The diversity present in 5140 human mitochondrial genomes - PubMed (original) (raw)

The diversity present in 5140 human mitochondrial genomes

Luísa Pereira et al. Am J Hum Genet. 2009 May.

Abstract

We analyzed the current status (as of the end of August 2008) of human mitochondrial genomes deposited in GenBank, amounting to 5140 complete or coding-region sequences, in order to present an overall picture of the diversity present in the mitochondrial DNA of the global human population. To perform this task, we developed mtDNA-GeneSyn, a computer tool that identifies and exhaustedly classifies the diversity present in large genetic data sets. The diversity observed in the 5140 human mitochondrial genomes was compared with all possible transitions and transversions from the standard human mitochondrial reference genome. This comparison showed that tRNA and rRNA secondary structures have a large effect in limiting the diversity of the human mitochondrial sequences, whereas for the protein-coding genes there is a bias toward less variation at the second codon positions. The analysis of the observed amino acid variations showed a tolerance of variations that convert between the amino acids V, I, A, M, and T. This defines a group of amino acids with similar chemical properties that can interconvert by a single transition.

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Figures

Figure 1

Figure 1

The Geographical Origin of the 5140 mtDNA Sequences Deposited in GenBank, as of the End of August 2008 African-American descendants were included in sub-Saharan Africa and European-American descendants were included in Eurasians given that they were homogeneous groups, bearing haplogroups belonging to these regions, whereas USA “Hispanics” constituted a mixed sample, with most lineages belonging to East Asian haplogroups observed in Native Americans.

Figure 2

Figure 2

Protein Diversity Correlation between the observed polymorphic positions and the gene size (bp) in the 13 protein-coding genes (A) and distributions of types of amino acids before and after the substitution (B).

Figure 3

Figure 3

Transitions and Transversions Correlation between the observed and maximum possible variations for (A) transitions and (B) transversions in the 13 protein-coding genes.

Figure 4

Figure 4

Synonymous and Nonsynonymous Sequence Changes Correlation between observed and maximum possible variations for (A) synonymous and (B) nonsynonymous substitutions in the 13 protein-coding genes.

Figure 5

Figure 5

Correlation between Observed and Maximum Possible Variations for Amino Acids Originated from Nonsynonymous Mutations The amino acids from group (VIAMT) are represented by red squares and the ones from group (FLPS) are represented by blue circles; the remaining amino acids are represented by black diamonds.

Figure 6

Figure 6

Distribution of Polymorphic Positions in the Various Structural Regions of the tRNA Genes

Figure 7

Figure 7

Variability in the Region of the Origin of the Light Strand Related to the Inferred DNA Secondary Structure Secondary structure of the OL region inferred in mfold with the observed polymorphic positions 5741, 5742, 5744, 5746, and 5747 indicated.

Figure 8

Figure 8

Variability in a tRNA Gene Related to the RNA Secondary Structure The secondary structure of the threonine tRNA and the observed polymorphic positions in the human database (gray hexagons), and positions that are 100% (square) and >90% (circle) conserved in mammalian species.

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References

    1. Benson D.A., Karsch-Mizrachi I., Lipman D.J., Ostell J., Wheeler D.L. GenBank. Nucleic Acids Res. 2008;36(Database issue):D25–D30. - PMC - PubMed
    1. Ingman M., Kaessmann H., Pääbo S., Gyllensten U. Mitochondrial genome variation and the origin of modern humans. Nature. 2000;408:708–713. - PubMed
    1. Ruiz-Pesini E., Lott M.T., Procaccio V., Poole J.C., Brandon M.C., Mishmar D., Yi C., Kreuziger J., Baldi P., Wallace D.C. An enhanced MITOMAP with a global mtDNA mutational phylogeny. Nucleic Acids Res. 2007;35(Database issue):D823–D828. - PMC - PubMed
    1. De Benedictis G., Rose G., Carreiri G., De Luca M., Falcone E., Passarino G., Bonafe M., Monti D., Baggio G., Bertolini S. Mitochondrial DNA inherited variants are associated with successful aging and longevity in humans. FASEB J. 1999;13:1532–1536. - PubMed
    1. Bilal E., Rabadan R., Alexe G., Fuku N., Ueno H., Nishigaki Y., Fujita Y., Ito M., Arai Y., Hirose N. Mitochondrial DNA haplogroups D4a is a marker for extreme longevity in Japan. PLoS ONE. 2008;3:e2421. - PMC - PubMed

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