Diagnosing mitochondrial DNA diversity: applications of a sentinel gene approach

Clare, E.L. and Hebert, P.D.N. and Wilson, J.J. and von Konigslow, T.E. and Kerr, K.C.R. (2008) Diagnosing mitochondrial DNA diversity: applications of a sentinel gene approach. Journal of Molecular Evolution, 66 (4). pp. 362-367. ISSN 0022-2844

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Abstract

Mitochondrial genomes show wide variation in their GC content. This study examines the correlations between mitochondrial genome-wide shifts in this feature and a fragment of the cytochrome c oxidase subunit I (COI) gene in animals, plants, and fungi. Because this approach utilizes COI as a sentinel, analyzing sequences from repositories such as GenBank and the Barcode of Life Data System (BOLD) can provide rapid insights into nucleotide usage. With this approach we probe nucleotide composition in a variety of taxonomic groups and establish the degree to which mitochondrial GC content varies among them. We then focus on two groups in particular, the classes Insecta and Aves, which possess the highest and lowest GC content, respectively. We establish that the sentinel approach provides strong indicators of mitochondrial GC content within divergent phyla (R values = 0.86-0.95, p < 0.001, in test cases) and provide evidence that selective pressures acting on GC content extend to noncoding regions of the plant and fungal mitochondrial genomes. We demonstrate that there is considerable variation in GC content of the mitochondrial genome within phyla and at each taxonomic level, leading to a substantial overlap zone in GC content between chordates and invertebrates. Our results provide a novel insight into the mitochondrial genome composition of animals, plants, and fungi and advocate this sentinel technique for the detection of rapid alterations in nucleotide usage as a measure of mitochondrial genome biodiversity.

Item Type: Article
Additional Information: Institute of Biological Sciences, Faculty of Science Building, University of Malaya, 50603 Kuala Lumpur, MALAYSIA
Uncontrolled Keywords: Cytochrome c oxidase i, Gc content, Nucleotide usage, Biodiversity, Dna, Barcoding, Nucleotide composition bias, Metabolic-rate, Evolution, Substitution, Barcodes, Trees
Subjects: Q Science > QH Natural history > QH301 Biology
Divisions: Faculty of Science > Institute of Biological Sciences
Depositing User: Miss Malisa Diana
Date Deposited: 05 Feb 2013 03:34
Last Modified: 25 Feb 2015 03:10
URI: http://eprints.um.edu.my/id/eprint/4644

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