ImtRDB: a database and software for mitochondrial imperfect interspersed repeats annotation.
Database
Imperfect repeats
Selection on dinucleotides
mtDNA
Journal
BMC genomics
ISSN: 1471-2164
Titre abrégé: BMC Genomics
Pays: England
ID NLM: 100965258
Informations de publication
Date de publication:
08 05 2019
08 05 2019
Historique:
entrez:
10
7
2019
pubmed:
10
7
2019
medline:
23
7
2019
Statut:
epublish
Résumé
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. 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. 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.
Sections du résumé
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.
Identifiants
pubmed: 31284879
doi: 10.1186/s12864-019-5536-1
pii: 10.1186/s12864-019-5536-1
pmc: PMC6614062
doi:
Substances chimiques
DNA, Circular
0
DNA, Mitochondrial
0
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
295Commentaires et corrections
Type : ErratumIn
Shamanskiy VN [corrected to Shamanskiy VA]
Références
Bioinformatics. 2018 Apr 1;34(7):1081-1085
pubmed: 29126205
Bioinformation. 2013 Jun 08;9(10):541-4
pubmed: 23861572
Gene. 1995 Dec 29;167(1-2):GC1-10
pubmed: 8566757
Trends Genet. 2004 May;20(5):226-9
pubmed: 15109774
Trends Genet. 2010 Aug;26(8):340-3
pubmed: 20591530
Mitochondrion. 2006 Aug;6(4):218-24
pubmed: 16854633
PLoS One. 2011 Jan 31;6(1):e16526
pubmed: 21304975
Bioinformatics. 2014 Jun 15;30(12):1765-6
pubmed: 24532721
Curr Protoc Bioinformatics. 2010 Dec;Chapter 9:Unit 9.13
pubmed: 21154710
Genome Res. 2002 Aug;12(8):1269-76
pubmed: 12176934
Mob DNA. 2015 Jun 02;6:11
pubmed: 26045719
J Comput Biol. 2006 Mar;13(2):296-308
pubmed: 16597241
Database (Oxford). 2015 Sep 27;2015:
pubmed: 26412851
Bioinformatics. 2004 Jun 12;20(9):1405-12
pubmed: 14976032
Nucleic Acids Res. 2016 Jan 4;44(D1):D81-9
pubmed: 26612867
Nucleic Acids Res. 2017 Jul 7;45(12):7237-7248
pubmed: 28486639
Genomics. 2010 Nov;96(5):316-21
pubmed: 20709168
Nucleic Acids Res. 1990 Dec 11;18(23):6927-33
pubmed: 2263455
Nucleic Acids Res. 2015 Apr 30;43(8):4098-108
pubmed: 25855815
Bioinformatics. 2002 Apr;18(4):634-6
pubmed: 12016062
Bioinformatics. 2006 Jan 15;22(2):134-41
pubmed: 16287941
Bioinformation. 2010 Nov 01;5(5):221-3
pubmed: 21364802
Genome Res. 2001 Aug;11(8):1441-52
pubmed: 11483586
Bioinformatics. 2005 Jun;21 Suppl 1:i152-8
pubmed: 15961452
BMC Bioinformatics. 2007 Oct 11;8:382
pubmed: 17931424
Bioinformatics. 2004 Nov 1;20(16):2812-20
pubmed: 15180940
Mol Cell. 2016 Oct 20;64(2):320-333
pubmed: 27720646
Trends Genet. 2000 Jun;16(6):276-7
pubmed: 10827456
Bioinformatics. 2005 Jun;21 Suppl 1:i351-8
pubmed: 15961478
J Hosp Infect. 1996 Dec;34(4):247-65
pubmed: 8971615
BMC Genomics. 2013 Sep 18;14:630
pubmed: 24047532
Nucleic Acids Res. 2012 Sep;40(16):7606-21
pubmed: 22661583
Nucleic Acids Res. 2019 Jan 25;47(2):e8
pubmed: 30304510
J Theor Biol. 2017 Jan 7;412:138-145
pubmed: 27816675
Bioinformatics. 2009 Oct 15;25(20):2632-8
pubmed: 19671691
Nucleic Acids Res. 1999 Jan 15;27(2):573-80
pubmed: 9862982
CSH Protoc. 2007 Jul 01;2007:pdb.top17
pubmed: 21357135
Front Plant Sci. 2016 Sep 13;7:1350
pubmed: 27679641
PLoS One. 2013 Sep 17;8(9):e73318
pubmed: 24069185
Bioinformatics. 2004 Jan 22;20(2):279-81
pubmed: 14734323
Mech Ageing Dev. 2006 Oct;127(10):808-12
pubmed: 16956646
Biomed Res Int. 2015;2015:394157
pubmed: 25811026
BMC Genomics. 2014 Aug 13;15:677
pubmed: 25124333
Bioinformatics. 2007 Jul 1;23(13):1683-5
pubmed: 17463017
Rejuvenation Res. 2008 Apr;11(2):409-17
pubmed: 18442324
Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W708-13
pubmed: 16845104
Mitochondrion. 2014 Nov;19 Pt B:334-7
pubmed: 24561221
PeerJ. 2018 Jun 4;6:e4958
pubmed: 29888139
Mol Cell. 2017 Feb 2;65(3):527-538.e6
pubmed: 28111015
Nucleic Acids Res. 2007;35(21):7197-208
pubmed: 17947320
Nucleic Acids Res. 1990 Feb 11;18(3):561-7
pubmed: 2308845
Bioinformatics. 2010 Feb 15;26(4):570-1
pubmed: 20015948
Biol Lett. 2009 Jun 23;5(3):413-6
pubmed: 19324654
Genome Res. 2009 Sep;19(9):1630-8
pubmed: 19570905
Int J Plant Genomics. 2008;2008:412696
pubmed: 18670612
Cell. 2009 Jan 23;136(2):215-33
pubmed: 19167326
Bioinformatics. 2013 Nov 1;29(21):2683-9
pubmed: 23958725
Bioinformatics. 2006 Mar 15;22(6):676-84
pubmed: 16403795
Nucleic Acids Res. 1999 Jun 1;27(11):2369-76
pubmed: 10325427
Genomics. 2013 Oct;102(4):403-8
pubmed: 23880222
BMC Genomics. 2005 Feb 18;6:23
pubmed: 15720707
Int Arch Med. 2009 Oct 28;2(1):33
pubmed: 19863780
PLoS One. 2015 Mar 03;10(3):e0118612
pubmed: 25734426
Ann N Y Acad Sci. 2005 May;1042:123-9
pubmed: 15965053
BMC Bioinformatics. 2003 Jun 5;4:22
pubmed: 12791171
Bioinformatics. 2004 Mar 22;20(5):701-8
pubmed: 14764564
Bioinformatics. 2007 Apr 15;23(8):1026-8
pubmed: 17309896
Proc Natl Acad Sci U S A. 1993 Aug 15;90(16):7671-5
pubmed: 8356068
Nucleic Acids Res. 2010 Jan;38(1):97-116
pubmed: 19946018
Bioinformatics. 2019 Mar 15;35(6):914-922
pubmed: 30165507
Bioinformatics. 2016 Jun 15;32(12):i209-i215
pubmed: 27307619
Investig Genet. 2015 Aug 05;6:10
pubmed: 26246889
Nucleic Acids Res. 2013 Mar 1;41(5):2779-96
pubmed: 23307556
Nucleic Acids Res. 2003 Jul 1;31(13):3672-8
pubmed: 12824391
PLoS Genet. 2014 Dec 04;10(12):e1004832
pubmed: 25474639
Nucleic Acids Res. 2001 Nov 15;29(22):4633-42
pubmed: 11713313
Mutat Res. 2006 Nov-Dec;613(2-3):76-102
pubmed: 16979375
Nucleic Acids Res. 2009 Apr;37(7):e53
pubmed: 19270064
PLoS One. 2014 Jan 30;9(1):e85363
pubmed: 24497926