent species conforms to the typical "general mammalian" isochore pattern.