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The evolution of isochore patterns in vertebrate genomes
Maria Costantini1, Rosalia Cammarano, Giorgio Bernardi
1Stazione Zoologica Anton Dohrn, Naples, Italy. mcosta@szn.it
BMC Genomics
|April 7, 2009
Summary
Vertebrate genomes feature DNA segments called isochores, which are conserved across species. Their patterns, influenced by GC levels and dinucleotide frequencies, are shaped by natural selection and linked to genome structure and function.
Area of Science:
- Genomics
- Molecular Biology
- Evolutionary Biology
Background:
- Vertebrate genomes are mosaics of isochores (large DNA segments with homogeneous base composition).
- Isochores form families with distinct GC levels, differing between fish/amphibians and mammals/birds.
- Isochores correlate with gene density, expression, replication timing, and recombination.
Purpose of the Study:
- To precisely quantify previous conclusions on isochore patterns using fully sequenced genomes.
- To investigate the conservation and changes in isochore family patterns across vertebrate evolution.
- To explore the evolutionary forces driving isochore pattern formation and maintenance.
Main Methods:
- Comparative genomics analysis of fully sequenced vertebrate genomes.
- Quantification of GC levels and dinucleotide frequencies within isochore families.
- Analysis of isochore size and pattern conservation across diverse vertebrate taxa.
Main Results:
- Isochore families are largely conserved in GC levels, dinucleotide frequencies, and size across vertebrate genomes.
- Isochore family patterns exhibit both conservation and change in warm- and cold-blooded vertebrates.
- Previous conclusions regarding isochore composition and genome properties were precisely quantified.
Conclusions:
- Conservation of GC levels and dinucleotide frequencies suggests conserved chromatin structures.
- Isochore size conservation may relate to chromosome structure and replication.
- Natural selection is proposed as the driving force for the formation, maintenance, and changes in isochore patterns.
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