Repeated regions in mitochondrial genomes: Distribution, origin and evolutionary significance

Nardi, Francesco; Carapelli, Antonio; Frati, Francesco

doi:10.1016/j.mito.2012.07.105

Cited by 15 publications

(14 citation statements)

References 53 publications

(70 reference statements)

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“…Table S5). Our data are therefore compatible with the idea that large repeats correlate with mtDNA deletion breakpoints in many diseases, as well as in normal ageing [Holt et al, 1988;Lakshmanan et al, 2012;Mita et al, 1990;Nardi et al, 2012;Sadikovic et al, 2010;Samuels et al, 2004;Schon et al, 1989]. It is however possible that these perfect repeats are part of large regions of partial or interrupted homology, which are in turn responsible for bringing together distant segments of the mtDNA during the deletion formation [Guo et al, 2010].…”

Section: Homology At Breakpointssupporting

confidence: 89%

Mitochondrial DNA Rearrangements in Health and Disease-A Comprehensive Study

et al. 2013

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Mitochondrial DNA (mtDNA) rearrangements cause a wide variety of highly debilitating and often fatal disorders and have been implicated in aging and age-associated disease. Here, we present a meta-analytical study of mtDNA deletions (n = 730) and partial duplications (n = 37) using information from more than 300 studies published over the last 30 years. We show that both classes of mtDNA rearrangements are unequally distributed among disorders and their breakpoints have different genomic locations. We also demonstrate that 100% of cases with sporadic mtDNA deletions and 97.3% with duplications have no breakpoints in the 16,071 breakage hotspot site, in contrast with deletions from healthy and aged tissues. Notably, most deletions removing a section of the D-loop are found in tumors. Deleted mtDNA molecules lacking the origin of L-strand replication (O(L)) represent only 9.5% of all reported cases, whereas extra origins of replication occur in all duplications. As previously shown for deletions, imperfect stretches of homology are common in duplication breakpoints. Finally, we provide a dedicated Website with detailed information on deleted/duplicated mtDNA regions to facilitate the design of efficient methods for identification and screening of rearranged mitochondrial genomes (available at http://www.portugene.com/mtDNArearrangements.html).

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Section: Homology At Breakpointssupporting

confidence: 89%

Mitochondrial DNA Rearrangements in Health and Disease-A Comprehensive Study

et al. 2013

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“…For these reasons, mitogenomes of animals are under selection for small size and are generally devoid of noncoding sequences ( Rand 1993 ; Zhang and Hewitt 1997 ). The mitogenomes of the seed beetle species studied here are extraordinary ( Nardi etal. 2012 ) in that two very long intergenic noncoding and TR-rich elements form a very large part of their complete sequence.…”

Section: Discussionmentioning

confidence: 99%

“…The mode by which LIGSs might affect transcription of PCGs is unknown. The fact that they are very AT rich suggests that they may provide secondary structure that, directly or indirectly, guide DNA-binding proteins that compartmentalize or otherwise affect transcription ( Nardi etal. 2012 ; Liu etal.…”

Section: Discussionmentioning

confidence: 99%

The Evolution of Dark Matter in the Mitogenome of Seed Beetles

Sayadi

Immonen

Tellgren-Roth

et al. 2017

Genome Biology and Evolution

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Animal mitogenomes are generally thought of as being economic and optimized for rapid replication and transcription. We use long-read sequencing technology to assemble the remarkable mitogenomes of four species of seed beetles. These are the largest circular mitogenomes ever assembled in insects, ranging from 24,496 to 26,613 bp in total length, and are exceptional in that some 40% consists of non-coding DNA. The size expansion is due to two very long intergenic spacers (LIGSs), rich in tandem repeats. The two LIGSs are present in all species but vary greatly in length (114–10,408 bp), show very low sequence similarity, divergent tandem repeat motifs, a very high AT content and concerted length evolution. The LIGSs have been retained for at least some 45 my but must have undergone repeated reductions and expansions, despite strong purifying selection on protein coding mtDNA genes. The LIGSs are located in two intergenic sites where a few recent studies of insects have also reported shorter LIGSs (>200 bp). These sites may represent spaces that tolerate neutral repeat array expansions or, alternatively, the LIGSs may function to allow a more economic translational machinery. Mitochondrial respiration in adult seed beetles is based almost exclusively on fatty acids, which reduces the need for building complex I of the oxidative phosphorylation pathway (NADH dehydrogenase). One possibility is thus that the LIGSs may allow depressed transcription of NAD genes. RNA sequencing showed that LIGSs are partly transcribed and transcriptional profiling suggested that all seven mtDNA NAD genes indeed show low levels of transcription and co-regulation of transcription across sexes and tissues.

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“…A word w is a repetitive sequence if it contains a substring of the form q r ′ where r′ is maximal and r′ ≥ r for a parameter r ≥ 2 that is called the repeat threshold. See [39] for a recent analysis of repeats in metazoan mitochondrial genomes.…”

Section: Methodsmentioning

confidence: 99%

Local Similarity Search to Find Gene Indicators in Mitochondrial Genomes

Moritz

Bernt

Middendorf

2014

Biology

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Given a set of nucleotide sequences we consider the problem of identifying conserved substrings occurring in homologous genes in a large number of sequences. The problem is solved by identifying certain nodes in a suffix tree containing all substrings occurring in the given nucleotide sequences. Due to the large size of the targeted data set, our approach employs a truncated version of suffix trees. Two methods for this task are introduced: (1) The annotation guided marker detection method uses gene annotations which might contain a moderate number of errors; (2) The probability based marker detection method determines sequences that appear significantly more often than expected. The approach is successfully applied to the mitochondrial nucleotide sequences, and the corresponding annotations that are available in RefSeq for 2989 metazoan species. We demonstrate that the approach finds appropriate substrings.

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Repeated regions in mitochondrial genomes: Distribution, origin and evolutionary significance

Cited by 15 publications

References 53 publications

Mitochondrial DNA Rearrangements in Health and Disease-A Comprehensive Study

Mitochondrial DNA Rearrangements in Health and Disease-A Comprehensive Study

The Evolution of Dark Matter in the Mitogenome of Seed Beetles

Local Similarity Search to Find Gene Indicators in Mitochondrial Genomes

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