Analysis of the complete mitochondrial genome and characterization of diverse NUMTs of Macaca leonina

Hu, Qiu-Xiang; Yu, Fan; Xu, Ling; Pang, Wei; Wang, Shuang; Zheng, Yong‐Tang; Lv, Lei; Yao, Yong‐Gang

doi:10.1016/j.gene.2015.06.085

Cited by 6 publications

(4 citation statements)

References 46 publications

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“…Second, the observation that chromosome sequences match transformed versions of the mitogenome suggests that chromosomes include inserts of mitogenomic origins that were transformed according to systematic rules. The observation that these are on average less similar to the transformed mitogenome than RNA contigs suggests that these transformed mitochondrial sequences inserted in nuclear chromosomes mutated apart from the original sequence, as expected for inserts lacking function in the cell's nucleus [16] , [24] , [29] , [34] , [35] , [36] , [38] , [40] , [52] , [54] , [63] , [65] , [71] , [77] , [113] , [116] , [117] , [118] , [119] , [126] , [128] , [129] .…”

Section: Discussionmentioning

confidence: 98%

Chimeric mitochondrial peptides from contiguous regular and swinger RNA

Seligmann

2016

Computational and Structural Biotechnology Journal

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Previous mass spectrometry analyses described human mitochondrial peptides entirely translated from swinger RNAs, RNAs where polymerization systematically exchanged nucleotides. Exchanges follow one among 23 bijective transformation rules, nine symmetric exchanges (X ↔ Y, e.g. A ↔ C) and fourteen asymmetric exchanges (X → Y → Z → X, e.g. A → C → G → A), multiplying by 24 DNA's protein coding potential. Abrupt switches from regular to swinger polymerization produce chimeric RNAs. Here, human mitochondrial proteomic analyses assuming abrupt switches between regular and swinger transcriptions, detect chimeric peptides, encoded by part regular, part swinger RNA. Contiguous regular- and swinger-encoded residues within single peptides are stronger evidence for translation of swinger RNA than previously detected, entirely swinger-encoded peptides: regular parts are positive controls matched with contiguous swinger parts, increasing confidence in results. Chimeric peptides are 200 × rarer than swinger peptides (3/100,000 versus 6/1000). Among 186 peptides with > 8 residues for each regular and swinger parts, regular parts of eleven chimeric peptides correspond to six among the thirteen recognized, mitochondrial protein-coding genes. Chimeric peptides matching partly regular proteins are rarer and less expressed than chimeric peptides matching non-coding sequences, suggesting targeted degradation of misfolded proteins. Present results strengthen hypotheses that the short mitogenome encodes far more proteins than hitherto assumed. Entirely swinger-encoded proteins could exist.

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Section: Discussionmentioning

confidence: 98%

Chimeric mitochondrial peptides from contiguous regular and swinger RNA

Seligmann

2016

Computational and Structural Biotechnology Journal

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“…The HV-I region of the D-loop has a faster mutation rate than other regions. So, it is useful to understand intra-species relationships, studies of population genetic diversity, and the reconstruction of the past demographic history (Whittaker et al 2007;Hu et al 2015).…”

Section: Phylogeny Analysis Based On Maternal Lineagementioning

confidence: 99%

“…The mitochondrial DNA is maternally inherited as a haploid with the size of is~16.6 kb. Its rapid rate of evolution thus makes it is used in phylogenetic reconstruction, phylogeographic, and population genetic studies (Allendorf et al 2012;Hu et al 2015). The D-loop is a non-recombinant and non-coding area, playing a role in the replication and translation process so the mtDNA control region (D-loop region) is the most variable portion of the mammalian mtDNA genome than others (Hu et al 2015).…”

Section: Introductionmentioning

confidence: 99%

“…Its rapid rate of evolution thus makes it is used in phylogenetic reconstruction, phylogeographic, and population genetic studies (Allendorf et al 2012;Hu et al 2015). The D-loop is a non-recombinant and non-coding area, playing a role in the replication and translation process so the mtDNA control region (D-loop region) is the most variable portion of the mammalian mtDNA genome than others (Hu et al 2015). It has a hypervariable (HV) region consisting of HV-I and HV-II and the most polymorphic region of the human MtDNA genome (Mondal and Ghosh 2013).…”

Section: Introductionmentioning

confidence: 99%

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Genetic characterization based on the D-loop MtDNA and the TSPY genes of the Dwarf Siamang (Hylobates klossii) of Mentawai Island, Indonesia

Hasanah

Saepuloh

Perwitasari-Farajallah

et al. 2020

Biodiversitas

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Abstract. Hasanah R, Saepuloh U, Perwitasari-Farajallah D, Sinaga W, Hastuti Y, Sajuthi D. 2020. Genetic characterization based on the D-loop MtDNA and the TSPY genes of the Dwarf Siamang (Hylobates klossii) of Mentawai Island, Indonesia. Biodiversitas 21: 2854-2861. Hylobates klossii is an endemic primate on the Mentawai Island, Indonesia that categorized as endangered species due to fragmentation, illegal hunting, and habitat loss. This study aimed to analyze the genetic characterization of H. klossii based on maternal and paternal lineages. The samples were collected from TSI (Bogor, Indonesia) cage consist of two males and two females (blood and fecal of four individuals) and Siberut Island, Mentawai, West Sumatra, Indonesia from one unknown gender (one individual fecal sample). PCR amplification was carried out on DNA and cDNA samples using specific primers for D-loop MtDNA and TSPY genes. The amplicon was analyzed with MEGA-7. The dimensional structure model of the TSPY protein was determined using I-TASSER and visualized with PyMol. The maternal analysis showed five samples consisted of four haplotypes revealed that Nam-nam and April were identic with 0% genetic distance. It’s revealed that Nam-nam and April were mother and son. The paternal analysis of two H. klossii males revealed that April was the closest relative to H. muelleri (99.56% identity) and Gou-gou to H. klossii (100% identity). Characterization of partial TSPY gene (990 bp) of April and Gou-Gou indicated four amino acids mutation, causing the shift in-amino acid structure position. The results assumed that April was a cross-breeding between H. klossii female and H. muelleri male. This genetic characterization is expected to support the conservation efforts through recommendations for good management in H. klossii preservation.

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