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It was recently shown that indels are responsible for more than twice as many unmatched nucleotides as are base substitutions between samples of chimpanzee and human DNA. A larger sample has now been examined and the result is similar. The number of indels is approximately 1/12th of the number of base substitutions and the average length of the indels is 36 nt, including indels up to 10 kb. The ratio (R(u)) of unpaired nucleotides attributable to indels to those attributable to substitutions is 3.0 for this 2 million-nt chimp DNA sample compared with human. There is similar evidence of a large value of R(u) for sea urchins from the polymorphism of a sample of Strongylocentrotus purpuratus DNA (R(u) = 3-4). Other work indicates that similarly, per nucleotide affected, large differences are seen for indels in the DNA polymorphism of the plant Arabidopsis thaliana (R(u) = 51). For the insect Drosophila melanogaster a high value of R(u) (4.5) has been determined. For the nematode Caenorhabditis elegans the polymorphism data are incomplete but high values of R(u) are likely. Comparison of two strains of Escherichia coli O157:H7 shows a preponderance of indels. Because these six examples are from very distant systematic groups the implication is that in general, for alignments of closely related DNA, indels are responsible for many more unmatched nucleotides than are base substitutions. Human genetic evidence suggests that indels are a major source of gene defects, indicating that indels are a significant source of evolutionary change.
Antonarakis,
Disease-causing mutations in the human genome.
2000, Pubmed
Antonarakis,
Disease-causing mutations in the human genome.
2000,
Pubmed
Berger,
Genetic mapping with SNP markers in Drosophila.
2001,
Pubmed
Britten,
Divergence between samples of chimpanzee and human DNA sequences is 5%, counting indels.
2002,
Pubmed
Britten,
Evidence that most human Alu sequences were inserted in a process that ceased about 30 million years ago.
1994,
Pubmed
Caccone,
DNA DIVERGENCE AMONG HOMINOIDS.
1989,
Pubmed
Dawson,
A SNP resource for human chromosome 22: extracting dense clusters of SNPs from the genomic sequence.
2001,
Pubmed
Ebersberger,
Genomewide comparison of DNA sequences between humans and chimpanzees.
2002,
Pubmed
Gu,
The size distribution of insertions and deletions in human and rodent pseudogenes suggests the logarithmic gap penalty for sequence alignment.
1995,
Pubmed
Hayashi,
Complete genome sequence of enterohemorrhagic Escherichia coli O157:H7 and genomic comparison with a laboratory strain K-12.
2001,
Pubmed
Jander,
Arabidopsis map-based cloning in the post-genome era.
2002,
Pubmed
Kudva,
Strains of Escherichia coli O157:H7 differ primarily by insertions or deletions, not single-nucleotide polymorphisms.
2002,
Pubmed
Lehrman,
Exon-Alu recombination deletes 5 kilobases from the low density lipoprotein receptor gene, producing a null phenotype in familial hypercholesterolemia.
1986,
Pubmed
Nickerson,
Molecular definition of pericentric inversion breakpoints occurring during the evolution of humans and chimpanzees.
1998,
Pubmed
Ohnishi,
Genomic diversity of enterohemorrhagic Escherichia coli O157 revealed by whole genome PCR scanning.
2002,
Pubmed
Ohnishi,
Diversification of Escherichia coli genomes: are bacteriophages the major contributors?
2001,
Pubmed
Perna,
Genome sequence of enterohaemorrhagic Escherichia coli O157:H7.
2001,
Pubmed
Petrov,
Mutational equilibrium model of genome size evolution.
2002,
Pubmed
Petrov,
DNA loss and evolution of genome size in Drosophila.
2002,
Pubmed
Robertson,
The large srh family of chemoreceptor genes in Caenorhabditis nematodes reveals processes of genome evolution involving large duplications and deletions and intron gains and losses.
2000,
Pubmed
Springer,
Calculation of sequence divergence from the thermal stability of DNA heteroduplexes.
1992,
Pubmed
Weber,
Human diallelic insertion/deletion polymorphisms.
2002,
Pubmed
Welch,
Extensive mosaic structure revealed by the complete genome sequence of uropathogenic Escherichia coli.
2002,
Pubmed
Wicks,
Rapid gene mapping in Caenorhabditis elegans using a high density polymorphism map.
2001,
Pubmed
Witherspoon,
Neutral evolution of ten types of mariner transposons in the genomes of Caenorhabditis elegans and Caenorhabditis briggsae.
2003,
Pubmed
