Genome Organization of Vertebrates


Compositional genomics, an approach relying on the base composition of genomes, helped to solve a long‐standing problem, namely the sequence organization of vertebrate and, more generally, of eukaryotic genomes.

Keywords: isochores; base composition; chromosomes; compositional genomics

Figure 1.

The two fundamental functions of DNA: replication and coding. During replication mistakes may occur, resulting in mutations. Some of these are repaired, but others persist and may spread into the progeny reaching 100% levels in the population: mutations are then said to be ‘fixed’ into nucleotide substitutions. The latter, after transcription of DNA into RNA and translation of RNA into proteins, may be silent (no amino acid change) or may appear as amino acid changes, which may be very rarely advantageous but more frequently are neutral or deleterious. Silent changes are also called synonymous, whereas nucleotide changes leading to aminoacid changes are called non‐synonymous. The symbols on the protein chain on the right indicate specific amino acids.

Figure 2.

The genetic code. The 1980 Grantham's representation of the genetic code was modified in that codons rather than anticodons are shown, a distinction is made among third position nucleotides of quartet, duet and odd number codons, and hydropathy values for amino acids using the scale of Kyte and Doolittle are shown. Codons are displayed vertically, the first position being on the top. One can observe that most third codon position changes are silent or synonymous, they do not lead to a change in the corresponding aminoacids. Reproduced from D'Onofrio G, Jabbari K, Musto H and Bernardi G (1999) The correlation of protein hydropathy with the composition of coding sequences. Gene 238: 3–14.

Figure 3.

DNA and gene distribution in the isochore families of the human genome. The major structural and functional properties associated with each gene space are listed (in blue for the genome desert and in red for the genome core). Reproduced from Bernardi G (2007) The neo‐selectionist theory of genome evolution. Proceedings of the National Academy of Sciences of the USA 104: 8385–8390.


Further Reading

Bernardi G (2004, reprinted in 2005) Structural and Evolutionary Genomics. Natural Selection in Genome Evolution. Elsevier: Amsterdam.

Bernardi G (2007) The neo‐selectionist theory of genome evolution. Proceedings of the National Academy of Sciences of the USA 104: 8385–8390.

Costantini M and Bernardi G (2008) Correlations between coding and contiguous non‐coding sequences in isochore families from vertebrate genomes. Gene 410: 241–248.

Costantini M and Bernardi G (2008). Replication timing, chromosomal bands and isochores. Proceedings of National Academy of Sciences USA (accepted for publication).

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Bernardi, Giorgio(Jul 2008) Genome Organization of Vertebrates. In: eLS. John Wiley & Sons Ltd, Chichester. [doi: 10.1002/9780470015902.a0005001.pub2]