The mitochondrial genome of yeast Hansenula wingei encodes NADH dehydrogenase subunit genes ND4L and ND5

1994 ◽  
Vol 243 (4) ◽  
pp. 473-476 ◽  
Author(s):  
K. Okamoto ◽  
T. Sekito ◽  
K. Yoshida
Keyword(s):  
Mitochondrial Genome ◽  
Nadh Dehydrogenase ◽  
Nadh Dehydrogenase Subunit ◽  
Hansenula Wingei

scholarly journals Nucleotide sequence of rat mitochondrial NADH dehydrogenase subunit 1. GTG, a new initiator codon in vertebrate mitochondrial genome

1988 ◽  
Vol 16 (13) ◽  
pp. 6233-6233 ◽  
Author(s):  
G. Gadaleta ◽  
G. Pepe ◽  
G. De Candia ◽  
C. Quagliariello ◽  
E. Sbisa ◽  
...  
Keyword(s):  
Nucleotide Sequence ◽  
Mitochondrial Genome ◽  
Nadh Dehydrogenase ◽  
Nadh Dehydrogenase Subunit ◽  
Initiator Codon

scholarly journals Complete mitochondrial genome of Indian tent turtle, Pangshura tentoria and comparative mitochondriomics

2018 ◽  
Author(s):  
Shantanu Kundu ◽  
Vikas Kumar ◽  
Kaomud Tyagi ◽  
Rajasree Chakraborty ◽  
Iftikar Rahaman ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Nadh Dehydrogenase ◽  
Tandem Repeats ◽  
Synonymous Codon ◽  
Complete Mitochondrial Genome ◽  
Mitochondrial Gene ◽  
Gene Arrangement ◽  
Bootstrap Support ◽  
Nadh Dehydrogenase Subunit ◽  
Strong Negative Selection

Complete mitochondrial genomes of Indian tent turtle, Pangshura tentoria was sequenced and annotated as 16,657 bp in length. This first assembly was encoded by 37 genes: 13 protein coding genes (PCGs), 22 transfer RNA (tRNAs), two ribosomal RNA (rRNAs) as similar to the typical vertebrate mitochondrial gene arrangement. The complete mitogenome has a base composition of A (33.30%), G (13.54%), C (27%), and T (26.13%). Most of the genes were encoded on major strand, except for the eight tRNAs and one PCG (nad6). Almost all PCGs were starting with an ATG initiation codon, except for cytochrome oxidase subunit 1 (cox1) with ‘GTG’ and NADH dehydrogenase subunit 5 (nad5) with ‘ATA’. The typical termination codons, ‘TAA’ and ‘AGA’ has been observed in NADH dehydrogenase subunit 4l (nad4l) and NADH dehydrogenase subunit 6 (nad6) respectively; and others were used incomplete stop codons. The Relative Synonymous Codon Usage (RSCU) analysis revealed the maximum abundance of Alanine, Isoleucine, Leucine, and Threonine in P. tentoria. Codon distribution per thousand codon (CDsPT) values for all the amino acids showed the maximum values were present for Leucine in all geoemydid turtles. Further, the PCGs showed non-synonymous (Ka)/synonymous (Ks) values were <1 that indicated a strong negative selection among the studied species. The tRNAs were folded into classic clover-leaf secondary structures, except for trnS (GCT), lacking of the conventional DHU arm or stem. Further, the 10 tRNAs showed G-T mismatches and forming weak bonds. In the control region (CR) of P. tentoria, a single tandem repeat of eight base pairs (TTCTCTTT) was resulted with two copy numbers. The comparative study of CR with other geoemydid turtles revealed the numbers of tandem repeats were frequent in the 3´ end and structural characteristic were species-specific. The Maximum Likelihood (ML) phylogeny showed 32 geoemydid turtles were clustered distinctly with high bootstrap support and congruent with the previous phylogenetic hypothesis. Further, the representative mitogenome sequences of other family/suborder were depicted discrete clades in the ML tree. The study argued the complete mitochondrial genome sequence of P. tentoria and comparative mitochondriomics of geoemydid turtles would be useful for further phylogenetic reconciliation and evolutionary research.

scholarly journals Complete mitochondrial genome of Indian tent turtle, Pangshura tentoria and comparative mitochondriomics

2018 ◽  
Author(s):  
Shantanu Kundu ◽  
Vikas Kumar ◽  
Kaomud Tyagi ◽  
Rajasree Chakraborty ◽  
Iftikar Rahaman ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Nadh Dehydrogenase ◽  
Tandem Repeats ◽  
Synonymous Codon ◽  
Complete Mitochondrial Genome ◽  
Mitochondrial Gene ◽  
Gene Arrangement ◽  
Bootstrap Support ◽  
Nadh Dehydrogenase Subunit ◽  
Strong Negative Selection

Complete mitochondrial genomes of Indian tent turtle, Pangshura tentoria was sequenced and annotated as 16,657 bp in length. This first assembly was encoded by 37 genes: 13 protein coding genes (PCGs), 22 transfer RNA (tRNAs), two ribosomal RNA (rRNAs) as similar to the typical vertebrate mitochondrial gene arrangement. The complete mitogenome has a base composition of A (33.30%), G (13.54%), C (27%), and T (26.13%). Most of the genes were encoded on major strand, except for the eight tRNAs and one PCG (nad6). Almost all PCGs were starting with an ATG initiation codon, except for cytochrome oxidase subunit 1 (cox1) with ‘GTG’ and NADH dehydrogenase subunit 5 (nad5) with ‘ATA’. The typical termination codons, ‘TAA’ and ‘AGA’ has been observed in NADH dehydrogenase subunit 4l (nad4l) and NADH dehydrogenase subunit 6 (nad6) respectively; and others were used incomplete stop codons. The Relative Synonymous Codon Usage (RSCU) analysis revealed the maximum abundance of Alanine, Isoleucine, Leucine, and Threonine in P. tentoria. Codon distribution per thousand codon (CDsPT) values for all the amino acids showed the maximum values were present for Leucine in all geoemydid turtles. Further, the PCGs showed non-synonymous (Ka)/synonymous (Ks) values were <1 that indicated a strong negative selection among the studied species. The tRNAs were folded into classic clover-leaf secondary structures, except for trnS (GCT), lacking of the conventional DHU arm or stem. Further, the 10 tRNAs showed G-T mismatches and forming weak bonds. In the control region (CR) of P. tentoria, a single tandem repeat of eight base pairs (TTCTCTTT) was resulted with two copy numbers. The comparative study of CR with other geoemydid turtles revealed the numbers of tandem repeats were frequent in the 3´ end and structural characteristic were species-specific. The Maximum Likelihood (ML) phylogeny showed 32 geoemydid turtles were clustered distinctly with high bootstrap support and congruent with the previous phylogenetic hypothesis. Further, the representative mitogenome sequences of other family/suborder were depicted discrete clades in the ML tree. The study argued the complete mitochondrial genome sequence of P. tentoria and comparative mitochondriomics of geoemydid turtles would be useful for further phylogenetic reconciliation and evolutionary research.

scholarly journals The complete mitochondrial genome of endangered Assam Roofed Turtle, Pangshura sylhetensis (Testudines: Geoemydidae): Genomic features and Phylogeny

2019 ◽  
Author(s):  
Shantanu Kundu ◽  
Vikas Kumar ◽  
Kaomud Tyagi ◽  
Kailash Chandra
Keyword(s):  
Mitochondrial Genome ◽  
Nadh Dehydrogenase ◽  
De Novo ◽  
Complete Mitochondrial Genome ◽  
Mitochondrial Gene ◽  
Genomic Feature ◽  
Trna Genes ◽  
Nadh Dehydrogenase Subunit ◽  
Sister Relationship ◽  
Protein Coding

AbstractAssam Roofed Turtle, Pangshura sylhetensis is an endangered and least studied species endemic to India and Bangladesh. The genomic feature of P. sylhetensis mitogenome is still anonymous to the scientific community. The present study decodes the first complete mitochondrial genome of P. sylhetensis (16,568 bp) by using next-generation sequencing. This de novo assembly encodes 13 Protein-coding genes (PCGs), 22 transfer RNAs (tRNAs), two ribosomal RNAs (rRNAs), and one control region (CR). Most of the genes were encoded on the majority strand, except NADH dehydrogenase subunit 6 (nad6) and eight tRNAs. Most of the PCGs were started with an ATG initiation codon, except for Cytochrome oxidase subunit 1 (cox1) and NADH dehydrogenase subunit 5 (nad5) with GTG. The study also found the typical cloverleaf secondary structure in most of the tRNA genes, except for serine (trnS1) with lack of conventional DHU arm and loop. Both, Bayesian and Maximum-likelihood topologies showed distinct clustering of all the Testudines species with their respective taxonomic ranks and congruent with the previous phylogenetic hypotheses (Pangshura and Batagur sister taxa). Nevertheless, the mitogenomic phylogeny with other amniotes corroborated the sister relationship of Testudines with Archosaurians (Birds and Crocodilians). Additionally, the mitochondrial Gene Order (GO) analysis indicated that, most of the Testudines species showed plesiomorphy with typical vertebrate GO.

Departure from Neutrality at the Mitochondrial NADH Dehydrogenase Subunit 2 Gene in Humans, but Not in Chimpanzees

Genetics ◽  
1998 ◽  
Vol 148 (1) ◽  
pp. 409-421 ◽  
Author(s):  
Cheryl A Wise ◽  
Michaela Sraml ◽  
Simon Easteal
Keyword(s):  
Nadh Dehydrogenase ◽  
Statistical Tests ◽  
Low Frequency ◽  
Nadh Dehydrogenase Subunit ◽  
Nadh Dehydrogenase Subunit 2 ◽  
Tests Of Neutrality ◽  
Slightly Deleterious Mutations ◽  
Neutral Marker ◽  
Transmembrane Regions ◽  
Interspecific Comparisons

Abstract To test whether patterns of mitochondrial DNA (mtDNA) variation are consistent with a neutral model of molecular evolution, nucleotide sequences were determined for the 1041 bp of the NADH dehydrogenase subunit 2 (ND2) gene in 20 geographically diverse humans and 20 common chimpanzees. Contingency tests of neutrality were performed using four mutational categories for the ND2 molecule: synonymous and nonsynonymous mutations in the transmembrane regions, and synonymous and nonsynonymous mutations in the surface regions. The following three topological mutational categories were also used: intraspecific tips, intraspecific interiors, and interspecific fixed differences. The analyses reveal a significantly greater number of nonsynonymous polymorphisms within human transmembrane regions than expected based on interspecific comparisons, and they are inconsistent with a neutral equilibrium model. This pattern of excess nonsynonymous polymorphism is not seen within chimpanzees. Statistical tests of neutrality, such as Tajima's D test, and the D and F tests proposed by Fu and Li, indicate an excess of low frequency polymorphisms in the human data, but not in the chimpanzee data. This is consistent with recent directional selection, a population bottleneck or background selection of slightly deleterious mutations in human mtDNA samples. The analyses further support the idea that mitochondrial genome evolution is governed by selective forces that have the potential to affect its use as a “neutral” marker in evolutionary and population genetic studies.

Molecular determination of the origin of acephalic cysticercus

Parasitology ◽  
2004 ◽  
Vol 130 (2) ◽  
pp. 239-246 ◽  
Author(s):  
J.-Y. CHUNG ◽  
W.-G. KHO ◽  
S.-Y. HWANG ◽  
E.-Y. JE ◽  
Y.-T. CHUNG ◽  
...  
Keyword(s):  
Nadh Dehydrogenase ◽  
Fatal Outcome ◽  
Constitutive Expression ◽  
Molecular Data ◽  
Molecular Characteristics ◽  
Nadh Dehydrogenase Subunit ◽  
Subarachnoidal Space ◽  
Species Specific ◽  
Molecular Determination

Acephalic cysticercus (Ac), a rarely developed multilobulated and nonencysted form of larval Taenia, causes hydrocephalus or adhesive arachnoiditis in the ventricles and subarachnoidal space that often lead to fatal outcome in affected patients. Ac has been proposed to originate from T. solium on the basis of morphological features, while no molecular data supporting the presumption have been available. In the present study, we investigated the immunological properties as well as molecular characteristics of Ac that was obtained surgically from 6 patients. Immunoblotting of the cyst fluid from Ac samples demonstrated the constitutive expression of a T. solium metacestode (TsM) 10 kDa protein. Specific antibodies against the truncated 10 kDa protein, which appears to be species specific for TsM cysticercosis, were detected in both serum and cerebrospinal fluid samples of Ac patients. Nucleotide sequences of mitochondrial cytochrome c oxidase subunit I (COI) and NADH dehydrogenase subunit 1 (ND1) genes of Ac were almost identical to those of T. solium but differed substantially from those of the other Taenia species. In phylogenetic analysis, Ac clustered with T. solium in a well-supported clade. Our results strongly suggest that Ac may have originated from T. solium.

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