{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,6]],"date-time":"2026-04-06T11:53:21Z","timestamp":1775476401821,"version":"3.50.1"},"reference-count":32,"publisher":"Oxford University Press (OUP)","issue":"7","license":[{"start":{"date-parts":[[2017,11,8]],"date-time":"2017-11-08T00:00:00Z","timestamp":1510099200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001824","name":"Czech Science Foundation","doi-asserted-by":"publisher","award":["15-21855S"],"award-info":[{"award-number":["15-21855S"]}],"id":[{"id":"10.13039\/501100001824","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2018,4,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>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.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>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\u2009bp 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.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>Data were produced using Palindrome analyser, freely available on the web at http:\/\/bioinformatics.ibp.cz.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btx729","type":"journal-article","created":{"date-parts":[[2017,11,7]],"date-time":"2017-11-07T12:11:44Z","timestamp":1510056704000},"page":"1081-1085","source":"Crossref","is-referenced-by-count":30,"title":["Complex analyses of inverted repeats in mitochondrial genomes revealed their importance and variability"],"prefix":"10.1093","volume":"34","author":[{"given":"Jana","family":"\u010cechov\u00e1","sequence":"first","affiliation":[{"name":"Department of Biophysical Chemistry and Molecular Oncology, Institute of Biophysics, The Czech Academy of Sciences, Brno, Czech Republic"}]},{"given":"Ji\u0159\u00ed","family":"L\u00fdsek","sequence":"additional","affiliation":[{"name":"Department of Informatics, Mendel University in Brno, Brno, Czech Republic"}]},{"given":"Martin","family":"Bartas","sequence":"additional","affiliation":[{"name":"Department of Biophysical Chemistry and Molecular Oncology, Institute of Biophysics, The Czech Academy of Sciences, Brno, Czech Republic"},{"name":"Department of Biology and Ecology\/Institute of Environmental Technologies, Faculty of Science, University of Ostrava, Ostrava, Czech Republic"}]},{"given":"V\u00e1clav","family":"Br\u00e1zda","sequence":"additional","affiliation":[{"name":"Department of Biophysical Chemistry and Molecular Oncology, Institute of Biophysics, The Czech Academy of Sciences, Brno, Czech Republic"}]}],"member":"286","published-online":{"date-parts":[[2017,11,8]]},"reference":[{"key":"2023012712564501000_btx729-B1","doi-asserted-by":"crossref","first-page":"R911","DOI":"10.1016\/j.cub.2015.07.055","article-title":"Endosymbiosis and eukaryotic cell evolution","volume":"25","author":"Archibald","year":"2015","journal-title":"Curr. Biol"},{"key":"2023012712564501000_btx729-B2","doi-asserted-by":"crossref","first-page":"39","DOI":"10.1111\/j.1469-8137.2005.01492.x","article-title":"Inheritance and recombination of mitochondrial genomes in plants, fungi and animals","volume":"168","author":"Barr","year":"2005","journal-title":"New Phytol"},{"key":"2023012712564501000_btx729-B3","doi-asserted-by":"crossref","first-page":"54","DOI":"10.1016\/j.sajb.2015.09.016","article-title":"Organelle genetic diversity in a global collection of Jute (Corchorus capsularis and C. olitorius, Malvaceae)","volume":"103","author":"Basu","year":"2016","journal-title":"South African J. Bot"},{"key":"2023012712564501000_btx729-B4","doi-asserted-by":"crossref","first-page":"570","DOI":"10.1128\/MMBR.00026-10","article-title":"Folded DNA in action: hairpin formation and biological functions in prokaryotes","volume":"74","author":"Bikard","year":"2010","journal-title":"Microbiol. Mol. Biol. Rev"},{"key":"2023012712564501000_btx729-B5","doi-asserted-by":"crossref","first-page":"1767","DOI":"10.1093\/nar\/27.8.1767","article-title":"Animal mitochondrial genomes","volume":"27","author":"Boore","year":"1999","journal-title":"Nucleic Acids Res"},{"key":"2023012712564501000_btx729-B6","doi-asserted-by":"crossref","first-page":"193","DOI":"10.1242\/jeb.200.2.193","article-title":"Regulation analysis of energy metabolism","volume":"200","author":"Brand","year":"1997","journal-title":"J. Exp. Biol"},{"key":"2023012712564501000_btx729-B7","doi-asserted-by":"crossref","first-page":"1739","DOI":"10.1016\/j.bbrc.2016.09.015","article-title":"Palindrome analyser \u2013 a new web-based server for predicting and evaluating inverted repeats in nucleotide sequences","volume":"478","author":"Brazda","year":"2016","journal-title":"Biochem. Biophys. Res. Commun"},{"key":"2023012712564501000_btx729-B8","doi-asserted-by":"crossref","first-page":"371","DOI":"10.1080\/07391102.2012.682205","article-title":"Superhelical DNA as a preferential binding target of 14-3-3gamma protein","volume":"30","author":"Brazda","year":"2012","journal-title":"J. Biomol. Struct. Dyn"},{"key":"2023012712564501000_btx729-B9","doi-asserted-by":"crossref","first-page":"516","DOI":"10.1016\/j.bbrc.2016.12.113","article-title":"The structure formed by inverted repeats in p53 response elements determines the transactivation activity of p53 protein","volume":"483","author":"Brazda","year":"2017","journal-title":"Biochem. Biophys. Res. Commun"},{"key":"2023012712564501000_btx729-B10","doi-asserted-by":"crossref","first-page":"33","DOI":"10.1186\/1471-2199-12-33","article-title":"Cruciform structures are a common DNA feature important for regulating biological processes","volume":"12","author":"Br\u00e1zda","year":"2011","journal-title":"BMC Mol. Biol"},{"key":"2023012712564501000_btx729-B11","doi-asserted-by":"crossref","DOI":"10.3390\/ijms18020375","article-title":"Recognition of Local DNA Structures by p53 Protein","volume":"18","author":"Brazda","year":"2017","journal-title":"Int. J. Mol. Sci"},{"key":"2023012712564501000_btx729-B12","first-page":"1","article-title":"Searching for non-B DNA-forming motifs using nBMST (non-B DNA motif search tool)","volume":"18","author":"Cer","year":"2012","journal-title":"Curr. Protoc. Hum. Genet"},{"key":"2023012712564501000_btx729-B13","doi-asserted-by":"crossref","first-page":"21","DOI":"10.1002\/cyto.a.20187","article-title":"DNA transitions induced by binding of PARP-1 to cruciform structures in supercoiled plasmids","volume":"68","author":"Chasovskikh","year":"2005","journal-title":"Cytometry A"},{"key":"2023012712564501000_btx729-B35","doi-asserted-by":"crossref","first-page":"D136","DOI":"10.1093\/nar\/gkr1178","article-title":"The NCBI taxonomy database","volume":"40","author":"Federhen","year":"2011","journal-title":"Nucleic Acids Res."},{"key":"2023012712564501000_btx729-B15","doi-asserted-by":"crossref","first-page":"107","DOI":"10.1016\/j.biochi.2013.09.016","article-title":"The plant mitochondrial genome: dynamics and maintenance","volume":"100","author":"Gualberto","year":"2014","journal-title":"Biochimie"},{"key":"2023012712564501000_btx729-B17","doi-asserted-by":"crossref","first-page":"367","DOI":"10.1093\/gbe\/evu290","article-title":"Extreme features of the Galdieria sulphuraria organellar genomes: a consequence of polyextremophily?","volume":"7","author":"Jain","year":"2015","journal-title":"Genome Biol. Evol"},{"key":"2023012712564501000_btx729-B18","doi-asserted-by":"crossref","first-page":"57","DOI":"10.1016\/j.cmet.2016.09.017","article-title":"Mammalian mitochondria and aging: an update","volume":"25","author":"Kauppila","year":"2017","journal-title":"Cell. Metab"},{"key":"2023012712564501000_btx729-B19","doi-asserted-by":"crossref","first-page":"619","DOI":"10.1146\/annurev.physiol.60.1.619","article-title":"The mitochondrial death\/life regulator in apoptosis and necrosis","volume":"60","author":"Kroemer","year":"1998","journal-title":"Annu. Rev. Physiol"},{"key":"2023012712564501000_btx729-B20","doi-asserted-by":"crossref","first-page":"W242","DOI":"10.1093\/nar\/gkw290","article-title":"Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees","volume":"44","author":"Letunic","year":"2016","journal-title":"Nucleic Acids Res"},{"key":"2023012712564501000_btx729-B21","doi-asserted-by":"crossref","first-page":"20","DOI":"10.1016\/j.jtbi.2017.02.031","article-title":"Symbiosis in eukaryotic evolution","volume":"434","author":"L\u00f3pez-Garc\u00eda","year":"2017","journal-title":"J. Theor. Biol"},{"key":"2023012712564501000_btx729-B22","doi-asserted-by":"crossref","first-page":"20140330.","DOI":"10.1098\/rstb.2014.0330","article-title":"Endosymbiotic theories for eukaryote origin","volume":"370","author":"Martin","year":"2015","journal-title":"Philos. Trans. R. Soc. B Biol. Sci"},{"key":"2023012712564501000_btx729-B23","doi-asserted-by":"crossref","first-page":"12998","DOI":"10.1021\/bi061002k","article-title":"Effect of DNA supercoiling on the geometry of holliday junctions","volume":"45","author":"Mikheikin","year":"2006","journal-title":"Biochemistry"},{"key":"2023012712564501000_btx729-B24","first-page":"151","author":"Pale\u010dek","year":"1991"},{"key":"2023012712564501000_btx729-B25","doi-asserted-by":"crossref","first-page":"11364","DOI":"10.1016\/S0021-9258(18)60968-8","article-title":"A native cruciform DNA structure probed in bacteria by recombinant T7 endonuclease","volume":"262","author":"Panayotatos","year":"1987","journal-title":"J. Biol. Chem"},{"key":"2023012712564501000_btx729-B26","doi-asserted-by":"crossref","first-page":"165","DOI":"10.1016\/j.ympev.2014.02.023","article-title":"Primate phylogenetic relationships and divergence dates inferred from complete mitochondrial genomes","volume":"75","author":"Pozzi","year":"2014","journal-title":"Mol. Phylogenet. Evol"},{"key":"2023012712564501000_btx729-B27","volume-title":"R: A Language and Environment for Statistical Computing","author":"R Core Team","year":"2014"},{"key":"2023012712564501000_btx729-B28","doi-asserted-by":"crossref","first-page":"1169","DOI":"10.1006\/jmbi.2000.3542","article-title":"A cruciform structural transition provides a molecular switch for chromosome structure and dynamics","volume":"296","author":"Shlyakhtenko","year":"2000","journal-title":"J. Mol. Biol"},{"key":"2023012712564501000_btx729-B29","author":"Sievert","year":"2016"},{"key":"2023012712564501000_btx729-B30","doi-asserted-by":"crossref","first-page":"602","DOI":"10.1016\/j.bbabio.2017.01.004","article-title":"Mitochondrial dysfunction and mitochondrial dynamics-The cancer connection","volume":"1858","author":"Srinivasan","year":"2017","journal-title":"Biochim. Biophys. Acta - Bioenerg"},{"key":"2023012712564501000_btx729-B32","first-page":"259","article-title":"Mitochondrial theory of aging matures \u2013 roles of mtDNA mutation and oxidative stress in human aging","volume":"64","author":"Wei","year":"2001","journal-title":"Zhonghua Yi Xue Za Zhi (Taipei)"},{"key":"2023012712564501000_btx729-B33","author":"Wickham","year":"2016"},{"key":"2023012712564501000_btx729-B34","doi-asserted-by":"crossref","first-page":"211","DOI":"10.1016\/0378-1119(84)90181-1","article-title":"The replication origin of pSC101: the nucleotide sequence and replication functions of the ori region","volume":"29","author":"Yamaguchi","year":"1984","journal-title":"Gene"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/34\/7\/1081\/48914301\/bioinformatics_34_7_1081.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/34\/7\/1081\/48914301\/bioinformatics_34_7_1081.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,27]],"date-time":"2023-01-27T13:45:06Z","timestamp":1674827106000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/34\/7\/1081\/4604597"}},"subtitle":[],"editor":[{"given":"John","family":"Hancock","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2017,11,8]]},"references-count":32,"journal-issue":{"issue":"7","published-print":{"date-parts":[[2018,4,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btx729","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2018,4,1]]},"published":{"date-parts":[[2017,11,8]]}}}