scholarly journals The mitochondrial genomes of Tortricidae: nucleotide composition, gene variation and phylogenetic performance

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Mingsheng Yang ◽  
Junhao Li ◽  
Silin Su ◽  
Hongfei Zhang ◽  
Zhengbing Wang ◽  
...  
Keyword(s):  
Nucleotide Composition ◽  
Mitochondrial Genomes ◽  
Protein Coding ◽  
Gene Variation ◽  
Protein Coding Genes ◽  
Phylogenetic Informativeness ◽  
Gc Skew ◽  
Effective Number Of Codons ◽  
First Time ◽  
Rna Genes

Abstract Background Mitochondrial genomes (mitogenomes) have greatly improved our understanding of the backbone phylogeny of Lepidoptera, but few studies on comparative mitogenomics below the family level have been conducted. Here, we generated 13 mitogenomes of eight tortricid species, reannotated 27 previously reported mitogenomes, and systematically performed a comparative analysis of nucleotide composition, gene variation and phylogenetic performance. Results The lengths of completely sequenced mitogenomes ranged from 15,440 bp to 15,778 bp, and the gene content and organization were conserved in Tortricidae and typical for Lepidoptera. Analyses of AT-skew and GC-skew, the effective number of codons and the codon bias index all show a base bias in Tortricidae, with little heterogeneity among the major tortricid groups. Variations in the divergence rates among 13 protein-coding genes of the same tortricid subgroup and of the same PCG among tortricid subgroups were detected. The secondary structures of 22 transfer RNA genes and two ribosomal RNA genes were predicted and comparatively illustrated, showing evolutionary heterogeneity among different RNAs or different regions of the same RNA. The phylogenetic uncertainty of Enarmoniini in Tortricidae was confirmed. The synonymy of Bactrini and Olethreutini was confirmed for the first time, with the representative Bactrini consistently nesting in the Olethreutini clade. Nad6 exhibits the highest phylogenetic informativeness from the root to the tip of the resulting tree, and the combination of the third coding positions of 13 protein-coding genes shows extremely high phylogenetic informativeness. Conclusions This study presents 13 mitogenomes of eight tortricid species and represents the first detailed comparative mitogenomics study of Tortricidae. The results further our understanding of the evolutionary architectures of tortricid mitogenomes and provide a basis for future studies of population genetics and phylogenetic investigations in this group.

scholarly journals Characterization and comparative analysis of the complete mitochondrial genome of Azygia hwangtsiyui Tsin, 1933 (Digenea), the first for a member of the family Azygiidae

ZooKeys ◽  
2020 ◽  
Vol 945 ◽  
pp. 1-16
Author(s):  
Yuan-An Wu ◽  
Jin-Wei Gao ◽  
Xiao-Fei Cheng ◽  
Min Xie ◽  
Xi-Ping Yuan ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Complete Mitochondrial Genome ◽  
Nucleotide Composition ◽  
Amino Acid Sequences ◽  
Phylogenetic Study ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
The Family ◽  
Close Relationship ◽  
Rna Genes

Azygia hwangtsiyui (Trematoda, Azygiidae), a neglected parasite of predatory fishes, is little-known in terms of its molecular epidemiology, population ecology and phylogenetic study. In the present study, the complete mitochondrial genome of A. hwangtsiyui was sequenced and characterized: it is a 13,973 bp circular DNA molecule and encodes 36 genes (12 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes) as well as two non-coding regions. The A+T content of the A. hwangtsiyui mitogenome is 59.6% and displays a remarkable bias in nucleotide composition with a negative AT skew (–0.437) and a positive GC skew (0.408). Phylogenetic analysis based on concatenated amino acid sequences of twelve protein-coding genes reveals that A. hwangtsiyui is placed in a separate clade, suggesting that it has no close relationship with any other trematode family. This is the first characterization of the A. hwangtsiyui mitogenome, and the first reported mitogenome of the family Azygiidae. These novel datasets of the A. hwangtsiyui mt genome represent a meaningful resource for the development of mitochondrial markers for the identification, diagnostics, taxonomy, homology and phylogenetic relationships of trematodes.

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 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 Molecular phylogeny inferred from the mitochondrial genomes of Plecoptera with Oyamia nigribasis (Plecoptera: Perlidae)

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Meng-Yuan Zhao ◽  
Qing-Bo Huo ◽  
Yu-Zhou Du
Keyword(s):  
Ribosomal Rna ◽  
Tandem Repeats ◽  
Phylogenetic Analyses ◽  
The Other ◽  
Mitochondrial Genomes ◽  
Stem Loop ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Noncoding Control Region ◽  
Rna Genes

AbstractIn this study, the mitochondrial genome of the stonefly, Oyamia nigribasis Banks, 1920 (Plecoptera: Perlidae), was sequenced and compared with the mtDNA genomes of 38 other stoneflies and two Ephemerae. The O. nigribasis mitogenome is a circular 15,923 bp molecule that encodes a large, noncoding control region (CR) and 37 typical mtDNA genes; these include 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), and two ribosomal RNA genes (rRNAs), respectively. Most of the PCGs initiated with ATN and terminated with TAN. The dihydrouridine (DHU) arm of tRNASer (AGN) was missing, whereas the other 21 tRNAs all exhibited the typical cloverleaf secondary structure. Stem-loop (SL) structures and tandem repeats were identified in the CR. Phylogenetic analyses using Bayesian inference and maximum likelihood were undertaken to determine relationships between stoneflies. Results indicated that the Antarctoperlaria, which contains Gripopterygidae, was absolutely separated from Arctoperlaria; this finding agrees with morphology. Finally, the overall relationships could be summarized as follows ((((Notonemouridae + Nemouridae) + Leuctridae) + (Scopuridae + (Capniidae + Taeniopterygidae))) + (((Perlodidae + Chloroperlidae) + Perlidae) + (Pteronarcyidae + (Peltoperlidae + Styloperlidae))) + ((Diamphipnoidae + Eustheniidae) + Gripopterygidae)).

scholarly journals The Complete Mitochondrial Genome of the American Palm Cixiid, Haplaxius crudus (Hemiptera: Cixiidae)

2021 ◽  
Vol 2021 ◽  
pp. 1-8
Author(s):  
Lidia Komondy ◽  
Jose Huguet-Tapia ◽  
Marina S. Ascunce ◽  
Ericka E. Helmick ◽  
Erica M. Goss ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Internal Control ◽  
Complete Mitochondrial Genome ◽  
Nucleotide Composition ◽  
Economic Losses ◽  
Mitochondrial Genomes ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Lethal Yellowing ◽  
Primer Sets

Haplaxius crudus Van Duzee is a pest of various economically important palms due to its ability to transmit lethal yellowing, a fatal phytoplasma infection. It is also the putative vector of lethal bronzing in Florida, another lethal phytoplasma disease causing significant economic losses. To date, no mitochondrial genomes for species in the family Cixiidae are sequenced. In this study, the complete mitochondrial genome of H. crudus was sequenced, assembled, and annotated from PacBio Sequel II long sequencing reads using the University of Florida’s HiPerGator. The mitogenome of H. crudus is 15,848 bp long and encodes 37 mitochondrial genes (including 13 protein-coding genes (PCGs), 22 tRNAs, and 2 rRNAs) in addition to a putative noncoding internal control region. The nucleotide composition of H. crudus is asymmetric with a bias toward A/T (44.8 %A, 13.4 %C, 8.5 %G, and 33.3 %T). Protein-coding genes (PCGs) possess the standard invertebrate mitochondrial start codons with few exceptions while the gene content and order of the H. crudus mitogenome is highly similar to most completely sequenced insect mitochondrial genomes. Phylogenetic analysis based on the entire mitogenome shows H. crudus resolving closely to Delphacidae, the accepted sister taxon of Cixiidae. These data provide a useful resource for developing novel primer sets that could aid in either phylogenetic studies or population genetic studies. As more full mitogenomes become available in the future for other planthopper species, more robust phylogenies can be constructed, giving more accurate perspectives on the evolutionary relationships within this fascinating and economically important group of insects.

scholarly journals The complete mitochondrial genome of Pentatoma rufipes (Hemiptera, Pentatomidae) and its phylogenetic implications

ZooKeys ◽  
2021 ◽  
Vol 1042 ◽  
pp. 51-72
Author(s):  
Ling Zhao ◽  
Jiufeng Wei ◽  
Wanqing Zhao ◽  
Chao Chen ◽  
Xiaoyun Gao ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Phylogenetic Trees ◽  
Complete Mitochondrial Genome ◽  
Genome Structure ◽  
Nucleotide Composition ◽  
Genome Database ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Phylogenetic Implications ◽  
Rna Genes

Pentatoma rufipes (Linnaeus, 1758) is an important agroforestry pest widely distributed in the Palaearctic region. In this study, we sequence and annotate the complete mitochondrial genome of P. rufipes and reconstruct the phylogenetic trees for Pentatomoidea using existing data for eight families published in the National Center for Biotechnology Information database. The mitogenome of P. rufipes is 15,887-bp-long, comprising 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and a control region, with an A+T content of 77.7%. The genome structure, gene order, nucleotide composition, and codon usage of the mitogenome of P. rufipes were consistent with those of typical Hemiptera insects. Among the protein-coding genes of Pentatomoidea, the evolutionary rate of ATP8 was the fastest, and COX1 was found to be the most conservative gene in the superfamily. Substitution saturation assessment indicated that neither transition nor transversion substitutions were saturated in the analyzed datasets. Phylogenetic analysis using the Bayesian inference method showed that P. rufipes belonged to Pentatomidae. The node support values based on the dataset concatenated from protein-coding and RNA genes were the highest. Our results enrich the mitochondrial genome database of Pentatomoidea and provide a reference for further studies of phylogenetic systematics.

scholarly journals Draft Genome Sequence of Mycobacterium boenickei CIP 107829

2017 ◽  
Vol 5 (18) ◽  
Author(s):  
Amar Bouam ◽  
Catherine Robert ◽  
Olivier Croce ◽  
Anthony Levasseur ◽  
Michel Drancourt
Keyword(s):  
United States ◽  
Dna Hybridization ◽  
Draft Genome ◽  
The United States ◽  
Mycobacterium Fortuitum ◽  
Protein Coding ◽  
Content Type ◽  
Protein Coding Genes ◽  
First Time ◽  
Rna Genes

ABSTRACT Mycobacterium boenickei is a rapidly growing mycobacterium isolated for the first time from a leg wound in the United States. Its 6,506,908-bp draft genome exhibits a 66.77% G+C content, 6,279 protein-coding genes, and 59 predicted RNA genes. In silico DNA-DNA hybridization confirms its assignment to the Mycobacterium fortuitum complex.

scholarly journals The complete mitogenome of  Lysmata vittata (Crustacea: Decapoda: Hippolytidae) and its phylogenetic position in Decapoda

2021 ◽  
Author(s):  
Longqiang Zhu ◽  
Zhihuang Zhu ◽  
Leiyu Zhu ◽  
Dingquan Wang ◽  
Jianxin Wang ◽  
...  
Keyword(s):  
Ribosomal Rna ◽  
Stop Codon ◽  
Nucleotide Composition ◽  
Start Codon ◽  
Phylogenetic Position ◽  
Base Pairs ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Complete Mitogenome ◽  
Rna Genes

In this study, the complete mitogenome of Lysmata vittata (Crustacea: Decapoda: Hippolytidae) has been determined. The genome sequence was 22003 base pairs (bp) and it included thirteen protein-coding genes (PCGs), twenty-two transfer RNA genes (tRNAs), two ribosomal RNA genes (rRNAs) and three putative control regions (CRs). The nucleotide composition of AT was 71.50%, with a slightly negative AT skewness (-0.04). Usually the standard start codon of the PCGs was ATN, while cox1, nad4L and cox3 began with TTG, TTG and GTG. The canonical termination codon was TAA, while nad5 and nad4 ended with incomplete stop codon T, and cox1 ended with TAG. We compared the order of genes of Decapoda ancestor and found that the positions of the two tRNAs genes ( trnA and trnR ) of the L. vittata were translocated. The phylogenetic tree showed that L. vittata was an independent clade, namely Hippolytidae.

scholarly journals Comparative analysis of the complete mitochondrial genomes of five Achilidae species (Hemiptera: Fulgoroidea) and other Fulgoroidea reveals conserved mitochondrial genome organization

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e6659 ◽  
Author(s):  
Shi-Yan Xu ◽  
Jian-Kun Long ◽  
Xiang-Sheng Chen
Keyword(s):  
Gene Rearrangement ◽  
Phylogenetic Analyses ◽  
Mitochondrial Genomes ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Close Relationship ◽  
First Time ◽  
Basal Position ◽  
Generation Sequencing ◽  
Complete Mitochondrial Genomes

In the present study, the complete mitochondrial genomes (mitogenomes) of five Achilidae (Hemiptera: Fulgoroidea), Betatropis formosana, two new species (Magadhaideus luodiana sp. nov and Peltatavertexalis horizontalis sp. nov), Plectoderini sp. and Paracatonidia sp., were sequenced for the first time through next-generation sequencing. The five mitogenomes ranged from 15,214 to 16,216 bp in length, with the typical gene content and arrangement usually observed in Hexapods. The motif “ATGATAA” between atp8 and atp6 was found in all the analyzed species. An overlap “AAGCTTA” between trnW and trnC was observed in the mitogenomes of most Fulgoroidea. The structural and compositional analyses of 26 Fulgoroidea mitogenomes, including the gene rearrangement of five tRNAs (trnW, trnC and trnY; trnT and trnP), the A + T content and AT-skew of the whole mitogenomes, and the nuclear acid and amino acid compositions of the protein-coding genes (PCGs), revealed family-level differences between Delphacidae and other families (Achilidae, Flatidae, Fulgoridae, Issidae and Ricaniidae). Phylogenetic analyses of 13 protein-coding genes from 26 Fulgoroidea species by maximum likelihood and Bayesian Inference were consistent and well supported the basal position of Delphacidae, a close affinity among the families Flatidae, Issidae and Ricaniidae, and a close relationship between Achilidae and Fulgoridae.

scholarly journals Sequencing and characterization of mitochondrial DNA genome for Brama japonica (Perciformes: Bramidae) with phylogenetic consideration

2016 ◽  
Author(s):  
Fenfang Chen ◽  
Hongyu Ma ◽  
Chunyan Ma ◽  
Heng Zhang ◽  
Mengdi Zhao ◽  
...  
Keyword(s):  
Control Region ◽  
Complete Mitochondrial Genome ◽  
Nucleotide Composition ◽  
Start Codon ◽  
12S Rrna ◽  
Rrna Gene ◽  
Protein Coding ◽  
Conserved Sequence ◽  
Protein Coding Genes ◽  
Rna Genes

In the present study, we isolated and characterized the complete mitochondrial genome sequence of Brama japonica by polymerase chain reaction (PCR) amplification and primer-walking sequencing. The complete DNA was 17,009 bp in length and contained a typical set of 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes and a long putative control region. The gene organization and nucleotide composition of complete mitogenome were identical to those of other Bramidae fishes. In contrast, the 12S rRNA gene contained a big poly C structure which was larger than those from other Bramidae species. Of 37 genes, twenty-eight were encoded by heavy strand, while nine were encoded by light strand. Among the 13 protein-coding genes, twelve employed ATG as start codon, while only COI utilized GTG as start codon. In the control region, the terminal associated sequence (TAS), the central and conserved sequence block (CSB-E and CSB-D) and a variable domain (CSB-1, CSB-2 and CSB-3) were identified, while the typical central conserved CSB-F could not be detected in B. japonica. The putative OL region can fold into a conserved secondary structure and the conserved motif (5’-GCCGG-3’) was found at the base of the stem in tRNACys. The overall nucleotide composition of this genome was 26.43% for A, 16.71% for G, 31.35% for C, and 25.50% for T, with a high A+T content of 51.93%. From the NJ phylogenetic tree, we can find that B. japonica was together with other five Bramidae species formed a monophyletic group among 24 species. This work provided a set of useful data for studying on population genetic diversity and molecular evolution in Bramidae and related fish species.

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