Nuclear mitochondrial pseudogenes

Gaziev, A.I.; Shaikhaev, G. O.

doi:10.1134/s0026893310030027

Cited by 52 publications

(41 citation statements)

References 114 publications

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“…20 We found a very slight increase in coverage deviation in autosomes with higher nuclear mtDNA segment content, but these are not sufficient to account for the large observed differences between LCLs and controls, and among autosomes.…”

Section: Resultscontrasting

confidence: 58%

Differences between the genomes of lymphoblastoid cell lines and blood-derived samples

Joesch-Cohen¹,

Glusman²

2017

AGG

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Lymphoblastoid cell lines (LCLs) represent a convenient research tool for expanding the amount of biologic material available from an individual. LCLs are commonly used as reference materials, most notably from the Genome in a Bottle Consortium. However, the question remains how faithfully LCL-derived genome assemblies represent the germline genome of the donor individual as compared to the genome assemblies derived from peripheral blood mononuclear cells. We present an in-depth comparison of a large collection of LCL- and peripheral blood mononuclear cell-derived genomes in terms of distributions of coverage and copy number alterations. We found significant differences in the depth of coverage and copy number calls, which may be driven by differential replication timing. Importantly, these copy number changes preferentially affect regions closer to genes and with higher GC content. This suggests that genomic studies based on LCLs may display locus-specific biases, and that conclusions based on analysis of depth of coverage and copy number variation may require further scrutiny.

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Section: Resultscontrasting

confidence: 58%

Differences between the genomes of lymphoblastoid cell lines and blood-derived samples

Joesch-Cohen¹,

Glusman²

2017

AGG

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“…All 786 sequences analyzed contained 267 polymorphic sites, 181 of which were phylogenetically informative, and 309 haplotypes were identified. No nuclear mitochondrial DNA segments (numts) [70, 71] were found. PCR amplifications always produced only one band and we found no ambiguities in the sequences obtained–there were no unexpected stop codons, deletions, insertions or changes in the reading frame; all sequences were in concordance with the rest of cyt b sequences of the common vole from GenBank.…”

Section: Resultsmentioning

confidence: 99%

Between the Balkans and the Baltic: Phylogeography of a Common Vole Mitochondrial DNA Lineage Limited to Central Europe

et al. 2016

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The common vole (Microtus arvalis) has been a model species of small mammal for studying end-glacial colonization history. In the present study we expanded the sampling from central and eastern Europe, analyzing contemporary genetic structure to identify the role of a potential ‘northern glacial refugium’, i.e. a refugium at a higher latitude than the traditional Mediterranean refugia. Altogether we analyzed 786 cytochrome b (cytb) sequences (representing mitochondrial DNA; mtDNA) from the whole of Europe, adding 177 new sequences from central and eastern Europe, and we conducted analyses on eight microsatellite loci for 499 individuals (representing nuclear DNA) from central and eastern Europe, adding data on 311 new specimens. Our new data fill gaps in the vicinity of the Carpathian Mountains, the potential northern refugium, such that there is now dense sampling from the Balkans to the Baltic Sea. Here we present evidence that the Eastern mtDNA lineage of the common vole was present in the vicinity of this Carpathian refugium during the Last Glacial Maximum and the Younger Dryas. The Eastern lineage expanded from this refugium to the Baltic and shows low cytb nucleotide diversity in those most northerly parts of the distribution. Analyses of microsatellites revealed a similar pattern but also showed little differentiation between all of the populations sampled in central and eastern Europe.

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“…This phenomenon would have resembled nuclear inserts of mitogenomes, which are frequent in eukaryotic chromosomes (for nuclear mitochondrial DNA segments, see Refs. [80][81][82][83][84][85][86][87][88][89][90][91][92][93][94][95].…”

Section: Focus On Poxviridae: Synteny Between Poxviral and Amoeban MImentioning

confidence: 99%

Giant viruses: spore‐like missing links between Rickettsia and mitochondria?

Seligmann

2019

Annals of the New York Academy of Sciences

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Phyloproteomics indicate common viral origin from ancient cells before archaea, bacteria, and eukaryota split and subsequent size and complexity reductions occurred. Further independent evidence for the cellular origin of viruses is reviewed for the virus order Megavirales, focusing on the family Poxviridae. Megavirales comprises giant viruses, double‐stranded DNA viruses whose genomes exceed some bacterial ones and large enough to parasitize large‐celled protists (amoeba). Giant viruses, virophages, and mitochondria have homologous DNA and RNA polymerases and share RNA splicing punctuation by stem–loop hairpins. Giant virus factories and amoeban mitochondria colocate, with viral proteins homologous to mitochondrial proteins specifically targeting mitochondrial inner membranes. Mitochondria share asexual budding with many bacterial endospores and membrane‐enveloped viruses. These megavirus−mitochondrion similarities are not coincidental: systematic alignment analyses have detected candidate megaviral homologs of each amoeban mitogene (including ribosomal RNAs) distributed across megaviral genomes. These candidate megaviral homologs overall follow mitogene order, and megaviral−mitogenome synteny increases with viral genome reduction. This analysis is repeated within Poxviridae, whose organellar‐like morphogenesis is reminiscent of mitochondria. More generally, the results confirm the patterns observed in Megavirales: synteny with amoeban mitogenomes increases with genome reduction. Parsimoniously interpreting this suggests Megavirales and mitochondria have a rickettsia‐like common ancestor. Megavirales could be the missing links between bacterial‐like cells and mitochondria, implying cellular‐to‐viral‐to‐subcellular macroevolution.

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Nuclear mitochondrial pseudogenes

Cited by 52 publications

References 114 publications

Differences between the genomes of lymphoblastoid cell lines and blood-derived samples

Differences between the genomes of lymphoblastoid cell lines and blood-derived samples

Between the Balkans and the Baltic: Phylogeography of a Common Vole Mitochondrial DNA Lineage Limited to Central Europe

Giant viruses: spore‐like missing links between Rickettsia and mitochondria?

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