Mitochondrial genome of the sweet potato hornworm, Agrius convolvuli (Lepidoptera: Sphingidae), and comparison with other Lepidoptera species

In the present study, we sequenced the complete mitochondrial genome (mitogenome) of Agrius convolvuli (Lepidoptera: Sphingidae) and compared it with previously sequenced mitogenomes of lepidopteran species. The mitogenome was a circular molecule, 15 349 base pairs (bp) long, containing 37 genes. The order and orientation of genes in the A. convolvuli mitogenome were similar to those in sequenced mitogenomes of other lepidopterans. All 13 protein-coding genes (PCGs) were initiated by ATN codons, except for the cytochrome c oxidase subunit 1 (cox1) gene, which seemed to be initiated by the codon CGA, as observed in other lepidopterans. Three of the 13 PCGs had the incomplete termination codon T, while the remainder terminated with TAA. Additionally, the codon distributions of the 13 PCGs revealed that Asn, Ile, Leu2, Lys, Phe, and Tyr were the most frequently used codon families. All transfer RNAs were folded into the expected cloverleaf structure except for tRNASer(AGN), which lacked a stable dihydrouridine arm. The length of the adenine (A) + thymine (T)-rich region was 331 bp. This region included the motif ATAGA followed by a 19-bp poly-T stretch and a microsatellite-like (TA)8 element next to the motif ATTTA. Phylogenetic analyses (maximum likelihood and Bayesian methods) showed that A. convolvuli belongs to the family Sphingidae.

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The complete mitochondrial genome of Flavoperla biocellata Chu, 1929 (Plecoptera: Perlidae) and the phylogenetic analyses of Plecoptera

PeerJ ◽

10.7717/peerj.8762 ◽

2020 ◽

Vol 8 ◽

pp. e8762

Author(s):

Yue Shen ◽

Yu-Zhou Du

Keyword(s):

Mitochondrial Genome ◽

Northern Hemisphere ◽

Phylogenetic Analyses ◽

Complete Mitochondrial Genome ◽

Gene Arrangement ◽

Trna Genes ◽

Protein Coding ◽

The Family ◽

Maximum Likelihood Methods ◽

Rna Genes

Of the roughly 400 species of Perlidae in the world, most species are widely distributed in the northern hemisphere, but a few can be found in South Africa and South America. There are only five species in the genus Flavoperla of the family Perlidae in China. To gain a better understanding of the architecture and evolution of mitochondrial genome in Flavoperla, the entire mitochondrial genome (mitogenome) of a Chinese Flavoperla biocellata Chu, 1929 from family Perlidae (Insecta: Plecoptera) was sequenced. The 15,805-bp long mitochondrial genome of F. biocellata contained 37 genes, including 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), two ribosomal RNA genes (rRNAs) and a putative control region (CR). The gene arrangement of F. biocellata was identical with that of other stoneflies and with the fly Drosophila yakuba. Most PCGs of F. biocellata used the standard ATN start codons and complete TAN termination codons. Twenty-one of the 22 tRNA genes exhibited cloverleaf secondary structures, but the dihydrouridine (DHU) arm of trnSer (AGN) was completely reduced. Phylogenetic analyses with both Bayesian inference (BI) and maximum likelihood methods (ML) generated similar topology, both supporting the monophyly of all stonefly families and the infraorder Systellognatha. The phylogenetic analysis based on mitochondrial genomic data from 30 stonefly species recovered a well-supported tree resolving higher-level relationships within Plecoptera. The northern hemisphere suborder Arctoperlaria divided into two groups, Euholognatha and Systellognatha. The southern hemisphere suborder Antarctoperlaria formed two clades: Eustheniidae+Diamphipnoidae and Austroperlidae+ Gripopterygidae; consistent with relationships proposed based on morphology. The final relationships within Plecoptera were recovered as (((Perlidae+(Perlodidae+Chloroperlidae))+(Pteronarcyidae+(Peltoperlidae+Styloperlidae))) +(Taeniopterygidae+(Capniidae+(Nemouridae+Notonemouridae))))+ (Gripopterygoidae+Eusthenioidae).

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The mitochondrial genome of Coridius chinensis (Hemiptera: Dinidoridae)

Zootaxa ◽

10.11646/zootaxa.3537.1.2 ◽

2012 ◽

Vol 3537 (1) ◽

pp. 29 ◽

Cited By ~ 5

Author(s):

LI LIU ◽

HU LI ◽

FAN SONG ◽

WEN SONG ◽

XUN DAI ◽

...

Keyword(s):

Mitochondrial Genome ◽

Complete Mitochondrial Genome ◽

Nucleotide Composition ◽

Rrna Genes ◽

Trna Genes ◽

Structural Domains ◽

Protein Coding ◽

Simple Loop ◽

Transfer Rnas ◽

Cloverleaf Structure

The nearly complete mitochondrial genome of Coridius chinensis (Dallas) is reported in this study. The mitogenome is a double-stranded circular molecule of more than 14,648 bp in length with an A+T content of 75.1%. It encoded 37 genes as in other insect mtDNAs, including 13 protein-coding genes (PCGs), 22 tRNA genes, 2 rRNA genes and a control region (unsuccessful sequencing), and the gene order is the same as most other known heteropteran mitogenomes. All of the 22 transfer RNAs can be folded into the typical cloverleaf structure except tRNASer(AGN), which can only form a simple loop at the site of dihydrouridine (DHU) arm as known in other metazoans. The secondary structures of the large and small ribosomal RNAs of C. chinensis are similar to other presented insects. The rrnL consisted of six structural domains and 40 helices, and the rrnS consisted of three structural domains and 26 helices. Nine PCGs are initiated with the standard initiation codons (ATN), while ND6 and ND1 use GTG, and COI and ATP8 use TTG. All PCGs stopped with TAA/TAG termination codons except the COII terminated with a single T residue. Asymmetry in the nucleotide composition between J-strand and N-strand was observed in this mitogenome.

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First complete mitochondrial genome of Rhodinia species (Lepidoptera: Saturniidae): genome description and phylogenetic implication

Bulletin of Entomological Research ◽

10.1017/s0007485321000808 ◽

2021 ◽

pp. 1-10

Author(s):

Dong-Bin Chen ◽

Ru-Song Zhang ◽

Xiang-Dong Jin ◽

Jian Yang ◽

Peng Li ◽

...

Keyword(s):

Mitochondrial Genome ◽

Ribosomal Rna ◽

Complete Mitochondrial Genome ◽

Repeat Sequence ◽

Rich Region ◽

Protein Coding ◽

Repeat Elements ◽

The Family ◽

Circular Molecule ◽

Rna Genes

Abstract To explore the characteristics of the mitochondrial genome (mitogenome) of the squeaking silkmoths Rhodinia, a genus of wild silkmoths in the family Saturniidae of Lepidoptera, and reveal phylogenetic relationships, the mitogenome of Rhodinia fugax Butler was determined. This wild silkmoth spins a green cocoon that has potential significance in sericulture, and exhibits a unique feature that its larvae can squeak loudly when touched. The mitogenome of R. fugax is a circular molecule of 15,334 bp long and comprises 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes, and an A + T-rich region, consistent with previous observations of Saturniidae species. The 370-bp A + T-rich region of R. fugax contains no tandem repeat elements and harbors several features common to the Bombycidea insects, but microsatellite AT repeat sequence preceded by the ATTTA motif is not present. Mitogenome-based phylogenetic analysis shows that R. fugax belongs to Attacini, instead of Saturniini. This study presents the first mitogenome for Rhodinia genus.

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Characteristics of the complete mitochondrial genome of the monotypic genus Arctictis (Family: Viverridae) and its phylogenetic implications

PeerJ ◽

10.7717/peerj.8033 ◽

2019 ◽

Vol 7 ◽

pp. e8033

Author(s):

Siuli Mitra ◽

Vaishnavi Kunteepuram ◽

Klaus-Peter Koepfli ◽

Neha Mehra ◽

Wajeeda Tabasum ◽

...

Keyword(s):

Mitochondrial Genome ◽

Phylogenetic Analyses ◽

Complete Mitochondrial Genome ◽

Mitochondrial Protein ◽

Divergence Time ◽

Protein Coding ◽

Divergence Time Estimates ◽

Time Estimates ◽

Phylogenetic Implications ◽

The Family

The binturong (Arctictis binturong) is classified as a member of the subfamily Paradoxurinae within the family Viverridae (Carnivora: Mammalia) and comprises nine subspecies spread across Southern and Southeast Asia. Here, we describe the complete mitochondrial genome of the Indian subspecies A. b. albifrons using next-generation sequencing methods. The total length of the A. b. albifrons mitogenome was 16,642 bp. Phylogenetic analyses based on 13 mitochondrial protein-coding genes placed the binturong as a sister taxon to Paguma larvata within the Paradoxurinae and supported the clustering of Genettinae and Viverrinae and the monophyly of Viverridae and six other families of feliforms, consistent with previous studies. Divergence time estimates suggest that the Viverridae diversified during the Miocene (22.62 Mya: 95% CI [20.78–24.54] Mya) and that Arctictis and Paguma split 12.57 Mya (95% CI [8.66–15.67] Mya). Further molecular studies are required to test the distinctiveness and diversity of the nine putative subspecies of binturong.

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Mitochondrial Genome of Eleutheronema rhadinum With an Additional Non-coding Region and Novel Insights Into the Phylogenetics

Frontiers in Marine Science ◽

10.3389/fmars.2021.746598 ◽

2021 ◽

Vol 8 ◽

Author(s):

Liqiang Zhong ◽

Minghua Wang ◽

Daming Li ◽

Shengkai Tang ◽

Xiaohui Chen

Keyword(s):

Mitochondrial Genome ◽

Complete Mitochondrial Genome ◽

Coding Region ◽

Significant Similarity ◽

Protein Coding ◽

Transfer Rnas ◽

The Family ◽

Sister Relationships ◽

First Time ◽

Eleutheronema Rhadinum

The complete mitochondrial genome of Eleutheronema rhadinum was determined for the first time. The E. rhadinum mitogenome was 16,718 bp in length, comprising 13 protein coding genes (PCGs), 2 ribosomal RNAs (rRNAs), 22 transfer RNAs (tRNAs), 1 control region (CR), and 1 L-strand replication origin (OL). The genome organization, and base composition were similar to other teleosts. An additional non-coding region detected in the HSL cluster, was with significant similarity to the nearby tRNA-Leu (CUN), which could be a useful marker for identifying E. rhadinum and Eleutheronema tetradactylum. Furthermore, phylogenetic analysis showed species in the family Polynemidae were well clustered together. But sister relationships between Polynemidae and Sciaenidae, Menidae plus Lactariidae were refused by present study.

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The complete mitochondrial genome of Amphinemura claviloba (Wu, 1973) (Plecoptera: Nemouridae)

Zootaxa ◽

10.11646/zootaxa.4732.3.8 ◽

2020 ◽

Vol 4732 (3) ◽

pp. 461-473

Author(s):

JIAJIA CHEN ◽

JINJUN CAO ◽

MENGDAN CHEN ◽

SIJIN CHEN ◽

WEIHAI LI ◽

...

Keyword(s):

Mitochondrial Genome ◽

Tandem Repeats ◽

Phylogenetic Analyses ◽

Complete Mitochondrial Genome ◽

Trna Genes ◽

Structural Elements ◽

Protein Coding ◽

Simple Loop ◽

The Family ◽

Secondary Structure Models

We sequenced the complete mitochondrial genome (mitogenome) of a stonefly, Amphinemura claviloba (Wu, 1973), of the family Nemouridae (Insecta: Plecoptera). The mitogenome was 15,707 bp long and contained typical 37 genes with an A+T content of 68.5%. All protein-coding genes (PCGs) use standard initiation codons (methionine and isoleucine), except ND1 and ND5 which starts with TTG and GTG, respectively. Two of the 13 PCGs harbor the incomplete termination codon. All tRNA genes have typical clover secondary structures, except the dihydrouridine (DHU) arm of tRNASer(AGN) forms a simple loop. Secondary structure models of the ribosomal RNA genes of A. claviloba are similar to those proposed for other insects. We also found some structural elements in the control region, such as tandem repeats, poly-C stretch and microsatellite-like elements, etc. Phylogenetic analyses showed the clades for the Nemoura, Amphinemura, and (Mesonemoura + Sphaeronemoura + Indonemoura + Protonemura) are well supported in a polytomy.

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The Complete Mitochondrial Genome of endemic giant tarantula, Lyrognathus crotalus (Araneae: Theraphosidae) and comparative analysis

Scientific Reports ◽

10.1038/s41598-019-57065-8 ◽

2020 ◽

Vol 10 (1) ◽

Cited By ~ 2

Author(s):

Vikas Kumar ◽

Kaomud Tyagi ◽

Rajasree Chakraborty ◽

Priya Prasad ◽

Shantanu Kundu ◽

...

Keyword(s):

Mitochondrial Genome ◽

Complete Mitochondrial Genome ◽

Start Codon ◽

Gene Arrangement ◽

Sister Relationship ◽

Protein Coding ◽

Relationship Of ◽

Rna Genes ◽

Boundary Mapping ◽

Cloverleaf Structure

AbstractThe complete mitochondrial genome of Lyrognathus crotalus is sequenced, annotated and compared with other spider mitogenomes. It is 13,865 bp long and featured by 22 transfer RNA genes (tRNAs), and two ribosomal RNA genes (rRNAs), 13 protein-coding genes (PCGs), and a control region (CR). Most of the PCGs used ATN start codon except cox3, and nad4 with TTG. Comparative studies indicated the use of TTG, TTA, TTT, GTG, CTG, CTA as start codons by few PCGs. Most of the tRNAs were truncated and do not fold into the typical cloverleaf structure. Further, the motif (CATATA) was detected in CR of nine species including L. crotalus. The gene arrangement of L. crotalus compared with ancestral arthropod showed the transposition of five tRNAs and one tandem duplication random loss (TDRL) event. Five plesiomophic gene blocks (A-E) were identified, of which, four (A, B, D, E) retained in all taxa except family Salticidae. However, block C was retained in Mygalomorphae and two families of Araneomorphae (Hypochilidae and Pholcidae). Out of 146 derived gene boundaries in all taxa, 15 synapomorphic gene boundaries were identified. TreeREx analysis also revealed the transposition of trnI, which makes three derived boundaries and congruent with the result of the gene boundary mapping. Maximum likelihood and Bayesian inference showed similar topologies and congruent with morphology, and previously reported multi-gene phylogeny. However, the Gene-Order based phylogeny showed sister relationship of L. crotalus with two Araneomorphae family members (Hypochilidae and Pholcidae) and other Mygalomorphae species.

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Complete Mitochondrial Genome Sequence Analysis and Phylogenetic Location Determination of Hydropsyche Fryeri (Insecta: Trichoptera)

10.21203/rs.3.rs-437236/v1 ◽

2021 ◽

Author(s):

Yimin Li ◽

Honglin Qin ◽

Xifa Zhong ◽

Jingcai Huang ◽

Yujun Wang ◽

...

Keyword(s):

Mitochondrial Genome ◽

Genome Sequence ◽

Complete Mitochondrial Genome ◽

Phylogenetic Tree Analysis ◽

Protein Coding ◽

Mitochondrial Genome Sequence ◽

Complete Mitochondrial Genome Sequence ◽

Location Determination ◽

The Family

Abstract Hydropsyche fryeri belongs to the Trichopteridae family and builds nests in clean and unpolluted streams using stones. It also can be used as an indicator of water quality. Here, we describe the complete mitochondrial genome sequence of Hydropsyche fryeri. The mitochondrial genome is 15,676 bp long and contains 13 protein-coding genes, 22 tRNAs, 2 rRNAs and an AT-rich control region. Phylogenetic tree analysis shows that Hydropsyche fryeri is more closely related to the family Hydroptera than other Trichoptera.

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Complete mitochondrial genome of Cultellus attenuatus and its phylogenetic implications

10.21203/rs.3.rs-868770/v1 ◽

2021 ◽

Author(s):

Haikun Li ◽

Ruihai Yu ◽

Peizhen Ma ◽

Chunhua Li

Keyword(s):

Mitochondrial Genome ◽

Complete Mitochondrial Genome ◽

Mitochondrial Genes ◽

Coding Region ◽

Protein Coding ◽

Sinonovacula Constricta ◽

Transfer Rnas ◽

Phylogenetic Implications ◽

Solen Grandis ◽

Relationship Of

Abstract The complete mitochondrial genome of Cultellus attenuates, a new aquaculture species, was sequenced and compared with mitogenomes from seven species of Heterodonta bivalve mollusk in the gene bank. The mitochondrial genome of C. attenuatus is 16888bp in length and contains 36 genes, including 12 protein-coding genes, 2 ribosomal RNAs and 22 transfer RNAs, and all genes are encoded on the same strand. In comparison with C. attenuates, the mitochondrial genes of the Sinonovacula constricta from the same family were not rearranged, but those of six other species from different family were rearranged to different degrees. The largest non-coding region of C. attenuatus is 1173bp in length and with the A + T content of 68.24%, located between nad2 and trnK. The results of phylogenetic analysis show that the C. attenuates and the S. constricta belonging to Cultellidae cluster into one branch while two species of Solenidae ( Solen grandis and Solen strictus) are clustering as their sister taxon. These data not only contribute to the understanding of the phylogenetic relationship of the Heterodonta, but also serve as a resource for the development of the genetic markers in aquaculture.

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Phylogenetic relationships and taxonomic position of genus Hyperacrius (Rodentia: Arvicolinae) from Kashmir based on evidences from analysis of mitochondrial genome and study of skull morphology

PeerJ ◽

10.7717/peerj.10364 ◽

2020 ◽

Vol 8 ◽

pp. e10364

Author(s):

Natalia I. Abramson ◽

Fedor N. Golenishchev ◽

Semen Yu. Bodrov ◽

Olga V. Bondareva ◽

Evgeny A. Genelt-Yanovskiy ◽

...

Keyword(s):

Mitochondrial Genome ◽

De Novo ◽

Phylogenetic Analyses ◽

Complete Mitochondrial Genome ◽

Morphological Characters ◽

Molecular Data ◽

Phylogenetic Position ◽

Skull Morphology ◽

Protein Coding ◽

Protein Coding Genes

In this article, we present the nearly complete mitochondrial genome of the Subalpine Kashmir vole Hyperacrius fertilis (Arvicolinae, Cricetidae, Rodentia), assembled using data from Illumina next-generation sequencing (NGS) of the DNA from a century-old museum specimen. De novo assembly consisted of 16,341 bp and included all mitogenome protein-coding genes as well as 12S and 16S RNAs, tRNAs and D-loop. Using the alignment of protein-coding genes of 14 previously published Arvicolini tribe mitogenomes, seven Clethrionomyini mitogenomes, and also Ondatra and Dicrostonyx outgroups, we conducted phylogenetic reconstructions based on a dataset of 13 protein-coding genes (PCGs) under maximum likelihood and Bayesian inference. Phylogenetic analyses robustly supported the phylogenetic position of this species within the tribe Arvicolini. Among the Arvicolini, Hyperacrius represents one of the early-diverged lineages. This result of phylogenetic analysis altered the conventional view on phylogenetic relatedness between Hyperacrius and Alticola and prompted the revision of morphological characters underlying the former assumption. Morphological analysis performed here confirmed molecular data and provided additional evidence for taxonomic replacement of the genus Hyperacrius from the tribe Clethrionomyini to the tribe Arvicolini.

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