The complete mitochondrial genomes of Notiophilus quadripunctatus Dejean, 1826 and Omophron limbatum (Fabricius, 1777): New insights into the mitogenome phylogeny of the Carabidae (Insecta, Coleoptera)

2022 ◽  
pp. 1-22
Author(s):  
Michael J. Raupach ◽  
Fabian Deister ◽  
Adrián Villastrigo ◽  
Michael Balke
Keyword(s):  
High Throughput Sequencing ◽  
Ground Beetle ◽  
Phylogenetic Study ◽  
Mitochondrial Genomes ◽  
Protein Coding ◽  
Circular Dna ◽  
Protein Coding Genes ◽  
Dna Molecule ◽  
Almost All ◽  
Complete Mitochondrial Genomes

Abstract The Carabidae is by far the largest family of the Adephaga, with more than 40,000 described species. Whereas their phylogeny has been extensively studied, convergences and reversals in morphological traits prevent a robust phylogenetic concept so far. In this study, we sequenced the complete mitochondrial genomes of Notiophilus quadripunctatus (Nebriinae) and Omophrom limbatum (Omophroninae) using high-throughput sequencing. Both mitogenomes consisted of a single circular DNA molecule that encoded the typical 13 protein-coding genes, two subunits of mitochondrial RNAs, 22 tRNAs and a putative control region. Our phylogenetic study placed Omophrom limbatum as sister taxon to all other analyzed ground beetle species whereas Notiophilus quadripunctatus was identified as sister to Nebria brevicollis as part of the Nebriinae. The analyses also support the monophyly of the Cicindelidae but place Trachypachus holmbergi (Trachypachidae) within the Carabidae. Nevertheless, almost all carabid subfamilies with more than one analyzed species were identified as monophyla.

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.

The Complete Mitochondrial Genomes of two Flying Fishes, Cheilopogon pinnatibarbatus japonicus and Hirundichthys rondeletii

2020 ◽  
Author(s):  
Liyan Qu ◽  
Heng Zhang ◽  
Fengying Zhang ◽  
Wei Wang ◽  
Fenghua Tang ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
Dna Sequences ◽  
Rrna Genes ◽  
Phylogenetic Position ◽  
Mitochondrial Genomes ◽  
Trna Genes ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Flying Fishes ◽  
Complete Mitochondrial Genomes

Background: Genome-scale approaches have played a significant role in the analysis of evolutionary relationships. Because of rich polymorphisms, high evolutionary rate and rare recombination, mitochondrial DNA sequences are commonly considered as effective markers for estimating population genetics, evolutionary and phylogenetic relationships. Flying fishes are important components of epipelagic ecosystems. Up to now, only few complete mitochondrial genomes of flying fishes have been reported. In the present study, the complete mitochondrial DNA sequences of the Cheilopogon pinnatibarbatus japonicus and Hirundichthys rondeletii had been determined. Methods: Based on the published mitogenome of Cheilopogon atrisignis (GenBank: KU360729), fifteen pairs of primers were designed by the software Primer Premier 5.0 to get the complete mitochondrial genomes of two flying fishes. According to the reported data, the phylogenetic position of two flying fishes were detected using the conserved 12 protein-coding genes. Result: The complete mitochondrial genomes of Cheilopogon pinnatibarbatus japonicus and Hirundichthys rondeletii are determined. They are 16532bp and 16525bp in length, respectively. And they both consists of 13 protein-coding genes, 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes and a control region. The OL regions are conserved in these two flying fishes and might have no function. From the tree topologies, we found C.p. japonicus and H. rondeletii clustered in a group. The findings of the study would contribute to the phylogenetic classification and the genetic conservation management of C.p. japonicus and H. rondeletii.

scholarly journals Ten complete mitochondrial genomes of Gymnocharacini (Stethaprioninae, Characiformes): evolutionary relationships and a repetitive element in the Control Region (D-loop)

2020 ◽  
Author(s):  
Rubens Pasa ◽  
Fabiano Bezerra Menegídio ◽  
Igor Henrique Rodrigues-Oliveira ◽  
Iuri Batista da Silva ◽  
Matheus Lewi Cruz Bonaccorsi de Campos ◽  
...  
Keyword(s):  
Neotropical Region ◽  
Rrna Genes ◽  
Mitochondrial Genomes ◽  
Trna Genes ◽  
Raw Data ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Species Complexes ◽  
D Loop ◽  
Complete Mitochondrial Genomes

AbstractWe are presenting the complete mitogenomes of eight fish species/cytotypes from Neotropical region belonging to the Astyanax and Psalidodon genus: A. aeneus, A. altiparanae, P. fasciatus (from two locations - Upper Paraná and São Francisco river basins), A. lacustris, P. rivularis (two cytotypes) and P. rioparanaibano. We perform the whole-genome sequencing for six of these species in a Novaseq 6000 - by Illumina, meanwhile two genomes were assembled from raw data available in databases. Plus, we reassembled and annotated the mitochondrial genomes for A. mexicanus and P. paranae, both already described and with raw data available online. All the genomes presented the same organization, with 13 protein-coding genes, 22 tRNA genes and two rRNA genes. Aiming to contribute to the understanding of the several cryptic species complexes and phylogeny of the genus, we perform Bayesian analysis using the 13 protein-coding genes from these species, plus Deuterodon giton and using a Brycon species as outgroup.

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.

scholarly journals The Gene Rearrangement, Loss, Transfer, and Deep Intronic Variation in Mitochondrial Genomes of Conidiobolus

2021 ◽  
Vol 12 ◽  
Author(s):  
Yong Nie ◽  
Heng Zhao ◽  
Zimin Wang ◽  
Zhengyu Zhou ◽  
Xiaoyong Liu ◽  
...  
Keyword(s):  
Gene Rearrangement ◽  
Core Protein ◽  
Gc Content ◽  
Mitochondrial Genomes ◽  
Phylogenomic Analysis ◽  
Protein Coding ◽  
Circular Dna ◽  
Protein Coding Genes ◽  
Main Factors ◽  
Insight Into

The genus Conidiobolus s.s. was newly delimited from Conidiobolus s.l. In order to gain insight into its mitochondrial genetic background, this study sequenced six mitochondrial genomes of the genus Conidiobolus s.s. These mitogenomes were all composed of circular DNA molecules, ranging from 29,253 to 48,417 bp in size and from 26.61 to 27.90% in GC content. The order and direction for 14 core protein-coding genes (PCGs) were identical, except for the atp8 gene lost in Conidiobolus chlamydosporus, Conidiobolus polyspermus, and Conidiobolus polytocus, and rearranged in the other Conidiobolus s.s. species. Besides, the atp8 gene split the cox1 gene in Conidiobolus taihushanensis. Phylogenomic analysis based on the 14 core PCGs confirmed that all Conidiobolus s.s. species formed a monophyly in the Entomophthoromycotina lineage. The number and length of introns were the main factors contributing to mitogenomic size, and deep variations and potential transfer were detected in introns. In addition, gene transfer occurred between the mitochondrial and nuclear genomes. This study promoted the understanding of the evolution and phylogeny of the Conidiobolus s.s. genus.

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 Characterization and Phylogenetic Implications of the Complete Mitochondrial Genome of Syrphidae

Genes ◽  
2019 ◽  
Vol 10 (8) ◽  
pp. 563 ◽  
Author(s):  
Hu Li
Keyword(s):  
Mitochondrial Genome ◽  
Stop Codon ◽  
Complete Mitochondrial Genome ◽  
Mitochondrial Genomes ◽  
Protein Coding ◽  
Future Studies ◽  
Protein Coding Genes ◽  
Phylogenetic Implications ◽  
Paraphyletic Group ◽  
Complete Mitochondrial Genomes

In this study, the complete mitochondrial genomes (mitogenomes) of two hoverfly species of Korinchia angustiabdomena (Huo, Ren, and Zheng) and Volucella nigricans Coquillett (Diptera: Syrphidae) were determined and analyzed. The circular mitogenomes were 16,473 bp in K. angustiabdomena (GenBank No. MK870078) and 15,724 bp in V. nigricans (GenBank No. MK870079). Two newly sequenced mitogenomes both contained 37 genes, and the gene order was similar with other syrphine species. All the protein-coding genes (PCGs) were started with the standard ATN codons; and most of PCGs were terminated with a TAA stop codon, while ND1 in K. angustiabdomena ended with a TAG codon, and ND5 terminated with truncated T stop codons in both species. The phylogenetic relationship between K. angustiabdomena and V. nigricans with related lineages was reconstructed using Bayesian inference and Maximum-likelihood analyses. The monophyly of each family considered within Muscomorpha was confirmed by the clades in the phylogenetic tree, and superfamily of the Oestroidea (Calliphoridae, Sarcophagidae, and Oestridae) was unexpectedly found to be a paraphyletic group based on our selected data. This mitogenome information for K. angustiabdomena and V. nigricans could facilitate future studies of evolutionarily related insects.

scholarly journals Complete Mitochondrial Genomes of Two Toxin-Accumulated Nassariids (Neogastropoda: Nassariidae: Nassarius) and Their Implication for Phylogeny

2020 ◽  
Vol 21 (10) ◽  
pp. 3545
Author(s):  
Yi Yang ◽  
Hongyue Liu ◽  
Lu Qi ◽  
Lingfeng Kong ◽  
Qi Li
Keyword(s):  
Biological Significance ◽  
Morphological Characteristics ◽  
Time Estimation ◽  
Rrna Genes ◽  
Mitochondrial Genomes ◽  
Sister Group Relationship ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Rna Genes ◽  
Complete Mitochondrial Genomes

The Indo-Pacific nassariids (genus Nassarius) possesses the highest diversity within the family Nassariidae. However, the previous shell or radula-based classification of Nassarius is quite confusing due to the homoplasy of certain morphological characteristics. The toxin accumulators Nassarius glans and Nassarius siquijorensis are widely distributed in the subtidal regions of the Indo-Pacific Ocean. In spite of their biological significance, the phylogenetic positions of N. glans and N. siquijorensis are still undetermined. In the present study, the complete mitochondrial genomes of N. glans and N. siquijorensis were sequenced. The present mitochondrial genomes were 15,296 and 15,337 bp in length, respectively, showing negative AT skews and positive GC skews as well as a bias of AT rich on the heavy strand. They contained 13 protein coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and several noncoding regions, and their gene order was identical to most caenogastropods. Based on the nucleotide sequences combining 13 protein coding genes and two rRNA genes, a well-supported phylogeny of Nassarius was reconstructed, and several morphological synapomorphies were observed corresponding to the phylogenetic framework. In addition, the sister group relationship between N. variciferus and the remaining toxin-accumulated nassariids was determined, suggesting that the phylogeny might be related to their diet. The divergence time estimation analysis revealed a correlation between speciation events of nassariids and glacial cycles during the Pliocene-Pleistocene epoch.

scholarly journals Comparative mitochondrial genomes of four species of Sinopodisma and phylogenetic implications (Orthoptera, Melanoplinae)

ZooKeys ◽  
2020 ◽  
Vol 969 ◽  
pp. 23-42
Author(s):  
Qiu Zhongying ◽  
Chang Huihui ◽  
Yuan Hao ◽  
Huang Yuan ◽  
Lu Huimeng ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Bayesian Inference ◽  
Mitochondrial Genomes ◽  
Rich Region ◽  
Stem Loop ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Phylogenetic Implications ◽  
Relationship Of ◽  
Complete Mitochondrial Genomes

In this study, the whole mitochondrial genomes (mitogenomes) from four species were sequenced. The complete mitochondrial genomes of Sinopodisma pieli, S. houshana, S. qinlingensis, and S. wulingshanensis are 15,857 bp, 15,818 bp, 15,843 bp, and 15,872 bp in size, respectively. The 13 protein-coding genes (PCGs) begin with typical ATN codons, except for COXI in S. qinlingensis, which begins with ACC. The highest A+T content in all the sequenced orthopteran mitogenomes is 76.8% (S. qinlingensis), followed by 76.5% (S. wulingshanensis), 76.4% (S. pieli) and 76.4% (S. houshana) (measured on the major strand). The long polythymine stretches (T-stretch) in the A+T-rich region of the four species are not adjacent to the trnI locus but are inside the stem-loop sequences on the major strand. Moreover, several repeated elements are found in the A+T-rich region of the four species. Phylogenetic analysis based on 53 mitochondrial genomes using Bayesian Inference (BI) and Maximum Likelihood (ML) revealed that Melanoplinae (Podismini) was a monophyletic group; however, the monophyly of Sinopodisma was not supported. These data will provide important information for a better understanding of the phylogenetic relationship of Melanoplinae.

Sign in / Sign up

Export Citation Format

Share Document