Comparative analysis of complete mitochondrial genomes suggests that relaxed purifying selection is driving high nonsynonymous evolutionary rate of the NADH2 gene in whitefish (Coregonus ssp.)

2016 ◽  
Vol 95 ◽  
pp. 161-170 ◽  
Author(s):  
Magnus W. Jacobsen ◽  
Rute R. da Fonseca ◽  
Louis Bernatchez ◽  
Michael M. Hansen
Keyword(s):  
Comparative Analysis ◽  
Evolutionary Rate ◽  
Purifying Selection ◽  
Mitochondrial Genomes ◽  
Complete Mitochondrial Genomes

scholarly journals Comparative Analysis of Complete Mitochondrial Genomes of Three Gerres Fishes (Perciformes: Gerreidae) and Primary Exploration of Their Evolution History

2020 ◽  
Vol 21 (5) ◽  
pp. 1874 ◽  
Author(s):  
Huiting Ruan ◽  
Min Li ◽  
Zhenhai Li ◽  
Jiajie Huang ◽  
Weiyuan Chen ◽  
...  
Keyword(s):  
Purifying Selection ◽  
Living Environment ◽  
Mitochondrial Genomes ◽  
Protein Coding ◽  
Marine Fishery ◽  
Gc Skew ◽  
The Difference ◽  
Early Paleogene ◽  
Complete Mitochondrial Genomes

Mitochondrial genome is a powerful molecule marker to explore phylogenetic relationships and reveal molecular evolution in ichthyological studies. Gerres species play significant roles in marine fishery, but its evolution has received little attention. To date, only two Gerres mitochondrial genomes were reported. In the present study, three mitogenomes of Gerres (Gerres filamentosus, Gerres erythrourus, and Gerres decacanthus) were systemically investigated. The lengths of the mitogenome sequences were 16,673, 16,728, and 16,871 bp for G. filamentosus, G. erythrourus, and G. decacanthus, respectively. Most protein-coding genes (PCGs) were initiated with the typical ATG codon and terminated with the TAA codon, and the incomplete termination codon T/TA could be detected in the three species. The majority of AT-skew and GC-skew values of the 13 PCGs among the three species were negative, and the amplitude of the GC-skew was larger than the AT-skew. The genetic distance and Ka/Ks ratio analyses indicated 13 PCGs were suffering purifying selection and the selection pressures were different from certain deep-sea fishes, were which most likely due to the difference in their living environment. The phylogenetic tree was constructed by molecular method (Bayesian Inference (BI) and maximum Likelihood (ML)), providing further supplement to the scientific classification of fish. Three Gerres species were differentiated in late Cretaceous and early Paleogene, and their evolution might link with the geological events that could change their survival environment.

scholarly journals Comparative analysis of the complete mitochondrial genomes of Aspergillus niger mtDNA type 1a and Aspergillus tubingensis mtDNA type 2b

2008 ◽  
Vol 281 (1) ◽  
pp. 51-57 ◽  
Author(s):  
ÁKos Juhász ◽  
Ilona Pfeiffer ◽  
Andrea Keszthelyi ◽  
Judit Kucsera ◽  
Csaba Vágvölgyi ◽  
...  
Keyword(s):  
Comparative Analysis ◽  
Aspergillus Niger ◽  
Mitochondrial Genomes ◽  
Aspergillus Tubingensis ◽  
Complete Mitochondrial Genomes

scholarly journals Comparative analysis of the complete mitochondrial genomes of four cordyceps fungi

2021 ◽  
Author(s):  
can zhong ◽  
jian jin ◽  
rongrong zhou ◽  
hao liu ◽  
jing xie ◽  
...  
Keyword(s):  
Comparative Analysis ◽  
Ribosomal Rna ◽  
Evolutionary Biology ◽  
Purifying Selection ◽  
Circular Dna ◽  
Close Relationship ◽  
Conserved Genes ◽  
Rna Genes ◽  
Entire Mitochondrial Genome ◽  
Complete Mitochondrial Genomes

Cordyceps is a large group of entomogenous, medicinally important fungi. In this study, we sequenced, assembled, and annotated the entire mitochondrial genome of O. xuefengensis, in addition to comparing it against three other complete cordyceps mitogenomes that were previously published. Comparative analysis indicated that the four complete mitogenomes are all composed of circular DNA molecules, although their sizes significantly differ due to high variability in intron and intergenic region sizes in the O. sinensis and O. xuefengensis mitogenomes. All mitogenomes contain 14 conserved genes and two ribosomal RNA genes, but varying numbers of tRNA introns. The Ka/Ks ratios for all 14 PCGs and rps3 were all less than 1, indicating that these genes have been subject to purifying selection. Phylogenetic analysis was conducted using concatenated amino acid and nucleotide sequences of the 14 PCGs and rps3 using two different methods (Maximum Likelihood and Bayesian analysis), revealing highly supported relationships between O. xuefengensis and other Ophiocordyceps species, in addition to a close relationship with O. sinensis. Further, the analyses indicated that cox1 and rps3 play important roles in population differentiation. These mitogenomes will allow further study of the population genetics, taxonomy, and evolutionary biology of medicinally important cordyceps species.

scholarly journals Mitogenomes Reveal Multiple Colonization of Mountains by Rattus in Sundaland

2020 ◽  
Author(s):  
Miguel Camacho-Sanchez ◽  
Jennifer A Leonard
Keyword(s):  
Genetic Diversity ◽  
Mitochondrial Dna ◽  
Purifying Selection ◽  
High Elevation ◽  
Mitochondrial Genomes ◽  
Tropical Mountains ◽  
Weak Evidence ◽  
History Of ◽  
Phylogenetic Framework ◽  
Complete Mitochondrial Genomes

Abstract Tropical mountains are cradles of biodiversity and endemism. Sundaland, tropical Southeast Asia, hosts 3 species of Rattus endemic to elevations above 2000 m with an apparent convergence in external morphology: Rattus korinchi and R. hoogerwerfi from Sumatra, and R. baluensis from Borneo. A fourth one, R. tiomanicus, is restricted to lowland elevations across the whole region. The origins of these endemics are little known due to the absence of a robust phylogenetic framework. We use complete mitochondrial genomes from the 3 high altitude Rattus, and several related species to determine their relationships, date divergences, reconstruct their history of colonization, and test for selection on the mitochondrial DNA. We show that mountain colonization happened independently in Borneo (<390 Kya) and Sumatra (~1.38 Mya), likely from lowland lineages. The origin of the Bornean endemic R. baluensis is very recent and its genetic diversity is nested within the diversity of R. tiomanicus. We found weak evidence of positive selection in the high-elevation lineages and attributed the greater nonsynonymous mutations on these branches (specially R. baluensis) to lesser purifying selection having acted on the terminal branches in the phylogeny.

scholarly journals Comparative Analysis of Gender-Associated Complete Mitochondrial Genomes in Marine Mussels (Mytilus spp.)

Genetics ◽  
2005 ◽  
Vol 172 (2) ◽  
pp. 1107-1119 ◽  
Author(s):  
Sophie Breton ◽  
Gertraud Burger ◽  
Donald T. Stewart ◽  
Pierre U. Blier
Keyword(s):  
Comparative Analysis ◽  
Mitochondrial Genomes ◽  
Marine Mussels ◽  
Complete Mitochondrial Genomes

scholarly journals Mitogenomics of Perumytilus purpuratus (Bivalvia: Mytilidae) and its implications for doubly uniparental inheritance of mitochondria

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e5593 ◽  
Author(s):  
Beata Śmietanka ◽  
Marek Lubośny ◽  
Aleksandra Przyłucka ◽  
Karin Gérard ◽  
Artur Burzyński
Keyword(s):  
Purifying Selection ◽  
Mitochondrial Genomes ◽  
Uniparental Inheritance ◽  
Maternal Lineage ◽  
Doubly Uniparental Inheritance ◽  
Reading Frame ◽  
Musculista Senhousia ◽  
Perumytilus Purpuratus ◽  
First Time ◽  
Complete Mitochondrial Genomes

Animal mitochondria are usually inherited through the maternal lineage. The exceptional system allowing fathers to transmit their mitochondria to the offspring exists in some bivalves. Its taxonomic spread is poorly understood and new mitogenomic data are needed to fill the gap. Here, we present for the first time the two divergent mitogenomes from Chilean mussel Perumytilus purpuratus. The existence of these sex-specific mitogenomes confirms that this species has the doubly uniparental inheritance (DUI) of mitochondria. The genetic distance between the two mitochondrial lineages in P. purpuratus is not only much bigger than in the Mytilus edulis species complex but also greater than the distance observed in Musculista senhousia, the only other DUI-positive member of the Mytilidae family for which both complete mitochondrial genomes were published to date. One additional, long ORF (open reading frame) is present exclusively in the maternal mitogenome of P. purpuratus. This ORF evolves under purifying selection, and will likely be a target for future DUI research.

scholarly journals Comparative analysis of twelve mitogenomes of Caliscelidae (Hemiptera: Fulgoromorpha) and their phylogenetic implications

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e12465
Author(s):  
Nian Gong ◽  
Lin Yang ◽  
Xiangsheng Chen
Keyword(s):  
Nucleotide Diversity ◽  
Stop Codon ◽  
Purifying Selection ◽  
Sister Group ◽  
Mitochondrial Genomes ◽  
Protein Coding ◽  
Phylogenetic Implications ◽  
Basal Position ◽  
High Support ◽  
Complete Mitochondrial Genomes

Here, the complete mitochondrial genomes (mitogenomes) of 12 Caliscelidae species, Augilina tetraina, Augilina triaina, Symplana brevistrata, Symplana lii, Neosymplana vittatum, Pseudosymplanella nigrifasciata, Symplanella brevicephala, Symplanella unipuncta, Augilodes binghami, Cylindratus longicephalus, Caliscelis shandongensis, and Peltonotellus sp., were determined and comparatively analyzed. The genomes varied from 15,424 to 16,746 bp in size, comprising 37 mitochondrial genes and an A+T-rich region. The typical gene content and arrangement were similar to those of most Fulgoroidea species. The nucleotide compositions of the mitogenomes were biased toward A/T. All protein-coding genes (PCGs) started with a canonical ATN or GTG codon and ended with TAN or an incomplete stop codon, single T. Among 13 PCGs in 16 reported Caliscelidae mitogenomes, cox1 and atp8 showed the lowest and highest nucleotide diversity, respectively. All PCGs evolved under purifying selection, with atp8 considered a comparatively fast-evolving gene. Phylogenetic relationships were reconstructed based on 13 PCGs in 16 Caliscelidae species and five outgroups using maximum likelihood and Bayesian inference analyses. All species of Caliscelidae formed a steadily monophyletic group with high support. Peltonotellini was present at the basal position of the phylogenetic tree. Augilini was the sister group to Caliscelini and Peltonotellini.

Sign in / Sign up

Export Citation Format

Share Document