Mitochondrial DNA insertions in the nuclear horse genome

Nergadze, Solomon G.; Lupotto, M.; Pellanda, Paola; Santagostino, Marco; Vitelli, Valerio; Giulotto, Elena

doi:10.1111/j.1365-2052.2010.02130.x

Cited by 38 publications

(31 citation statements)

References 40 publications

(68 reference statements)

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“…However, there is lack of consensus over whether the majority of human numts represent independent mtDNA insertions or arose by duplication events in the nuclear genome [6], [8]. In the horse genome, which contains very few duplicate copies of genes [11], the extant numt complement does not appear to contain any duplicates [12]. Analyses of the structure of numts in human and horse have revealed that many numts contain structural changes that have occured post-insertion, including inversions, deletions and insertions [2], [12].…”

Section: Introductionmentioning

confidence: 99%

“…In the horse genome, which contains very few duplicate copies of genes [11], the extant numt complement does not appear to contain any duplicates [12]. Analyses of the structure of numts in human and horse have revealed that many numts contain structural changes that have occured post-insertion, including inversions, deletions and insertions [2], [12]. Some numts are very large or complete copies of the mitochondrial genome; the largest human numt for example covers 90% of the human mitochondrial genome [10].…”

Section: Introductionmentioning

confidence: 99%

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Mitochondrial Pseudogenes in the Nuclear Genomes of Drosophila

Rogers

Griffiths-Jones

2012

PLoS ONE

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Mitochondrial pseudogenes in nuclear chromosomes (numts) have been detected in the genomes of a diverse range of eukaryotic species. However, the numt content of different genomes and their properties is not uniform, and study of these differences provides insight into the mechanisms and dynamics of genome evolution in different organisms. In the genus Drosophila, numts have previously only been identified on a genome-wide scale in the melanogaster subgroup. The present study extends the identification to 11 species of the Drosophila genus. We identify a total of 302 numts and show that the numt complement is highly variable in Drosophilids, ranging from just 4 in D. melanogaster to 67 in D. willistoni, broadly correlating with genome size. Many numts have undergone large-scale rearrangements in the nucleus, including interruptions, inversions, deletions and duplications of sequence of variable size. Estimating the age of the numts in the nucleus by phylogenetic tree reconstruction reveals the vast majority of numts to be recent gains, 90% having arisen on terminal branches of the species tree. By identifying paralogs and counting duplications among the extant numts we estimate that 23% of extant numts arose through post-insertion duplications. We estimate genus average rates of insertion of 0.75 per million years, and a duplication rate of 0.010 duplications per numt per million years.

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Mitochondrial Pseudogenes in the Nuclear Genomes of Drosophila

Rogers

Griffiths-Jones

2012

PLoS ONE

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“…It is therefore possible that an unusually high mutation rate of HV1 in gorillas has obliterated the overall sequence similarity between the HV1 sequences and their nuclear copies, leading to an apparent deficit of numts from this region. As the peripheral regions of the MCR in mammals exhibit exceptionally high variation in length and sequence associated with the presence of nucleotide repeats (Saccone et al 1991; Sbisà et al 1997), rapid sequence evolution of this region would be expected to lead to loss of sequence identity with nuclear copies and a generalized deficit of numts from this region across mammals, as evidenced so far not only in primates but also in taxa as distant as Perissodactyla (Mourier et al 2001; Nergadze et al 2010; Soto-Calderón et al 2012). …”

Section: Discussionmentioning

confidence: 99%

Identification of species-specific nuclear insertions of mitochondrial DNA (numts) in gorillas and their potential as population genetic markers

Soto-Calderón

Clark

Wildschutte

et al. 2014

Molecular Phylogenetics and Evolution

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The first hyper-variable region (HV1) of the mitochondrial control region (MCR) has been widely used as a molecular tool in population genetics, but inadvertent amplification of nuclear translocated copies of mitochondrial DNA (numts) in gorillas has compromised the use of mitochondrial DNA in population genetic studies. At least three putative classes (I, II, III) of gorilla-specific HV1 MCR numts have been uncovered over the past decade. However, the number, size and location of numt loci in gorillas and other apes are completely unknown. Furthermore, little work to date has assessed the utility of numts as candidate population genetic markers. In the present study, we screened Bacterial Artificial Chromosome (BAC) genomic libraries in the chimpanzee and gorilla to compare patterns of mitochondrial-wide insertion in both taxa. We conducted an intensive BLAST search for numts in the gorilla genome and compared the prevalence of numt loci originating from the MCR with other great ape taxa. Additional gorilla-specific MCR numts were retrieved either through BAC library screens or using an anchored-PCR (A-PCR) amplification using genomic DNA from five unrelated gorillas. Locus-specific primers were designed to identify numt insertional polymorphisms and evaluate their potential as population genetic markers. Mitochondrial-wide surveys of chimpanzee and gorilla BACs showed that the number of numts does not differ between these two taxa. However, MCR numts are more abundant in chimpanzees than in other great apes. We identified and mapped 67 putative gorilla-specific numts, including two that contain the entire HV1 domain, cluster with sequences from two numt classes (I, IIb) and will likely co-amplify with mitochondrial sequences using most published HV1 primers. However, phylogenetic analysis coupled with post-hoc analysis of mitochondrial variation can successfully differentiate nuclear sequences. Insertional polymorphisms were evident in three out of five numts examined, indicating their potential utility as molecular markers. Taken together, these findings demonstrate the potentially powerful insight that numts could make in uncovering population history in gorillas and other mammals.

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“…Since their first discovery (du Buy and Riley, 1967), numts have been found in numerous species (Bensasson et al, 2001;Leister, 2005;Liu and Zhao, 2007;Hassanin et al, 2010;Hazkani-Covo et al, 2010;Nergadze et al, 2010;Song et al, 2013). An increasing research effort is now directed at determining the evolution of numts and their possible function and influence on studies involving mitochondrial genes (Ricchetti et al, 2004;Thalmann et al, 2004;Schmitz et al, 2005;Cleaver et al, 2014).…”

Section: Introductionmentioning

confidence: 99%

“…As in the field of animal genetics, studies of mtDNA polymorphism and genetic variation are also increasing in numbers. Due to their homology with the counterpart mtDNA fragments, numts could severely influence the results of analyses involving polymerase chain reaction (PCR) methods and might even result in completely erroneous conclusions (Wallace et al, 1997;Nergadze et al, 2010). An example of such a case, is the argument about the relationship between Alzheimer's disease and mtDNA polymorphisms (Davis et al, 1997;Hirano et al, 1997;Wallace et al, 1997;Wang et al, 2014).…”

Section: Introductionmentioning

confidence: 99%

Mitochondrial DNA insertions in the nuclear Capra hircus genome

Ning

2017

Genet. Mol. Res.

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ABSTRACT. Nuclear mitochondrial pseudogenes (numts), originating from mtDNA insertions into the nuclear genome, have been detected in many species. However, the distribution of numts in the newly published nuclear genome of domestic goat (Capra hircus) has not yet been explored. We used the entire goat mtDNA sequence and nuclear genome, to identify 118 numts using BLAST. Of these, 79 were able to map sequences to the genome. Further analysis showed that the size of the numts ranged from 318 to 9608 bp, and the homologous identity between numts and their respective corresponding mtDNA fragments varied between 65 and 99%. The identified Yunnan black goat numts covered nearly all the mitochondrial genes including mtDNA control region, and were distributed over all chromosomes with the exception of chromosomes 18, 21, and 25. The Y chromosome was excluded from our analysis, as sequence data are currently not available. Among the discovered 79 numts that we were able to map to the genome, 26 relatively complete mitochondrial genes were detected. Our results constitute valuable information for subsequent studies related to mitochondrial genes and goat evolution.

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Mitochondrial DNA insertions in the nuclear horse genome

Cited by 38 publications

References 40 publications

Mitochondrial Pseudogenes in the Nuclear Genomes of Drosophila

Mitochondrial Pseudogenes in the Nuclear Genomes of Drosophila

Identification of species-specific nuclear insertions of mitochondrial DNA (numts) in gorillas and their potential as population genetic markers

Mitochondrial DNA insertions in the nuclear Capra hircus genome

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