Variable Number Tandem Repeats in the Mitochondrial DNA of Lentinula edodes

Kim, Sinil; Song, Yelin; Ha, Byeongsuk; Moon, Yoon Jung; Kim, Minseek; Ryu, Hojin; Ro, Hyeon-Su

doi:10.3390/genes10070542

Cited by 10 publications

(10 citation statements)

References 49 publications

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“…60 The tandem repeats in animals and plants have been reported to be involved in mtDNA stability by insertion and deletion of the repeat array. 61 Thus, it is not excluded that the decreased number of repetitive elements in one of the examined dogs might be a result of such slippage during replication. The in silico analyses revealed that there might be a 313 bp-long CpG island at the positions 16 137…16 449 (%GC = 0.40) in the canine mitochondrial VNTR region, which in some circumstances might be methylated or demethylated.…”

Section: Discussionmentioning

confidence: 99%

“…VNTRs are thought to have arisen due to slippages during DNA replication or as a consequence of unequal crossing‐over, and due to the repetitive nature of the sequence have allowed further increases/decreases in the number of repeats resulting in the polymorphisms observed 60 . The tandem repeats in animals and plants have been reported to be involved in mtDNA stability by insertion and deletion of the repeat array 61 . Thus, it is not excluded that the decreased number of repetitive elements in one of the examined dogs might be a result of such slippage during replication.…”

Section: Discussionmentioning

confidence: 99%

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Molecular differences in mitochondrial DNA genomes of dogs with malignant mammary tumours

Kowal

Tkaczyk-Wlizło

Pierzchała

et al. 2021

Vet Comparative Oncology

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The aim of this study was to determine molecular defects in mitochondrial DNA (mtDNA) with the use of large-scale genome analysis in malignant canine mammary gland tumours and indicate whether these changes were linked with the carcinogenesis process. With the use of the NGS technology, we sequenced 27 samples of mtDNA isolated from blood and tumours obtained from 13 dogs with mammary gland tumours.The total number of mutations and polymorphisms in the analysed mitochondrial genomes was 557. We identified 383 single nucleotide polymorphisms (SNP), 32 indels (or length polymorphisms), 4 mutations, 137 heteroplasmic positions and 1 indel mutation. The highest variability (132 changes) was observed in the variable number of tandem repeats (VNTR) region. The heteroplasmy rate in VNTR varied among individuals and even between two tumours in one organism. Our previous study resulted in determination of a probable CpG island in this region, thus it is not excluded that these changes might alter mtDNA methylation. Only the ATP8 gene was not affected by any polymorphisms or mutations, whereas the COX1 gene had the highest number of polymorphisms from all protein-coding genes. One change m.13594G>A was detected in a region spanning two genes: ND5 and ND6, from which a deleterious effect was observed for the ND5 protein. Molecular changes were frequently observed in the TΨC loop, which is thought to interact with ribosomal RNA.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Molecular differences in mitochondrial DNA genomes of dogs with malignant mammary tumours

Kowal

Tkaczyk-Wlizło

Pierzchała

et al. 2021

Vet Comparative Oncology

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“…But at the same time, GHA79 has gained unique TR regions and lost a common TR region (Supplementary Excel File 2). Comparative analysis of the mitogenomes from three isolates of L. edodes, another Agaricales also revealed variable number TR regions (Kim et al, 2019). The authors proposed that the elongation of the repeat regions occurs through reciprocal incorporation of basic repeat units.…”

Section: Mitogenome Size Variation and Sources Of Genome Expansionmentioning

confidence: 99%

Mitochondrial Genomics of Six Cacao Pathogens From the Basidiomycete Family Marasmiaceae

et al. 2021

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Thread blight disease has recently been described as an emerging disease on cacao (Theobroma cacao) in Ghana. In Ghana, thread blight disease is caused by multiple species of the Marasmiaceae family: Marasmius tenuissimus, M. crinis-equi, M. palmivorus, and Marasmiellus scandens. Interestingly, two additional members of the Marasmiaceae; Moniliophthora roreri (frosty pod rot) and Moniliophthora perniciosa (witches’ broom disease), are major pathogens of cacao in the Western hemisphere. It is important to accurately characterize the genetic relationships among these economically important species in support of their disease management. We used data from Illumina NGS-based genome sequencing efforts to study the mitochondrial genomes (mitogenomes) of the four cacao thread blight associated pathogens from Ghana and compared them with published mitogenomes of Mon. roreri and Mon. perniciosa. There is a remarkable interspecies variation in mitogenome size within the six cacao-associated Marasmiaceae species, ranging from 43,121 to 109,103 bp. The differences in genome lengths are primarily due to the number and lengths of introns, differences in intergenic space, and differences in the size and numbers of unidentified ORFs (uORF). Among seven M. tenuissimus mitogenomes sequenced, there is variation in size and sequence pointing to divergent evolution patterns within the species. The intronic regions show a high degree of sequence variation compared to the conserved sequences of the 14 core genes. The intronic ORFs identified, regardless of species, encode GIY-YIG or LAGLIDADG domain-containing homing endonuclease genes. Phylogenetic relationships using the 14 core proteins largely mimic the phylogenetic relationships observed in gene order patterns, grouping M. tenuissimus with M. crinis-equi, and M. palmivorus with Mon. roreri and Mon. perniciosa, leaving Mar. scandens as an outlier. The results from this study provide evidence of independent expansion/contraction events and sequence diversification in each species and establish a foundation for further exploration of the evolutionary trajectory of the fungi in Marasmiaceae family.

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“…Ustilago maydis also shows uniparental inheritance associated with a defined mating type, where the result is strongly affected by mating-type locus ( Xu et al, 2000 ; Yan and Xu, 2003 ; Fedler et al, 2009 ). In the mating of filamentous basidiomyceteous fungi, two types of dikaryotic cells, which carry one of the two mtDNAs originated from the two monokaryotic cells, are generated through reciprocal entrance of nuclei to the cytoplasms of monokaryotic cells after hyphal fusion between monokaryotic hyphae with compatible mating types ( Kim et al, 2019 ).…”

Section: Introductionmentioning

confidence: 99%

“…The genetic diversity analysis using the mating type genes of 127 strains of L. edodes showed a high degree of diversity particularly in the A mating type locus of the wild strains ( Ha et al, 2018 ). The diverse nature of the A mating type genes enabled the discrimination of nuclei in dikaryons as well as monokaryons of different origins ( Kim et al, 2019 ). The mtDNA is another source of genetic information.…”

Section: Introductionmentioning

confidence: 99%

Comparative structural analysis on the mitochondrial DNAs from various strains of Lentinula edodes

et al. 2022

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The evolution of mitochondria through variations in mitochondrial DNA (mtDNA) is one of the intriguing questions in eukaryotic cells. In order to assess the causes of the variations in mitochondria, the mtDNAs of the 21 strains of Lentinula edodes were assembled for this study, and analyzed together with four published mtDNA sequences. The mtDNAs were within the sizes of 117 kb ~ 122 kb. The gene number was observed consistent except for two mtDNAs, which carry a duplicated trnG1-trnG2 unit or a putative gene deletion. The size variation was largely attributed to the number of introns, repeated sequences, transposable elements (TEs), and plasmid-related sequences. Intron loss and gain were found from cox1, rnl, and rns of three mtDNAs. Loss of two introns in cox1 of KY217797.1 reduced its size by 2.7 kb, making it the smallest cox1 gene (8.4 kb) among the cox1s of the 25 mtDNAs, whereas gain of a Group II intron (2.65 kb) and loss of a Group I intron (1.7 kb) in cox1 of MF774813.1 resulted in the longest cox1 (12 kb). In rnl of L. edodes, we discovered four intron insertion consensus sequences which were unique to basidiomycetes but not ascomycetes. Differential incorporation of introns was the primary cause of the rnl size polymorphism. Homing endonucleases (HEGs) were suggestively involved in the mobilization of the introns because all of the introns have HEG genes of the LAGRIDADG or GIY-YIG families with the conserved HEG cleavage sites. TEs contributed to 11.04% of the mtDNA size in average, of which 7.08% was LTR-retrotransposon and 3.96% was DNA transposon, whereas the repeated sequences covered 4.6% of the mtDNA. The repeat numbers were variable in a strain-dependent manner. Both the TEs and repeated sequences were mostly found in the intronic and intergenic regions. Lastly, two major deletions were found in the plasmid-related sequence regions (pol2-pol3 and pol1-atp8) in the five mtDNAs. Particularly, the 6.8 kb-long deletion at pol2-pol3 region made MF774813.1 the shortest mtDNA of all. Our results demonstrate that mtDNA is a dynamic molecule that persistently evolves over a short period of time by insertion/deletion and repetition of DNA segments at the strain level.

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Variable Number Tandem Repeats in the Mitochondrial DNA of Lentinula edodes

Cited by 10 publications

References 49 publications

Molecular differences in mitochondrial DNA genomes of dogs with malignant mammary tumours

Molecular differences in mitochondrial DNA genomes of dogs with malignant mammary tumours

Mitochondrial Genomics of Six Cacao Pathogens From the Basidiomycete Family Marasmiaceae

Comparative structural analysis on the mitochondrial DNAs from various strains of Lentinula edodes

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