Insect mitochondrial genomics 3: the complete mitochondrial genome sequences of representatives from two neuropteroid orders: a dobsonfly (order Megaloptera) and a giant lacewing and an owlfly (order Neuroptera)

Genome ◽  
2009 ◽  
Vol 52 (1) ◽  
pp. 31-38 ◽  
Author(s):  
Andrew T. Beckenbach ◽  
James Bruce Stewart
Keyword(s):  
Complete Mitochondrial Genome ◽  
Mitochondrial Gene ◽  
Noncoding Region ◽  
Gene Arrangement ◽  
Mitochondrial Genomes ◽  
Trna Genes ◽  
Base Pairs ◽  
Major Noncoding Region ◽  
Myrmeleon Immaculatus ◽  
Complete Mitochondrial Genomes

We describe the complete mitochondrial genomes from representatives of two orders of the Neuropterida: a dobsonfly, Corydalus cornutus (Megaloptera: Corydalidae, GenBank Accession No. FJ171323), a giant lacewing Polystoechotes punctatus (Neuroptera: Polystoechotidae, FJ171325), and an owlfly, Ascaloptynx appendiculatus (Neuroptera: Ascalaphidae, FJ171324). The dobsonfly sequence is 15 687 base pairs with a major noncoding (A+T rich) region of approximately 967 bp. The gene content and organization of the dobsonfly is identical to that of most insects. The giant lacewing sequence is 16 036 bp with a major noncoding region of about 1123 bp, while the owlfly sequence is 15 877 bp with a major noncoding region of about 1066 bp. The two Neuroptera sequences include a transposition of two tRNA genes, tRNATrp and tRNACys. These tRNA genes are coded on opposite strands and overlap by seven residues in the standard insect mitochondrial gene arrangement. Thus, the transposition required a duplication of at least the region of overlap. It is likely that the transposition occurred by a duplication of both genes followed by deletion of one copy of each gene. Examination of this region in two other neuropteroid species, a snakefly, Agulla sp. (Raphidioptera: Raphidiidae), and an antlion, Myrmeleon immaculatus (Neuroptera: Myrmeleontidae), shows that the rearrangement is widespread in the order Neuroptera but not present in either of the other two orders of Neuropterida.

Characterization and Phylogenetic Analysis of the Complete Mitochondrial Genomes of Two Tiny Necrophagous Phorid Flies, Metopina sagittata and Puliciphora borinquenensis (Diptera: Phoridae)

2021 ◽  
Author(s):  
Shu-Tong Dai ◽  
Dian-Xing Feng ◽  
Da-Peng Sun
Keyword(s):  
Mitochondrial Genome ◽  
Species Identification ◽  
Stop Codon ◽  
Complete Mitochondrial Genome ◽  
Mitochondrial Genomes ◽  
Base Pairs ◽  
Protein Coding ◽  
Phylogenetic Studies ◽  
Rna Genes ◽  
Complete Mitochondrial Genomes

Abstract The mitochondrial genome is frequently used for species identification and phylogenetic studies. In this study, we first sequenced and annotated the complete mitochondrial genomes of two phorid species that are forensically important in buried or enclosed environments: Metopina sagittata (Liu) and Puliciphora borinquenensis (Wheeler). The complete mitochondrial genome sequences of M. sagittata and P. borinquenensis were 15,640 bp with an A+T content of 75.97% and 15,429 bp with an A+T content of 75.38%, respectively. Their circular genomes both contained 13 protein-coding genes (PCGs), 22 transfer RNA genes, 2 ribosomal RNA genes, and 1 control region located between rrnS and trnI which was 808 bp for M. sagittata and 746 bp for P. borinquenensis. All the PCGs of both species started with ATN codons except for cox1 which used TTG codon. In addition to the common stop codon TAA and TAG, the incomplete stop codon T was used in two PCGs (cox1 and nad4) of M. sagittata and five PCGs (cox1, cox2, cox3, nad5, and nad4) of P. borinquenensis. There were 3 and 10 mismatched base pairs in the tRNA secondary structures from M. sagittata and P. borinquenensis, respectively. Both maximum likelihood and Bayesian inference analyses indicated that Platypezidae and Phoridae are sister taxa. M. sagittata is closely related to P. borinquenensis within the subfamily Metopininae. This work enhances the databases of Phoridae genomes and contributes to the further study of species identification and phylogenetics of this family.

scholarly journals The highly rearranged mitochondrial genomes of three economically important scale insects and the mitochondrial phylogeny of Coccoidea (Hemiptera: Sternorrhyncha)

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e9932 ◽  
Author(s):  
Hong-Ling Liu ◽  
Qing-Dong Chen ◽  
Song Chen ◽  
De-Qiang Pu ◽  
Zhi-Teng Chen ◽  
...  
Keyword(s):  
Tandem Repeats ◽  
Phylogenetic Analyses ◽  
Mitochondrial Gene ◽  
Scale Insects ◽  
Rrna Genes ◽  
Gene Arrangement ◽  
Planococcus Citri ◽  
Mitochondrial Genomes ◽  
Trna Genes ◽  
Stem Loop

The mitochondrial genomes (mitogenomes) of scale insects are less known in comparison to other insects, which hinders the phylogenetic and evolutionary studies of Coccoidea and higher taxa. Herein, the complete mitogenomes of Unaspis yanonensis, Planococcus citri and Ceroplastes rubens were sequenced for Coccoidea. The 15,220-bp long mitogenome of U. yanonensis contained the typical set of 37 genes including 13 PCGs, 22 tRNA genes and two rRNA genes; the 15,549-bp long mitogenome of P. citri lacked the tRNA gene trnV; the 15,387-bp long mitogenome of C. rubens exhibited several shortened PCGs and lacked five tRNA genes. The mitochondrial gene arrangement of the three mitogenomes was different from other scale insects and Drosophila yakuba. Most PCGs used standard ATN (ATA, ATT, ATC and ATG) start codons and complete TAN (TAA or TAG) termination codons. The ND4L had the highest evolutionary rate but COX1 and CYTB were the lowest. Most tRNA genes had cloverleaf secondary structures, whereas the reduction of dihydrouridine (DHU) arms and TψC arms were detected. Tandem repeats, stem-loop (SL) structures and poly-[TA]n stretch were found in the control regions (CRs) of the three mitogenomes. The phylogenetic analyses using Bayesian inference (BI) and maximum likelihood methods (ML) showed identical results, both supporting the inner relationship of Coccoidea as Coccidae + (Pseudococcidae + Diaspididae).

scholarly journals Complete Mitochondrial Genome of Phoneutria Boliviensis (Araneae, Ctenidae): New Insights Into the Phylogeny and Evolution of Spider

2021 ◽  
Author(s):  
Carlos Fernando Prada ◽  
Lida Marcela Franco ◽  
Felipe Cabarcas
Keyword(s):  
Mitochondrial Genome ◽  
Gene Order ◽  
Complete Mitochondrial Genome ◽  
Mitochondrial Gene ◽  
High Rate ◽  
Mitochondrial Genomes ◽  
Trna Genes ◽  
Order Analysis ◽  
Phylogeny And Evolution ◽  
The Relationship

Abstract Spiders are the most abundant land predators and megadiverse on earth. In recent years, the mitochondrial genome has been sequenced, mainly for ecological and commercial purposes, reporting some level of rearrangements in this genome. However, there is poor genetic information in several taxonomic families of spiders. The aim of this study was to obtain the sequence of the complete genome of Phoneutria boliviensis and, based on this, extract the mitogenomes of other species of the family Ctenidae from published transcriptomes to perform a comparative study among spider species to determine the relationship between the level of mitochondrial rearrangement and its possible relationship with molecular variability in spiders. Complete mitochondrial genomes of eighteen spiders (including nine Ctenidae species) were obtained by two different methodologies (sequencing and transcriptome extraction). Fifty-eight spider mitochondrial genomes were downloaded from the NCBI database for gene order analysis. After verifying the annotation of each mitochondrial gene, a phylogeny and gene order, analysis from 76 spider mitochondrial genomes was obtained. Our results show a high rate of annotation error in the mitochondrial genomes of spiders published in databases, which could lead to false phylogenetic relationships. Moreover, to provide new mitochondrial genomes in spiders by two different methodologies to obtain them, our analysis identifies six different mitochondrial architectures among all spiders. Translocation or tandem duplication random loss (TDRL) events in tRNA genes were identified to explain the evolution of the spider mitochondrial genome. In addition, our findings provide new insights into spider mitochondrial evolution.

scholarly journals The Insights into Mitochondrial Genomes of Sunflowers

Plants ◽  
2021 ◽  
Vol 10 (9) ◽  
pp. 1774
Author(s):  
Maksim S. Makarenko ◽  
Denis O. Omelchenko ◽  
Alexander V. Usatov ◽  
Vera A. Gavrilova
Keyword(s):  
Mitochondrial Genome ◽  
Mitochondrial Gene ◽  
Nuclear Genome ◽  
Jerusalem Artichoke ◽  
Mitochondrial Genomes ◽  
Trna Genes ◽  
Genetic Studies ◽  
Protein Coding ◽  
Significant Difference ◽  
Complete Mitochondrial Genomes

The significant difference in the mtDNA size and structure with simultaneous slow evolving genes makes the mitochondrial genome paradoxical among all three DNA carriers in the plant cell. Such features make mitochondrial genome investigations of particular interest. The genus Helianthus is a diverse taxonomic group, including at least two economically valuable species—common sunflower (H. annuus) and Jerusalem artichoke (H. tuberosus). The successful investigation of the sunflower nuclear genome provided insights into some genomics aspects and significantly intensified sunflower genetic studies. However, the investigations of organelles’ genetic information in Helianthus, especially devoted to mitochondrial genomics, are presented by limited studies. Using NGS sequencing, we assembled the complete mitochondrial genomes for H. occidentalis (281,175 bp) and H. tuberosus (281,287 bp) in the current investigation. Besides the master circle chromosome, in the case of H. tuberosus, the 1361 bp circular plasmid was identified. The mitochondrial gene content was found to be identical for both sunflower species, counting 32 protein-coding genes, 3 rRNA, 23 tRNA genes, and 18 ORFs. The comparative analysis between perennial sunflowers revealed common and polymorphic SSR and SNPs. Comparison of perennial sunflowers with H. annuus allowed us to establish similar rearrangements in mitogenomes, which have possibly been inherited from a common ancestor after the divergence of annual and perennial sunflower species. It is notable that H. occidentalis and H. tuberosus mitogenomes are much more similar to H. strumosus than H. grosseserratus.

scholarly journals Complete Mitochondrial Genomes of Babylonia Formosae and Babylonia Zeylanica (Neogastropoda: Babyloniidae) and Increased Sampling Give New Insights Into Neogastropoda Phylogeny

2021 ◽  
Author(s):  
Hongwei Huang ◽  
huai Yang ◽  
Jiji Li ◽  
baoying Guo ◽  
Yingying Ye
Keyword(s):  
Phylogenetic Trees ◽  
Mitochondrial Gene ◽  
Gene Arrangement ◽  
Trna Genes ◽  
Phylogenetic Studies ◽  
Marine Snails ◽  
Fundamental Information ◽  
Complete Mitogenome ◽  
Genome Arrangement ◽  
Complete Mitochondrial Genomes

Abstract The phylogenetic relationships of Neogastropoda, a group of highly complex predatory marine snails, have been controversial. The two newly sequenced mitogenomes of Babylonia formosae and Babylonia zeylanica (Neogastropoda: Babyloniidae) are described. The mitogenomes of B. zeylanica and B. formosae were 16, 214 bp and 16, 181 bp in length, respectively. The mitogenomes of both species contain 13 PCGs, 22 tRNA genes, and 2 ribosomal RNA genes. The sequence of genes differed from the ancestral mitochondrial gene arrangement of Caenogastropoda mitogenomes. Also, 63 Neogastropoda species were analyzed for the genome organization of seventeen major lineage of Neogastropoda, five types of mitochondrial genome arrangement were identified. Bayesian Inference phylogenetic trees and Maximum likehood of Neogastropoda were established according to complete mitogenome. The monophyly of Neogastropoda families is strongly supported by this study, in contrast to previous molecular studies. Our results shed light on gene sequence distribution/arrangement characteristics of Neogastropoda mitogenomes, provide fundamental information for further phylogenetic studies on Neogastropoda.

scholarly journals Mitochondrial Genomes from Two Specialized Subfamilies of Reduviidae (Insecta: Hemiptera) Reveal Novel Gene Rearrangements of True Bugs

Genes ◽  
2021 ◽  
Vol 12 (8) ◽  
pp. 1134
Author(s):  
Fei Ye ◽  
Hu Li ◽  
Qiang Xie
Keyword(s):  
Gene Rearrangement ◽  
Hot Spot ◽  
Phylogenetic Analyses ◽  
Mitochondrial Gene ◽  
Deep Understanding ◽  
Gene Arrangement ◽  
Mitochondrial Genomes ◽  
Current View ◽  
Novel Gene ◽  
Spot Group

Reduviidae, a hyper-diverse family, comprise 25 subfamilies with nearly 7000 species and include many natural enemies of crop pests and vectors of human disease. To date, 75 mitochondrial genomes (mitogenomes) of assassin bugs from only 11 subfamilies have been reported. The limited sampling of mitogenome at higher categories hinders a deep understanding of mitogenome evolution and reduviid phylogeny. In this study, the first mitogenomes of Holoptilinae (Ptilocnemus lemur) and Emesinae (Ischnobaenella hainana) were sequenced. Two novel gene orders were detected in the newly sequenced mitogenomes. Combined 421 heteropteran mitogenomes, we identified 21 different gene orders and six gene rearrangement units located in three gene blocks. Comparative analyses of the diversity of gene order for each unit reveal that the tRNA gene cluster trnI-trnQ-trnM is the hotspot of heteropteran gene rearrangement. Furthermore, combined analyses of the gene rearrangement richness of each unit and the whole mitogenome among heteropteran lineages confirm Reduviidae as a ‘hot-spot group’ of gene rearrangement in Heteroptera. The phylogenetic analyses corroborate the current view of phylogenetic relationships between basal groups of Reduviidae with high support values. Our study provides deeper insights into the evolution of mitochondrial gene arrangement in Heteroptera and the early divergence of reduviids.

scholarly journals The mitochondrial genome of Dipetalonema gracile from a squirrel monkey in China

2018 ◽  
Vol 94 ◽  
Author(s):  
P. Zhang ◽  
R.K. Ran ◽  
A.Y. Abdullahi ◽  
X.L. Shi ◽  
Y. Huang ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Squirrel Monkey ◽  
Complete Mitochondrial Genome ◽  
Mitochondrial Gene ◽  
Rrna Genes ◽  
Saimiri Sciureus ◽  
Trna Genes ◽  
Loop Structure ◽  
Protein Coding ◽  
Protein Coding Genes

AbstractDipetalonema gracile is a common parasite in squirrel monkeys (Saimiri sciureus), which can cause malnutrition and progressive wasting of the host, and lead to death in the case of massive infection. This study aimed to identify a suspected D. gracile worm from a dead squirrel monkey by means of molecular biology, and to amplify its complete mitochondrial genome by polymerase chain reaction (PCR) and sequence analysis. The results identified the worm as D. gracile, and the full length of its complete mitochondrial genome was 13,584 bp, which contained 22 tRNA genes, 12 protein-coding genes, two rRNA genes, one AT-rich region and one small non-coding region. The nucleotide composition included A (16.89%), G (20.19%), T (56.22%) and C (6.70%), among which A + T = 73.11%. The 12 protein-coding genes used TTG and ATT as start codons, and TAG and TAA as stop codons. Among the 22 tRNA genes, only trnS1AGN and trnS2UCN exhibited the TΨC-loop structure, while the other 20 tRNAs showed the TV-loop structure. The rrnL (986 bp) and rrnS (685 bp) genes were single-stranded and conserved in secondary structure. This study has enriched the mitochondrial gene database of Dipetalonema and laid a scientific basis for further study on classification, and genetic and evolutionary relationships of Dipetalonema nematodes.

scholarly journals Complete mitochondrial genome of Glomeridesmus spelaeus (Diplopoda), a troglobitic species from Carajás iron-ore caves (Pará, Brazil)

2017 ◽  
Author(s):  
Gisele Lopes Nunes ◽  
Renato Renison Moreira Oliveira ◽  
Eder Soares Pires ◽  
Santelmo Vasconcelos ◽  
Thadeu Pietrobon ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Base Composition ◽  
Iron Ore ◽  
Complete Mitochondrial Genome ◽  
Rrna Genes ◽  
Significant Advance ◽  
Mitochondrial Genomes ◽  
Trna Genes ◽  
Rich Region ◽  
The Public

AbstractWe report the complete mitochondrial genome sequence of Glomeridesmus spelaeus, the first sequenced genome of the order Gomeridesmida. The genome is 14,825 pb in length and encodes 37 mitochondrial (13 PCGs, 2 rRNA genes, 22 tRNA) genes and contains a typical AT-rich region. The base composition of the genome was A (40.1%), T (36.4%), C (15.8%), and G (7.6%), with an AT content of 76.5%. Our results indicated that Glomeridesmus spelaeus only distantly related to the other Diplopoda species with available mitochondrial genomes in the public databases. The publication of the mitogenome of G. spelaeus will contribute to the identification of troglobitic invertebrates, a very significant advance for the conservation of the troglofauna.

The complete mitochondrial genomes of four Baikal molluscs from the endemic family Baicaliidae (Caenogastropoda: Truncatelloida)

2020 ◽  
Vol 86 (3) ◽  
pp. 201-209
Author(s):  
T E Peretolchina ◽  
T Ya Sitnikova ◽  
D Yu Sherbakov
Keyword(s):  
Lake Baikal ◽  
Ribosomal Rna ◽  
Rrna Genes ◽  
Trna Genes ◽  
Coding Region ◽  
Base Pairs ◽  
Protein Coding ◽  
Phylogenetic Studies ◽  
Canonical Base ◽  
Complete Mitochondrial Genomes

Abstract Here, we present the complete mitochondrial (mt) genomes of four members of the Baicaliidae Fisher, 1885, a truncatelloidean family that is endemic to Lake Baikal (East Siberia). The mt genomes are those of Korotnewia korotnevi (15,171 bp), Godlewskia godlewskii (15,224 bp), Baicalia turriformis (15,127) and Maackia herderiana (15,154 bp). All these mt genomes contain 13 protein-coding genes, 2 ribosomal RNA (rRNA) genes and 22 transfer RNA (tRNA) genes. We detected non-canonical base pairs in some of the tRNA genes and variable numbers of non-coding spacers; some tRNAs do not have a TψC loop. We found gene order to be highly conserved in these Lake Baikal species and similar to the majority of caenogastropod mt genomes available on GenBank. A position of the putative control region is delimited to the non-coding region between trnF and the cox3 gene. It contains the ‘GAA(A)nT’ motif at the 3′ end and is similar to the replication origin found in most Caenogastropoda studied to date. We also compared the evolutionary rates of different genes to evaluate their use in different kinds of population or phylogenetic studies of this group of gastropods.

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