scholarly journals Signals of positive selection in mitochondrial protein‐coding genes of woolly mammoth: Adaptation to extreme environments?

2019 ◽  
Vol 9 (12) ◽  
pp. 6821-6832 ◽  
Author(s):  
Jacob Njaramba Ngatia ◽  
Tian Ming Lan ◽  
Thi Dao Dinh ◽  
Le Zhang ◽  
Ahmed Khalid Ahmed ◽  
...  
Keyword(s):  
Positive Selection ◽  
Mitochondrial Protein ◽  
Extreme Environments ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Woolly Mammoth

scholarly journals Preliminary assessment of adaptive evolution of mitochondrial protein coding genes in darters (Percidae: Etheostomatinae)

F1000Research ◽  
2019 ◽  
Vol 8 ◽  
pp. 464 ◽  
Author(s):  
Leos G. Kral ◽  
Sara Watson
Keyword(s):  
Positive Selection ◽  
Adaptive Evolution ◽  
Gene Evolution ◽  
Mitochondrial Gene ◽  
Mitochondrial Protein ◽  
Preliminary Assessment ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Show Evidence ◽  
Selection Of

Background: Mitochondrial DNA of vertebrates contains genes for 13 proteins involved in oxidative phosphorylation. Some of these genes have been shown to undergo adaptive evolution in a variety of species. This study examines all mitochondrial protein coding genes in 11 darter species to determine if any of these genes show evidence of positive selection. Methods: The mitogenome from four darter was sequenced and annotated. Mitogenome sequences for another seven species were obtained from GenBank. Alignments of each of the protein coding genes were subject to codon-based identification of positive selection by Selecton, MEME and FEL. Results: Evidence of positive selection was obtained for six of the genes by at least one of the methods. CYTB was identified as having evolved under positive selection by all three methods at the same codon location. Conclusions: Given the evidence for positive selection of mitochondrial protein coding genes in darters, a more extensive analysis of mitochondrial gene evolution in all the extant darter species is warranted.

scholarly journals Preliminary assessment of adaptive evolution of mitochondrial protein coding genes in darters (Percidae: Etheostomatinae)

F1000Research ◽  
2019 ◽  
Vol 8 ◽  
pp. 464
Author(s):  
Leos G. Kral ◽  
Sara Watson
Keyword(s):  
Positive Selection ◽  
Adaptive Evolution ◽  
Gene Evolution ◽  
Mitochondrial Gene ◽  
Mitochondrial Protein ◽  
Preliminary Assessment ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Show Evidence ◽  
Selection Of

Background: Mitochondrial DNA of vertebrates contains genes for 13 proteins involved in oxidative phosphorylation. Some of these genes have been shown to undergo adaptive evolution in a variety of species. This study examines all mitochondrial protein coding genes in 11 darter species to determine if any of these genes show evidence of positive selection. Methods: The mitogenome from four darter was sequenced and annotated. Mitogenome sequences for another seven species were obtained from GenBank. Alignments of each of the protein coding genes were subject to codon-based identification of positive selection by Selecton, MEME and FEL. Results: Evidence of positive selection was obtained for six of the genes by at least one of the methods. CYTB was identified as having evolved under positive selection by all three methods at the same codon location. Conclusions: Given the evidence for positive selection of mitochondrial protein coding genes in darters, a more extensive analysis of mitochondrial gene evolution in all the extant darter species is warranted.

Polyphyletic Origins of Schizothoracinae Fishes (Cyprinidae) in Respect to Their Mitochondrial Protein-Coding Genes

2019 ◽  
Vol 07 (02) ◽  
Author(s):  
Saira Bibi ◽  
Muhammad Fiaz Khan ◽  
Aqsa Rehman ◽  
Faisal Nouroz
Keyword(s):  
Mitochondrial Protein ◽  
Protein Coding ◽  
Protein Coding Genes

Patterns of Nucleotide Substitution in Mitochondrial Protein Coding Genes of Vertebrates

Genetics ◽  
1996 ◽  
Vol 143 (1) ◽  
pp. 537-548 ◽  
Author(s):  
Sudhir Kumar
Keyword(s):  
Nucleotide Substitution ◽  
Mitochondrial Protein ◽  
Likelihood Estimation ◽  
Nucleotide Composition ◽  
Substitution Rates ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Conserved Genes ◽  
Maximum Likelihood Methods ◽  
Position Data

Abstract Maximum likelihood methods were used to study the differences in substitution rates among the four nucleotides and among different nucleotide sites in mitochondrial protein-coding genes of vertebrates. In the lst+2nd codon position data, the frequency of nucleotide G is negatively correlated with evolutionary rates of genes, substitution rates vary substantially among sites, and the transition / transversion rate bias (R) is two to five times larger than that expected at random. Generally, largest transition biases and greatest differences in substitution rates among sites are found in the highly conserved genes. The 3rd positions in placental mammal genes exhibit strong nucleotide composition biases and the transitional rates exceed transversional rates by one to two orders of magnitude. Tamura-Nei and Hasegawa-Kishino-Yano models with gamma distributed variable rates among sites (gamma parameter, α) adequately describe the nucleotide substitution process in 1st+2nd position data. In these data, ignoring differences in substitution rates among sites leads to largest biases while estimating substitution rates. Kimura's two-parameter model with variable-rates among sites performs satisfactorily in likelihood estimation of R, α, and overall amount of evolution for lst+2nd position data. It can also be used to estimate pairwise distances with appropriate values of α for a majority of genes.

Analysis of codon usage pattern of mitochondrial protein-coding genes in different hookworms

2018 ◽  
Vol 219 ◽  
pp. 24-32 ◽  
Author(s):  
Bornali Deb ◽  
Arif Uddin ◽  
Gulshana Akthar Mazumder ◽  
Supriyo Chakraborty
Keyword(s):  
Codon Usage ◽  
Mitochondrial Protein ◽  
Codon Usage Pattern ◽  
Usage Pattern ◽  
Protein Coding ◽  
Protein Coding Genes

scholarly journals Phylogenetic Analysis and Substitution Rate Estimation of Colonial Volvocine Algae Based on Mitochondrial Genomes

Genes ◽  
2020 ◽  
Vol 11 (1) ◽  
pp. 115
Author(s):  
Yuxin Hu ◽  
Weiyue Xing ◽  
Zhengyu Hu ◽  
Guoxiang Liu
Keyword(s):  
Phylogenetic Analysis ◽  
Mitochondrial Genome ◽  
Phylogenetic Relationship ◽  
Phylogenetic Analyses ◽  
Mitochondrial Protein ◽  
Substitution Rates ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Chloroplast Genomes ◽  
Volvocine Algae

We sequenced the mitochondrial genome of six colonial volvocine algae, namely: Pandorina morum, Pandorina colemaniae, Volvulina compacta, Colemanosphaera angeleri, Colemanosphaera charkowiensi, and Yamagishiella unicocca. Previous studies have typically reconstructed the phylogenetic relationship between colonial volvocine algae based on chloroplast or nuclear genes. Here, we explore the validity of phylogenetic analysis based on mitochondrial protein-coding genes. We found phylogenetic incongruence of the genera Yamagishiella and Colemanosphaera. In Yamagishiella, the stochastic error and linkage group formed by the mitochondrial protein-coding genes prevent phylogenetic analyses from reflecting the true relationship. In Colemanosphaera, a different reconstruction approach revealed a different phylogenetic relationship. This incongruence may be because of the influence of biological factors, such as incomplete lineage sorting or horizontal gene transfer. We also analyzed the substitution rates in the mitochondrial and chloroplast genomes between colonial volvocine algae. Our results showed that all volvocine species showed significantly higher substitution rates for the mitochondrial genome compared with the chloroplast genome. The nonsynonymous substitution (dN)/synonymous substitution (dS) ratio is similar in the genomes of both organelles in most volvocine species, suggesting that the two counterparts are under a similar selection pressure. We also identified a few chloroplast protein-coding genes that showed high dN/dS ratios in some species, resulting in a significant dN/dS ratio difference between the mitochondrial and chloroplast genomes.

Universal DNA primers for amplification of complete mitochondrial protein-coding genes and ribosomal RNA genes from Crocodilia

2013 ◽  
Vol 5 (3) ◽  
pp. 873-877
Author(s):  
Yishu Wang ◽  
Dinglong Feng ◽  
Hui Xue ◽  
Chuanpeng Nie ◽  
En Li ◽  
...  
Keyword(s):  
Ribosomal Rna ◽  
Mitochondrial Protein ◽  
Ribosomal Rna Genes ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Dna Primers ◽  
Rna Genes

Poly(T) Variation Within Mitochondrial Protein-Coding Genes in Globodera (Nematoda: Heteroderidae)

2008 ◽  
Vol 66 (3) ◽  
pp. 197-209 ◽  
Author(s):  
Angelique H. Riepsamen ◽  
Vivian C. Blok ◽  
Mark Phillips ◽  
Tracey Gibson ◽  
Mark Dowton
Keyword(s):  
Mitochondrial Protein ◽  
Protein Coding ◽  
Protein Coding Genes
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