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. 2019 May 8;20(Suppl 3):295.
doi: 10.1186/s12864-019-5536-1.

ImtRDB: A Database and Software for Mitochondrial Imperfect Interspersed Repeats Annotation

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Free PMC article

ImtRDB: A Database and Software for Mitochondrial Imperfect Interspersed Repeats Annotation

Viktor A Shamanskiy et al. BMC Genomics. .
Free PMC article

Erratum in

Abstract

Background: Mitochondria is a powerhouse of all eukaryotic cells that have its own circular DNA (mtDNA) encoding various RNAs and proteins. Somatic perturbations of mtDNA are accumulating with age thus it is of great importance to uncover the main sources of mtDNA instability. Recent analyses demonstrated that somatic mtDNA deletions depend on imperfect repeats of various nature between distant mtDNA segments. However, till now there are no comprehensive databases annotating all types of imperfect repeats in numerous species with sequenced complete mitochondrial genome as well as there are no algorithms capable to call all types of imperfect repeats in circular mtDNA.

Results: We implemented naïve algorithm of pattern recognition by analogy to standard dot-plot construction procedures allowing us to find both perfect and imperfect repeats of four main types: direct, inverted, mirror and complementary. Our algorithm is adapted to specific characteristics of mtDNA such as circularity and an excess of short repeats - it calls imperfect repeats starting from the length of 10 b.p. We constructed interactive web available database ImtRDB depositing perfect and imperfect repeats positions in mtDNAs of more than 3500 Vertebrate species. Additional tools, such as visualization of repeats within a genome, comparison of repeat densities among different genomes and a possibility to download all results make this database useful for many biologists. Our first analyses of the database demonstrated that mtDNA imperfect repeats (i) are usually short; (ii) associated with unfolded DNA structures; (iii) four types of repeats positively correlate with each other forming two equivalent pairs: direct and mirror versus inverted and complementary, with identical nucleotide content and similar distribution between species; (iv) abundance of repeats is negatively associated with GC content; (v) dinucleotides GC versus CG are overrepresented on light chain of mtDNA covered by repeats.

Conclusions: ImtRDB is available at http://bioinfodbs.kantiana.ru/ImtRDB/ . It is accompanied by the software calling all types of interspersed repeats with different level of degeneracy in circular DNA. This database and software can become a very useful tool in various areas of mitochondrial and chloroplast DNA research.

Keywords: Database; Imperfect repeats; Selection on dinucleotides; mtDNA.

Conflict of interest statement

The authors declare that they have no competing interests.

Figures

Fig. 1
Fig. 1
Four interspersed repeat types. Colors mark the repeated nucleotide pattern, arrows indicate the pattern direction
Fig. 2
Fig. 2
Block scheme of repeats searching algorithm. A - recognition of similar short nucleotide patterns; B - short patterns merging
Fig. 3
Fig. 3
Pseudocode of Perl script for calculating midpoint position for each repeat monomer. Abbreviations: gp, genome position of nucleotide; Sgp, start genome position of repeat monomer; Egp, end genome position of repeat monomer
Fig. 4
Fig. 4
Number of nucleotides between neighbor mismatches in imperfect repeats found by our algorithm and Vmatch in (A) Homo sapiens mtDNA and (B) Mus musculus mtDNA
Fig. 5
Fig. 5
The number of all four types of repeats normalized by mtDNA lengths of each species. Taxon codes: 1, Chondrichthyes; 2, Actinopterygii; 3, Amphibia; 4, Testudines; 5, Squamata; 6, Aves; 7, Mammalia
Fig. 6
Fig. 6
The analysis of repeat densities evolution in Hominidae. Upper screenshot shows ‘Search results’ page with selected mtDNAs for subsequent comparative analysis. Middle screenshot demonstrate the resulted tab-delimited table containing the alignment of repeat densities (per nucleotide). Bottom screenshot shows the plot generated in MS Excel based on tab-delimited table described in the middle screenshot
Fig. 7
Fig. 7
The analysis of repeat densities and repeat physico-chemical properties correlation in Pongo abelii. Upper screenshot shows ‘Search results’ page with Pongo abelii mtDNAs. Middle screenshot demonstrates the graphical comparison of Pongo abelii mtDNAs repeat densities with the melting temperatures of repeat regions base-pairing in a context of mtDNA genes. Bottom screenshot shows table that summarises the relations between Pongo abelii mtDNAs repeat densities and their physico-chemical properties
Fig. 8
Fig. 8
Taxa-specific repeat densities and repeat length characteristics. A, species-specific mean of repeat densities per mtDNA nucleotide; B, species-specific mean of turns number in B-DNA duplex structure forming by repeat sequence; C, species-specific mean of twist degrees in DNA duplex structure forming by repeat sequence
Fig. 9
Fig. 9
Taxa-specific repeat features related to GC content. A, species-specific averages of GC percent in repeats; B, species-specific averages of changes in absolute value of Gibbs free energy for DNA duplex structure formation by repeated sequences; C, species-specific averages of melting temperature for DNA duplex structure formation by repeated sequences; D, species-specific averages of Stacking energies for DNA duplex structure formation by repeated sequences; E, species-specific averages of changes in absolute value of Enthalpy for DNA duplex structure formation by repeated sequences; F, species-specific averages of changes in absolute value of Entropy for DNA duplex structure formation by repeated sequences

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