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 The complete mitochondrial genomes of two erythroneurine leafhoppers (Hemiptera, Cicadellidae, Typhlocybinae, Erythroneurini) with assessment of the phylogenetic status and relationships of tribes of Typhlocybinae

ZooKeys ◽  
2021 ◽  
Vol 1037 ◽  
pp. 137-159
Author(s):  
Xiaoxiao Chen ◽  
Can Li ◽  
Yuehua Song
Keyword(s):  
Nucleotide Diversity ◽  
Molecular Data ◽  
Rrna Genes ◽  
Mitochondrial Genomes ◽  
Morphological Classification ◽  
Protein Coding ◽  
Phylogenetic Status ◽  
The Relationship ◽  
Complete Mitochondrial Genomes

The number and classification of tribes in the leafhopper subfamily Typhlocybinae are not yet fully clear, and molecular data has recently been used to help resolve the problem. In this study, the mitochondrial genomes of Mitjaevia shibingensis Chen, Song & Webb, 2020 and M. dworakowskae Chen, Song & Webb, 2020 of the tribe Erythroneurini (Cicadellidae, Typhlocybinae) were sequenced. Most protein-coding genes (PCGs) start with ATN and end with TAA or TAG, and the AT content of these three codons were found differ from previous results that show that the first codon has the highest incidence. Two rRNA genes are highly conserved, and the AT content in 16S is higher than that of 12S. The nucleotide diversity and genetic distance among 13 PCGs of the four tribes from Typhlocybinae show that Empoascini nucleotide diversity is significantly less than in the other three tribes, and have the largest distance from the others, while Typhlocybini and Zyginellini have the smallest distance, indicating that the relationship between the two is the closest. The nad2, nad4, nad4L, and nad5 genes have greater nucleotide diversity, showing potential for use as the main markers for species identification. The phylogenetic analysis yielded a well-supported topology with most branches receiving maximum support and a few branches pertaining to relationships within Zyginellini and Typhlocybini receiving lower support. The species of these two tribes are intertwined, and it was impossible to resolve them into separate branches. In addition, the tribes Empoascini and Erythroneurini were recovered as monophyletic, and Alebrini was placed at the base of the tree as the most primitive. These results are broadly in line with other molecular phylogenetical studies which differ from traditional morphological classification.

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.

The mitochondrial genomes of Panorpidae: sequence, structure and phylogenetic analysis

2020 ◽  
Author(s):  
Yuan Hua ◽  
Ning Li ◽  
Jie Chen ◽  
Bao-Zhen Hua ◽  
Shi-Heng Tao
Keyword(s):  
Nucleotide Diversity ◽  
Mitochondrial Genomes ◽  
Trna Genes ◽  
Sequence Structure ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Gc Skew ◽  
Paraphyletic Group ◽  
Complete Mitogenome ◽  
Complete Mitochondrial Genomes

Abstract Background: Mitochondrial genomes play a significant role in reconstructing phylogenetic relationships and revealing molecular evolution in insects. However, only two species of Panorpidae have been documented for mitochondrial genomes in Mecoptera to date.Results: We obtained complete mitochondrial genomes of 17 species of Panorpidae. The results show that the complete mitogenome sequences of Panorpidae all contain 37 genes (13 protein-coding genes (PCGs), two rRNAs, 22 tRNAs) and one control region. The mitogenomes exhibit a strong AT bias. The AT-skew can either be slightly positive or slightly negative, while the GC-skew is usually negative. The 22 tRNA genes can fold into a common cloverleaf secondary structure except trnS1. The sliding window and genetic distance analyses demonstrate highly variable nucleotide diversity among the 13 protein-coding genes, with comparatively low evolutionary rate of cox1, cox2 and nad1, and high variability of nad2 and nad6. The phylogeny of Panorpidae can be presented as (Neopanorpa + Furcatopanorpa) + (Dicerapanorpa + (Panorpa debilis + (Sinopanorpa + (Cerapanorpa + Panorpa)))).Conclusions: Our analyses indicate that the genes nad2 and nad6 can be regarded as potential markers for population genetics and species delimitation in Panorpidae. Panorpa is reconfirmed a paraphyletic group.

scholarly journals One Hundred Mitochondrial Genomes of Cicadas

2018 ◽  
Vol 110 (2) ◽  
pp. 247-256 ◽  
Author(s):  
Piotr Łukasik ◽  
Rebecca A Chong ◽  
Katherine Nazario ◽  
Yu Matsuura ◽  
De Anna C Bublitz ◽  
...  
Keyword(s):  
Phylogenetic Analyses ◽  
Purifying Selection ◽  
Evolutionary Rates ◽  
Future Research ◽  
Mitochondrial Genomes ◽  
Protein Coding ◽  
Coding Regions ◽  
Mitochondrial Genome Evolution ◽  
Taxonomic Framework

Abstract Mitochondrial genomes can provide valuable information on the biology and evolutionary histories of their host organisms. Here, we present and characterize the complete coding regions of 107 mitochondrial genomes (mitogenomes) of cicadas (Insecta: Hemiptera: Auchenorrhyncha: Cicadoidea), representing 31 genera, 61 species, and 83 populations. We show that all cicada mitogenomes retain the organization and gene contents thought to be ancestral in insects, with some variability among cicada clades in the length of a region between the genes nad2 and cox1, which encodes 3 tRNAs. Phylogenetic analyses using these mitogenomes recapitulate a recent 5-gene classification of cicadas into families and subfamilies, but also identify a species that falls outside of the established taxonomic framework. While protein-coding genes are under strong purifying selection, tests of relative evolutionary rates reveal significant variation in evolutionary rates across taxa, highlighting the dynamic nature of mitochondrial genome evolution in cicadas. These data will serve as a useful reference for future research into the systematics, ecology, and evolution of the superfamily Cicadoidea.

scholarly journals Three Complete Mitochondrial Genomes of Orestes guangxiensis, Peruphasma schultei, and Phryganistria guangxiensis (Insecta: Phasmatodea) and Their Phylogeny

Insects ◽  
2021 ◽  
Vol 12 (9) ◽  
pp. 779 ◽  
Author(s):  
Ke-Ke Xu ◽  
Qing-Ping Chen ◽  
Sam Pedro Galilee Ayivi ◽  
Jia-Yin Guan ◽  
Kenneth B. Storey ◽  
...  
Keyword(s):  
Sister Group ◽  
Recent Common Ancestor ◽  
Mitochondrial Genomes ◽  
Sister Group Relationship ◽  
Protein Coding ◽  
Most Recent Common Ancestor ◽  
Stick Insects ◽  
Long Time ◽  
Relationship Of ◽  
Complete Mitochondrial Genomes

Insects of the order Phasmatodea are mainly distributed in the tropics and subtropics and are best known for their remarkable camouflage as plants. In this study, we sequenced three complete mitochondrial genomes from three different families: Orestes guangxiensis, Peruphasma schultei, and Phryganistria guangxiensis. The lengths of the three mitochondrial genomes were 15,896 bp, 16,869 bp, and 17,005 bp, respectively, and the gene composition and structure of the three stick insects were identical to those of the most recent common ancestor of insects. The phylogenetic relationships among stick insects have been chaotic for a long time. In order to discuss the intra- and inter-ordinal relationship of Phasmatodea, we used the 13 protein-coding genes (PCGs) of 85 species for maximum likelihood (ML) and Bayesian inference (BI) analyses. Results showed that the internal topological structure of Phasmatodea had a few differences in both ML and BI trees and long-branch attraction (LBA) appeared between Embioptera and Zoraptera, which led to a non-monophyletic Phasmatodea. Consequently, after removal of the Embioptera and Zoraptera species, we re-performed ML and BI analyses with the remaining 81 species, which showed identical topology except for the position of Tectarchus ovobessus (Phasmatodea). We recovered the monophyly of Phasmatodea and the sister-group relationship between Phasmatodea and Mantophasmatodea. Our analyses also recovered the monophyly of Heteropterygidae and the paraphyly of Diapheromeridae, Phasmatidae, Lonchodidae, Lonchodinae, and Clitumninae. In this study, Peruphasma schultei (Pseudophasmatidae), Phraortes sp. YW-2014 (Lonchodidae), and species of Diapheromeridae clustered into the clade of Phasmatidae. Within Heteropterygidae, O. guangxiensis was the sister clade to O. mouhotii belonging to Dataminae, and the relationship of (Heteropteryginae + (Dataminae + Obriminae)) was recovered.

scholarly journals Eusociality Shapes Convergent Patterns of Molecular Evolution across Mitochondrial Genomes of Snapping Shrimps

2020 ◽  
Author(s):  
Solomon T C Chak ◽  
Juan Antonio Baeza ◽  
Phillip Barden
Keyword(s):  
Molecular Evolution ◽  
Genome Evolution ◽  
Purifying Selection ◽  
Synonymous Substitution ◽  
Mitochondrial Genomes ◽  
Comparative Genomic ◽  
Effective Population ◽  
Protein Coding ◽  
Marine Realm ◽  
Snapping Shrimps

Abstract Eusociality is a highly conspicuous and ecologically impactful behavioral syndrome that has evolved independently across multiple animal lineages. So far, comparative genomic analyses of advanced sociality have been mostly limited to insects. Here, we study the only clade of animals known to exhibit eusociality in the marine realm—lineages of socially diverse snapping shrimps in the genus Synalpheus. To investigate the molecular impact of sociality, we assembled the mitochondrial genomes of eight Synalpheus species that represent three independent origins of eusociality and analyzed patterns of molecular evolution in protein-coding genes. Synonymous substitution rates are lower and potential signals of relaxed purifying selection are higher in eusocial relative to noneusocial taxa. Our results suggest that mitochondrial genome evolution was shaped by eusociality-linked traits—extended generation times and reduced effective population sizes that are hallmarks of advanced animal societies. This is the first direct evidence of eusociality impacting genome evolution in marine taxa. Our results also strongly support the idea that eusociality can shape genome evolution through profound changes in life history and demography.

scholarly journals Population genetics of Paramecium mitochondrial genomes: recombination, mutational spectrum, and efficacy of selection

2018 ◽  
Author(s):  
Parul Johri ◽  
Georgi K. Marinov ◽  
Thomas G. Doak ◽  
Michael Lynch
Keyword(s):  
Gc Content ◽  
Purifying Selection ◽  
Mitochondrial Genomes ◽  
Unique Combination ◽  
Protein Coding ◽  
Unicellular Eukaryotes ◽  
Population Genomic ◽  
Outgroup Species ◽  
Multiple Species ◽  
Mutation Spectra

ABSTRACTThe evolution of mitochondrial genomes and their population-genetic environment among unicellular eukaryotes are understudied. Ciliate mitochondrial genomes exhibit a unique combination of characteristics, including a linear organization and the presence of multiple genes with no known function or detectable homologs in other eukaryotes. Here we study the variation of ciliate mitochondrial genomes both within and across thirteen highly diverged Paramecium species, including multiple species from the P. aurelia species complex, with four outgroup species: P. caudatum, P. multimicronucleatum, and two strains that may represent novel related species. We observe extraordinary conservation of gene order and protein-coding content in Paramecium mitochondria across species. In contrast, significant differences are observed in tRNA content and copy number, which is highly conserved in species belonging to the P. aurelia complex but variable among and even within the other Paramecium species. There is an increase in GC content from ~20% to ~40% on the branch leading to the P. aurelia complex. Patterns of polymorphism in population-genomic data and mutation-accumulation experiments suggest that the increase in GC content is primarily due to changes in the mutation spectra in the P. aurelia species. Finally, we find no evidence of recombination in Paramecium mitochondria and find that the mitochondrial genome appears to experience either similar or stronger efficacy of purifying selection than the nucleus.

scholarly journals Utility of Complete Mitochondrial Genomes in Phylogenetic Classification of the Species of Anopheles (Culicidae: Anophelinae)

2021 ◽  
Author(s):  
Taghi Ghassemi-Khademi ◽  
Mohammad Ali Oshaghi ◽  
Hassan Vatandoost ◽  
Seyed Massoud Madjdzadeh ◽  
Mohammad Amin Gorouhi
Keyword(s):  
Evolutionary Biology ◽  
Phylogenetic Trees ◽  
Complete Mitochondrial Genome ◽  
Malaria Vectors ◽  
Mitochondrial Genomes ◽  
Phylogenetic Classification ◽  
Anopheles Mosquitoes ◽  
Blood Sucking ◽  
Complete Mitochondrial Genomes

Background: Among the blood-sucking insects, Anopheles mosquitoes have a very special position, because they transmit parasites of the genus Plasmodium, which cause malaria as one of the main vector-borne disease worldwide. The aim of this review study was to evaluate utility of complete mitochondrial genomes in phylogenetic classification of the species of Anopheles. Methods: The complete mitochondrial genome sequences belonging to 28 species of the genus Anopheles (n=32) were downloaded from NCBI. The phylogenetic trees were constructed using the ML, NJ, ME, and Bayesian inference methods. Results: In general, the results of the present survey revealed that the complete mitochondrial genomes act very accu- rately in recognition of the taxonomic and phylogenetic status of these species and provide a higher level of support than those based on individual or partial mitochondrial genes so that by using them, we can meticulously reconstruct and modify Anopheles classification. Conclusion: Understanding the taxonomic position of Anopheles, can be a very effective step in better planning for controlling these malaria vectors in the world and will improve our knowledge of their evolutionary biology.

scholarly journals Complete mitochondrial genomes of five raptors and implications for the phylogenetic relationships between owls and nightjars

2019 ◽  
Author(s):  
Gang Liu ◽  
Lizhi Zhou ◽  
Guanghong Zhao
Keyword(s):  
Control Region ◽  
Phylogenetic Relationships ◽  
Phylogenetic Trees ◽  
Stop Codon ◽  
Mitochondrial Genomes ◽  
Closely Related Species ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Independent Families ◽  
Complete Mitochondrial Genomes

The phylogenetic relationships between owls and nightjars are rather complex and controversial. To clarify these relationships, we determined the complete mitochondrial genomes of Glaucidium cuculoides, Otus scops, Glaucidium brodiei, Caprimulgus indicus, and Strix leptogrammica, and estimated phylogenetic trees based on the complete mitochondrial genomes and aligned sequences from closely related species that were obtained in GenBank. The complete mitochondrial genomes were 17392, 17317, 17549, 17536, and 16307 bp in length. All mitochondrial genomes contained 13 protein-coding genes, two rRNAs, 22 tRNAs, and a putative control region. All mitochondrial genomes except for that of Strix leptogrammica contained a pseudo-control region. ATG, GTG, and ATA are generally start codons, whereas TAA is the most frequent stop codon. All tRNAs in the new mtDNAs could be folded into canonical cloverleaf secondary structures except for tRNASer (AGY) and tRNALeu (CUN) , which missing the “DHU” arm. The phylogenetic relationships demonstrated that Strigiformes and Caprimulgiformes are independent orders, and Aegothelidae is a family within Caprimulgiformes. The results also revealed that Accipitriformes is an independent order, and Pandionidae and Sagittariidae are independent families. The results also supported that Apodiformes is polyphyletic, and hummingbirds (family Trochilidae) belong to Apodiformes. Piciformes was most distantly related to all other analyzed orders.

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