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Lucas T, Vincent B, Eric P. Translocation of mitochondrial DNA into the nuclear genome blurs phylogeographic and conservation genetic studies in seabirds. ROYAL SOCIETY OPEN SCIENCE 2022; 9:211888. [PMID: 35719890 PMCID: PMC9198517 DOI: 10.1098/rsos.211888] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 04/19/2022] [Indexed: 05/03/2023]
Abstract
Mitochondrial DNA (mtDNA) translocated into the nuclear genome (numt), when co-analysed with genuine mtDNA, could plague phylogeographic studies. To evaluate numt-related biases in population genetics parameters in birds, which are prone to accumulating numts, we targeted the mitochondrial mt-cytb gene. We looked at 13 populations of Audubon's shearwater (Puffinus lherminieri), including five mitochondrial lineages. mt-cytb homologue and paralogue (numt) sequences were determined by Sanger sequencing with and without prior exonuclease digestion of nuclear DNA. Numts formed monophyletic clades corresponding to three of the five mitochondrial lineages tested (the remaining two forming a paraphyletic group). Nineteen percent of numt alleles fell outside of their expected mitochondrial clade, a pattern consistent with multiple translocation events, incomplete lineage sorting (ILS), and/or introgression. When co-analysing mt-cytb paralogues and homologues, excluding individuals with ambiguities underestimates genetic diversity (4%) and differentiation (11%) among least-sampled populations. Removing ambiguous sites drops the proportion of inter-lineage genetic variance by 63%. While co-analysing numts with mitochondrial sequences can lead to severe bias and information loss in bird phylogeographic studies, the separate analysis of genuine mitochondrial loci and their nuclear paralogues can shed light on numt molecular evolution, as well as evolutionary processes such as ILS and introgression.
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Affiliation(s)
- Torres Lucas
- Centre d'Etudes Biologiques de Chizé, UMR 7372, CNRS - La Rochelle Universite, Villiers en Bois, France
- Littoral, Environnement et Sociétés, UMR 7266 CNRS - La Rochelle Université, La Rochelle, France
| | - Bretagnolle Vincent
- Centre d'Etudes Biologiques de Chizé, UMR 7372, CNRS - La Rochelle Universite, Villiers en Bois, France
| | - Pante Eric
- Littoral, Environnement et Sociétés, UMR 7266 CNRS - La Rochelle Université, La Rochelle, France
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2
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Willcox JAL, Geiger JT, Morton SU, McKean D, Quiat D, Gorham JM, Tai AC, DePalma S, Bernstein D, Brueckner M, Chung WK, Giardini A, Goldmuntz E, Kaltman JR, Kim R, Newburger JW, Shen Y, Srivastava D, Tristani-Firouzi M, Gelb B, Porter GA, Seidman JG, Seidman CE. Neither cardiac mitochondrial DNA variation nor copy number contribute to congenital heart disease risk. Am J Hum Genet 2022; 109:961-966. [PMID: 35397206 PMCID: PMC9118105 DOI: 10.1016/j.ajhg.2022.03.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 03/11/2022] [Indexed: 11/28/2022] Open
Abstract
The well-established manifestation of mitochondrial mutations in functional cardiac disease (e.g., mitochondrial cardiomyopathy) prompted the hypothesis that mitochondrial DNA (mtDNA) sequence and/or copy number (mtDNAcn) variation contribute to cardiac defects in congenital heart disease (CHD). MtDNAcns were calculated and rare, non-synonymous mtDNA mutations were identified in 1,837 CHD-affected proband-parent trios, 116 CHD-affected singletons, and 114 paired cardiovascular tissue/blood samples. The variant allele fraction (VAF) of heteroplasmic variants in mitochondrial RNA from 257 CHD cardiovascular tissue samples was also calculated. On average, mtDNA from blood had 0.14 rare variants and 52.9 mtDNA copies per nuclear genome per proband. No variation with parental age at proband birth or CHD-affected proband age was seen. mtDNAcns in valve/vessel tissue (320 ± 70) were lower than in atrial tissue (1,080 ± 320, p = 6.8E-21), which were lower than in ventricle tissue (1,340 ± 280, p = 1.4E-4). The frequency of rare variants in CHD-affected individual DNA was indistinguishable from the frequency in an unaffected cohort, and proband mtDNAcns did not vary from those of CHD cohort parents. In both the CHD and the comparison cohorts, mtDNAcns were significantly correlated between mother-child, father-child, and mother-father. mtDNAcns among people with European (mean = 52.0), African (53.0), and Asian haplogroups (53.5) were calculated and were significantly different for European and Asian haplogroups (p = 2.6E-3). Variant heteroplasmic fraction (HF) in blood correlated well with paired cardiovascular tissue HF (r = 0.975) and RNA VAF (r = 0.953), which suggests blood HF is a reasonable proxy for HF in heart tissue. We conclude that mtDNA mutations and mtDNAcns are unlikely to contribute significantly to CHD risk.
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Affiliation(s)
- Jon A L Willcox
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Joshua T Geiger
- Department of Pediatrics, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Sarah U Morton
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; Division of Newborn Medicine, Department of Medicine, Boston Children's Hospital, Boston, MA 02115, USA
| | - David McKean
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Daniel Quiat
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; Department of Cardiology, Boston Children's Hospital, Boston, MA 02115, USA
| | - Joshua M Gorham
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Angela C Tai
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Steven DePalma
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Daniel Bernstein
- Department of Pediatrics, Stanford University, Palo Alto, CA 94305, USA
| | - Martina Brueckner
- Departments of Genetics and Pediatric Cardiology, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Wendy K Chung
- Departments of Pediatrics and Medicine, Columbia University Medical Center, New York, NY 10019, USA
| | - Alessandro Giardini
- Cardiorespiratory Unit, Great Ormond Street Hospital, Great Ormond Street, London WC1N 3JH, UK
| | - Elizabeth Goldmuntz
- Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jonathan R Kaltman
- Heart Development and Structural Diseases Branch, Division of Cardiovascular Sciences, NHLBI/NIH, Bethesda, MD 20892, USA
| | - Richard Kim
- Cardiothoracic Surgery, Children's Hospital Los Angeles, Los Angeles, CA 90027, USA
| | - Jane W Newburger
- Department of Cardiology, Boston Children's Hospital, Boston, MA 02115, USA
| | - Yufeng Shen
- Departments of Systems Biology and Biomedical Informatics, Columbia University Medical Center, New York, NY 10019, USA
| | - Deepak Srivastava
- Gladstone Institute of Cardiovascular Disease, San Francisco, CA 94158, USA
| | - Martin Tristani-Firouzi
- Nora Eccles Harrison Cardiovascular Research and Training Institute, University of Utah, Salt Lake City, UT 84132, USA
| | - Bruce Gelb
- Mindich Child Health and Development Institute and Departments of Pediatrics, Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - George A Porter
- Department of Pediatrics, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - J G Seidman
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.
| | - Christine E Seidman
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Department of Cardiology, Brigham and Women's Hospital, Boston, MA 02115, USA; Howard Hughes Medical Institute, Harvard University, Boston, MA 02138, USA
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3
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Ko YJ, Yang EC, Lee JH, Lee KW, Jeong JY, Park K, Chung O, Bhak J, Lee JH, Yim HS. Characterization of cetacean Numt and its application into cetacean phylogeny. Genes Genomics 2015. [DOI: 10.1007/s13258-015-0353-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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Song H, Moulton MJ, Whiting MF. Rampant nuclear insertion of mtDNA across diverse lineages within Orthoptera (Insecta). PLoS One 2014; 9:e110508. [PMID: 25333882 PMCID: PMC4204883 DOI: 10.1371/journal.pone.0110508] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2014] [Accepted: 09/23/2014] [Indexed: 02/06/2023] Open
Abstract
Nuclear mitochondrial pseudogenes (numts) are non-functional fragments of mtDNA inserted into the nuclear genome. Numts are prevalent across eukaryotes and a positive correlation is known to exist between the number of numts and the genome size. Most numt surveys have relied on model organisms with fully sequenced nuclear genomes, but such analyses have limited utilities for making a generalization about the patterns of numt accumulation for any given clade. Among insects, the order Orthoptera is known to have the largest nuclear genome and it is also reported to include several species with a large number of numts. In this study, we use Orthoptera as a case study to document the diversity and abundance of numts by generating numts of three mitochondrial loci across 28 orthopteran families, representing the phylogenetic diversity of the order. We discover that numts are rampant in all lineages, but there is no discernable and consistent pattern of numt accumulation among different lineages. Likewise, we do not find any evidence that a certain mitochondrial gene is more prone to nuclear insertion than others. We also find that numt insertion must have occurred continuously and frequently throughout the diversification of Orthoptera. Although most numts are the result of recent nuclear insertion, we find evidence of very ancient numt insertion shared by highly divergent families dating back to the Jurassic period. Finally, we discuss several factors contributing to the extreme prevalence of numts in Orthoptera and highlight the importance of exploring the utility of numts in evolutionary studies.
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Affiliation(s)
- Hojun Song
- Department of Biology, University of Central Florida, Orlando, Florida, United States of America
| | - Matthew J. Moulton
- Department of Human Genetics, University of Utah, Salt Lake City, Utah, United States of America
- Department of Biology and M. L. Bean Museum, Brigham Young University, Provo, Utah, United States of America
| | - Michael F. Whiting
- Department of Biology and M. L. Bean Museum, Brigham Young University, Provo, Utah, United States of America
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Song H, Moulton MJ, Hiatt KD, Whiting MF. Uncovering historical signature of mitochondrial DNA hidden in the nuclear genome: the biogeography ofSchistocercarevisited. Cladistics 2013; 29:643-662. [DOI: 10.1111/cla.12013] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Affiliation(s)
- Hojun Song
- Department of Biology; University of Central Florida; Orlando FL 32816 USA
- Department of Biology and M. L. Bean Life Science Museum; Brigham Young University; Provo UT 84602 USA
| | - Matthew J. Moulton
- Department of Biology and M. L. Bean Life Science Museum; Brigham Young University; Provo UT 84602 USA
| | - Kevin D. Hiatt
- Department of Biology and M. L. Bean Life Science Museum; Brigham Young University; Provo UT 84602 USA
| | - Michael F. Whiting
- Department of Biology and M. L. Bean Life Science Museum; Brigham Young University; Provo UT 84602 USA
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Polymorphic NumtS trace human population relationships. Hum Genet 2011; 131:757-71. [DOI: 10.1007/s00439-011-1125-3] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2011] [Accepted: 11/30/2011] [Indexed: 11/26/2022]
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Hazkani-Covo E. Mitochondrial insertions into primate nuclear genomes suggest the use of numts as a tool for phylogeny. Mol Biol Evol 2009; 26:2175-9. [PMID: 19578158 DOI: 10.1093/molbev/msp131] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Homoplasy-free characters are a valuable and highly desired tool for molecular systematics. Nuclear sequences of mitochondrial origin (numts) are fragments of mitochondrial DNA that have been transferred into the nuclear genome. numts are passively captured into genomes and have no transposition activity, which suggests they may have utility as phylogenetic markers. Here, five fully sequenced primate genomes (human, chimpanzee, orangutan, rhesus macaque, and marmoset) are used to reconstruct the evolutionary dynamics of recent numt accumulation in a phylogenetic context. The status of 367 numt loci is used as categorical data, and a maximum parsimony approach is used to trace numt insertions on different branches of the taxonomically undisputed primate phylogenetic tree. The presence of a given numt in related taxa implies orthologous integration, whereas the absence of a numt indicates the plesiomorphic condition prior to integration. An average rate of 5.65 numts per 1 My is estimated on the tree, but insertion rates vary significantly on different branches. Two instances in which the presence-absence pattern of numts does not agree with the phylogenetic tree were identified. These events may be the result of either lineage sorting or reversal. Using the numts reported here to reconstruct primate phylogeny produces the canonical primate tree topology with high bootstrap support. Moreover, numts identified in gorilla Supercontigs were used to test the human-chimp-gorilla trichotomy, yielding a high level of support for the sister relationship of human and chimpanzee. These analyses suggest that numts are valuable phylogenetic markers that can be used for molecular systematics. It remains to be tested whether numts are useful at deeper phylogenetic levels.
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Dunshea G, Barros NB, Wells RS, Gales NJ, Hindell MA, Jarman SN. Pseudogenes and DNA-based diet analyses: a cautionary tale from a relatively well sampled predator-prey system. BULLETIN OF ENTOMOLOGICAL RESEARCH 2008; 98:239-248. [PMID: 18439341 DOI: 10.1017/s0007485308005993] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Mitochondrial ribosomal DNA is commonly used in DNA-based dietary analyses. In such studies, these sequences are generally assumed to be the only version present in DNA of the organism of interest. However, nuclear pseudogenes that display variable similarity to the mitochondrial versions are common in many taxa. The presence of nuclear pseudogenes that co-amplify with their mitochondrial paralogues can lead to several possible confounding interpretations when applied to estimating animal diet. Here, we investigate the occurrence of nuclear pseudogenes in fecal samples taken from bottlenose dolphins (Tursiops truncatus) that were assayed for prey DNA with a universal primer technique. We found pseudogenes in 13 of 15 samples and 1-5 pseudogene haplotypes per sample representing 5-100% of all amplicons produced. The proportion of amplicons that were pseudogenes and the diversity of prey DNA recovered per sample were highly variable and appear to be related to PCR cycling characteristics. This is a well-sampled system where we can reliably identify the putative pseudogenes and separate them from their mitochondrial paralogues using a number of recommended means. In many other cases, it would be virtually impossible to determine whether a putative prey sequence is actually a pseudogene derived from either the predator or prey DNA. The implications of this for DNA-based dietary studies, in general, are discussed.
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Affiliation(s)
- G Dunshea
- Antarctic Wildlife Research Unit, School of Zoology, University of Tasmania, Hobart, TAS, Australia.
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Zbawicka M, Burzyński A, Wenne R. Complete sequences of mitochondrial genomes from the Baltic mussel Mytilus trossulus. Gene 2007; 406:191-8. [PMID: 17980515 DOI: 10.1016/j.gene.2007.10.003] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2007] [Accepted: 10/01/2007] [Indexed: 11/28/2022]
Abstract
Marine mussels Mytilus possess two mitochondrial (mt) genomes, which undergo doubly uniparental inheritance (DUI). Female (F) and male (M) genomes are usually highly diverged at the sequence level. Both genomes contain the same set of metazoan genes (for 12 proteins, 2 rRNAs and 23 tRNAs), both lack the atp8 gene and have two tRNAs for methionine. However, recently recombination between those variants has been reported. Both original F and M mt genomes of M. trossulus were replaced by M. edulis mtDNA in the Baltic populations. Highly diverged M genome occurs rarely in the Baltic mussels. Full sequences of the M genome identified in males (sperm) and F genome in females (eggs) were obtained. Both genomes were diverged by 24% in nucleotide sequence, but had similar nucleotide composition and codon usage bias. Constant domain (CD) of the control region (CR), the tRNA and rRNA genes were the most conserved. The most diverged was the variable domain 1 (VD1) of the control region. The F genome was longer than M by 147 bp. and the main difference was localised in the VD1 region. No recombination was observed in whole mtDNA of both studied variants. Nuclear mitochondrial pseudogenes (numts) have not been found by hybridisation with probes complementary to several fragments of the Baltic M. trossulus mtDNA.
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Affiliation(s)
- Małgorzata Zbawicka
- Department of Genetics and Marine Biotechnology, Institute of Oceanology, Polish Academy of Sciences, Powstańców Warszawy 55, 81-712, Poland
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Hazkani-Covo E, Graur D. A Comparative Analysis of numt Evolution in Human and Chimpanzee. Mol Biol Evol 2006; 24:13-8. [PMID: 17056643 DOI: 10.1093/molbev/msl149] [Citation(s) in RCA: 90] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Mitochondrial DNA sequences are frequently transferred into the nuclear genome, giving rise to numts (nuclear DNA sequences of mitochondrial origin). So far, the evolutionary history of numts has largely been studied by using single genomes. Here, we present the first attempt to study numt evolution in a comparative manner by using a pairwise genomic alignment. The total number of numts was estimated to be 452 in human and 469 in chimpanzee. numts that were found in both genomes at identical loci were deemed to be orthologous; 391 numts (>80%) were classified as such. The preponderance of orthologous numts is due to the very short divergence time between the 2 hominoids. The rest of numts were deemed to be nonorthologous. Nonorthologous numts were subdivided into 1) ancestral numts that have lost an ortholog in one species through deletion (12 in human and 11 in chimpanzee), 2) new numts acquired by the insertion of a mitochondrial sequence after the divergence of the 2 species (34 in human and 46 in chimpanzee), and 3) paralogous numts created by the tandem duplication of a preexisting numt (2 in human). This approach also enabled us to reconstruct the numt repertoire in the common ancestor of humans and chimpanzees (409 numts). Our comparative approach is also useful in identifying the exact boundaries of numts.
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Abstract
Mitochondria play important roles in cellular energy metabolism, free radical generation, and apoptosis. Defects in mitochondrial function have long been suspected to contribute to the development and progression of cancer. In this review article, we aim to provide a brief summary of our current understanding of mitochondrial genetics and biology, review the mtDNA alterations reported in various types of cancer, and offer some perspective as to the emergence of mtDNA mutations, their functional consequences in cancer development, and therapeutic implications.
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Affiliation(s)
- Jennifer S Carew
- Department of Molecular Pathology, The University of Texas M. D. Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, Texas 77030, USA
- The Graduate School of Biomedical Sciences, University of Texas Health Sciences Center, 1515 Holcombe Boulevard, Houston, Texas 77030, USA
| | - Peng Huang
- Department of Molecular Pathology, The University of Texas M. D. Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, Texas 77030, USA
- The Graduate School of Biomedical Sciences, University of Texas Health Sciences Center, 1515 Holcombe Boulevard, Houston, Texas 77030, USA
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Bensasson D, Zhang DX, Hartl DL, Hewitt GM. Mitochondrial pseudogenes: evolution's misplaced witnesses. Trends Ecol Evol 2001; 16:314-321. [PMID: 11369110 DOI: 10.1016/s0169-5347(01)02151-6] [Citation(s) in RCA: 671] [Impact Index Per Article: 29.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Nuclear copies of mitochondrial DNA (mtDNA) have contaminated PCR-based mitochondrial studies of over 64 different animal species. Since the last review of these nuclear mitochondrial pseudogenes (Numts) in animals, Numts have been found in 53 of the species studied. The recent evidence suggests that Numts are not equally abundant in all species, for example they are more common in plants than in animals, and also more numerous in humans than in Drosophila. Methods for avoiding Numts have now been tested, and several recent studies demonstrate the potential utility of Numt DNA sequences in evolutionary studies. As relics of ancient mtDNA, these pseudogenes can be used to infer ancestral states or root mitochondrial phylogenies. Where they are numerous and selectively unconstrained, Numts are ideal for the study of spontaneous mutation in nuclear genomes.
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