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, 34 (7), 1081-1085

Complex Analyses of Inverted Repeats in Mitochondrial Genomes Revealed Their Importance and Variability

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Complex Analyses of Inverted Repeats in Mitochondrial Genomes Revealed Their Importance and Variability

Jana Cechová et al. Bioinformatics.

Abstract

Motivation: The NCBI database contains mitochondrial DNA (mtDNA) genomes from numerous species. We investigated the presence and locations of inverted repeat sequences (IRs) in these mtDNA sequences, which are known to be important for regulating nuclear genomes.

Results: IRs were identified in mtDNA in all species. IR lengths and frequencies correlate with evolutionary age and the greatest variability was detected in subgroups of plants and fungi and the lowest variability in mammals. IR presence is non-random and evolutionary favoured. The frequency of IRs generally decreased with IR length, but not for IRs 24 or 30 bp long, which are 1.5 times more abundant. IRs are enriched in sequences from the replication origin, followed by D-loop, stem-loop and miscellaneous sequences, pointing to the importance of IRs in regulatory regions of mitochondrial DNA.

Availability and implementation: Data were produced using Palindrome analyser, freely available on the web at http://bioinformatics.ibp.cz.

Contact: vaclav@ibp.cz.

Supplementary information: Supplementary data are available at Bioinformatics online.

Figures

Fig. 1.
Fig. 1.
Variability of length and amount of mtDNAs. Box plots show sequence length interquartile ranges for different species groups. The whiskers represent the minimum and maximum values. Numbers of species in each group is visualized with bars (scale is on the secondary vertical axis)
Fig. 2.
Fig. 2.
Frequency of IRs in mtDNAs for subgroups and numbers of mtDNAs. The box plot shows the interquartile ranges of IR frequencies per 1000 bp in different species groups. Whiskers represent the minimum and maximum values
Fig. 3.
Fig. 3.
Differences in IR frequency by DNA locus. The chart shows IR frequencies comparison per 1000 bp between ‘gene’ annotation and other annotated locations from the NCBI database. We analyzed frequencies of all IRs (all) and of IRs with lengths 8 bp and longer (8+), 10 bp and longer (10+) and 12 bp and longer (12+) within annotated locations (inside) and before and after annotated locations (Color version of this figure is available at Bioinformatics online.)

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