scholarly journals First mitochondrial genome from Yponomeutidae (Lepidoptera, Yponomeutoidea) and the phylogenetic analysis for Lepidoptera

ZooKeys ◽  
2019 ◽  
Vol 879 ◽  
pp. 137-156
Author(s):  
Mingsheng Yang ◽  
Bingyi Hu ◽  
Lin Zhou ◽  
Xiaomeng Liu ◽  
Yuxia Shi ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Phylogenetic Analyses ◽  
Complete Mitochondrial Genome ◽  
Start Codon ◽  
Length Variation ◽  
Protein Coding ◽  
Conserved Sequence ◽  
Protein Coding Genes ◽  
The One ◽  
Rna Genes

The complete mitochondrial genome (mitogenome) of Yponomeuta montanatus is sequenced and compared with other published yponomeutoid mitogenomes. The mitogenome is circular, 15,349 bp long, and includes the typical metazoan mitochondrial genes (13 protein-coding genes, two ribosomal RNA genes, and 22 transfer RNA genes) and an A + T-rich region. All 13 protein-coding genes use a typical start codon ATN, the one exception being cox1, which uses CGA across yponomeutoid mitogenomes. Comparative analyses further show that the secondary structures of tRNAs are conserved, including loss of the Dihydorouidine (DHU) arm in trnS1 (AGN), but remarkable nucleotide variation has occurred mainly in the DHU arms and pseudouridine (TψC) loops. A + T-rich regions exhibit substantial length variation among yponomeutoid mitogenomes, and conserved sequence blocks are recognized but some of them are not present in all species. Multiple phylogenetic analyses confirm the position of Y. montanatus in Yponomeutoidea. However, the superfamily-level relationships in the Macroheterocera clade in Lepidoptera recovered herein show considerable difference with that recovered in previous mitogenomic studies, raising the necessity of extensive phylogenetic investigation when more mitogenomes become available for this clade.

scholarly journals The complete mitochondrial genome of Dysgonia stuposa (Lepidoptera: Erebidae) and phylogenetic relationships within Noctuoidea

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e8780
Author(s):  
Yuxuan Sun ◽  
Yeshu Zhu ◽  
Chen Chen ◽  
Qunshan Zhu ◽  
Qianqian Zhu ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Phylogenetic Analyses ◽  
Complete Mitochondrial Genome ◽  
Intergenic Spacer ◽  
Nucleotide Composition ◽  
Start Codon ◽  
Phylogenetic Position ◽  
Protein Coding ◽  
Conserved Sequence ◽  
Rna Genes

To determine the Dysgonia stuposa mitochondrial genome (mitogenome) structure and to clarify its phylogenetic position, the entire mitogenome of D. stuposa was sequenced and annotated. The D. stuposa mitogenome is 15,721 bp in size and contains 37 genes (protein-coding genes, transfer RNA genes, ribosomal RNA genes) usually found in lepidopteran mitogenomes. The newly sequenced mitogenome contained some common features reported in other Erebidae species, e.g., an A+T biased nucleotide composition and a non-canonical start codon for cox1 (CGA). Like other insect mitogenomes, the D. stuposa mitogenome had a conserved sequence ‘ATACTAA’ in an intergenic spacer between trnS2 and nad1, and a motif ‘ATAGA’ followed by a 20 bp poly-T stretch in the A+T rich region. Phylogenetic analyses supported D. stuposa as part of the Erebidae family and reconfirmed the monophyly of the subfamilies Arctiinae, Catocalinae and Lymantriinae within Erebidae.

scholarly journals The complete mitochondrial genome of stag beetle Lucanus cervus (Coleoptera: Lucanidae) and phylogenetic analysis

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e8274 ◽  
Author(s):  
Dan Chen ◽  
Jing Liu ◽  
Luca Bartolozzi ◽  
Xia Wan
Keyword(s):  
Mitochondrial Genome ◽  
Bayesian Methods ◽  
Phylogenetic Relationships ◽  
Phylogenetic Analyses ◽  
Complete Mitochondrial Genome ◽  
Illumina Platform ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Rna Genes ◽  
Generation Sequencing

Background The stag beetle Lucanus cervus (Coleoptera: Lucanidae) is widely distributed in Europe. Habitat loss and fragmentation has led to significant reductions in numbers of this species. In this study, we sequenced the complete mitochondrial genome of L. cervus and reconstructed phylogenetic relationships among Lucanidae using complete mitochondrial genome sequences. Methods Raw data sequences were generated by the next generation sequencing using Illumina platform from genomic DNA of L. cervus. The mitochondrial genome was assembled by IDBA and annotated by MITOS. The aligned sequences of mitochondrial genes were partitioned using PartitionFinder 2. Phylogenetic relationships among 19 stag beetle species were constructed using Maximum Likelihood (ML) method implemented in IQ-TREE web server and Bayesian method implemented in PhyloBayes MPI 1.5a. Three scarab beetles were used as outgroups. Results The complete mitochondrial genome of L. cervus is 20,109 bp in length, comprising 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNAs and a control region. The A + T content is 69.93% for the majority strand. All protein-coding genes start with the typical ATN initiation codons except for cox1, which uses AAT. Phylogenetic analyses based on ML and Bayesian methods shown consistent topologies among Lucanidae.

scholarly journals First Complete Mitochondrial Genome of Melyridae(Coleoptera, Cleroidea): Genome Description and Phylogenetic Implications

Insects ◽  
2021 ◽  
Vol 12 (2) ◽  
pp. 87
Author(s):  
Lilan Yuan ◽  
Xueying Ge ◽  
Guanglin Xie ◽  
Haoyu Liu ◽  
Yuxia Yang
Keyword(s):  
Mitochondrial Genome ◽  
Phylogenetic Analyses ◽  
Complete Mitochondrial Genome ◽  
Repeat Sequence ◽  
Start Codon ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Phylogenetic Implications ◽  
Independent Families ◽  
First Time

To explore the characteristics of the mitogenome of Melyridae and reveal phylogenetic relationships, the mitogenome of Cordylepherus sp. was sequenced and annotated. This is the first time a complete mitochondrial genome has been generated in this family. Consistent with previous observations of Cleroidea species, the mitogenome of Cordylepherus sp. is highly conserved in gene size, organization and codon usage, and secondary structures of tRNAs. All protein-coding genes (PCGs) initiate with the standard start codon ATN, except ND1, which starts with TTG, and terminate with the complete stop codons of TAA and TAG, or incomplete forms, TA- and T-. Most tRNAs have the typical clover-leaf structure, except trnS1 (Ser, AGN), whose dihydrouridine (DHU) arm is reduced. In the A+T-rich region, three types of tandem repeat sequence units are found, including a 115 bp sequence tandemly repeated twice, a 16 bp sequence tandemly repeated three times with a partial third repeat and a 10 bp sequence tandemly repeated seven times. Phylogenetic analyses based on 13 protein-coding genes by both Bayesian inference (BI) and maximum likelihood (ML) methods suggest that Melyridae sensu lato is polyphyletic, and Dasytinae and Malchiinae are supported as independent families.

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.

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.

The complete mitochondrial genome of Orthocoelium streptocoelium (Digenea: Paramphistomidae) for comparison with other digeneans

2016 ◽  
Vol 91 (2) ◽  
pp. 255-261 ◽  
Author(s):  
Y.Y. Zhao ◽  
X. Yang ◽  
H.M. Chen ◽  
L.X. Wang ◽  
H.L. Feng ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Phylogenetic Analyses ◽  
Complete Mitochondrial Genome ◽  
Small Ruminants ◽  
Amino Acid Sequences ◽  
Population Variation ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Mt Genome ◽  
Rna Genes

AbstractOrthocoelium streptocoelium is a common paramphistome species parasitizing the rumen and/or reticulum of small ruminants, leading to significant losses. This study first determined the complete mitochondrial (mt) genome of O. streptocoelium. The complete mt genome of O. streptocoelium was amplified, sequenced, assembled, analysed and then compared with those of other digeneans. The entire mt genome of O. streptocoelium is 13,800 bp in length, which is smaller than those of other digeneans except for Opisthorchis viverrini. This mt genome contains 12 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes and two non-coding regions. The arrangement of the O. streptocoelium mt genome is the same as those of other digeneans except for Schistosoma haematobium and Schistosoma spindale. Phylogenetic analyses based on concatenated amino acid sequences of the 12 protein-coding genes representing 16 digeneans were conducted to assess the relationship of O. streptocoelium with other digeneans. The result indicated that O. streptocoelium is closely related to Paramphistomum cervi and Fischoederius elongates, which is in accordance with their relationships by taxonomy. This complete mt genome of O. streptocoelium enriched the mitochondrial genome data of paramphistomes and provided important molecular markers for diagnostics and studies of population variation, epidemiology, ecology and evolution of O. streptocoelium and other digeneans.

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

2020 ◽  
Vol 10 (1) ◽  
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.

scholarly journals 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 ◽  
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.

scholarly journals The complete mitochondrial genome of a cold seep gastropod Phymorhynchus buccinoides (Neogastropoda: Conoidea: Raphitomidae)

PLoS ONE ◽  
2020 ◽  
Vol 15 (11) ◽  
pp. e0242541
Author(s):  
Lvpei Du ◽  
Shanya Cai ◽  
Jun Liu ◽  
Ruoyu Liu ◽  
Haibin Zhang
Keyword(s):  
Mitochondrial Genome ◽  
Complete Mitochondrial Genome ◽  
Cold Seep ◽  
Start Codon ◽  
Rrna Genes ◽  
Trna Genes ◽  
Protein Coding ◽  
Future Studies ◽  
Protein Coding Genes ◽  
High Support

Phymorhynchus is a genus of deep-sea snails that are most distributed in hydrothermal vent or cold seep environments. In this study, we presented the complete mitochondrial genome of P. buccinoides, a cold seep snail from the South China Sea. It is the first mitochondrial genome of a cold seep member of the superfamily Conoidea. The mitochondrial genome is 15,764 bp in length, and contains 13 protein-coding genes (PCGs), 2 rRNA genes, and 22 tRNA genes. These genes are encoded on the positive strand, except for 8 tRNA genes that are encoded on the negative strand. The start codon ATG and 3 types of stop codons, TAA, TAG and the truncated termination codon T, are used in the 13 PCGs. All 13 PCGs in the 26 species of Conoidea share the same gene order, while several tRNA genes have been translocated. Phylogenetic analysis revealed that P. buccinoides clustered with Typhlosyrinx sp., Eubela sp., and Phymorhynchus sp., forming the Raphitomidae clade, with high support values. Positive selection analysis showed that a residue located in atp6 (18 S) was identified as the positively selected site with high posterior probabilities, suggesting potential adaption to the cold seep environment. Overall, our data will provide a useful resource on the evolutionary adaptation of cold seep snails for future studies.

The mitochondrial genome of Leuctra sp. (Plecoptera: Leuctridae) and its performance in phylogenetic analyses

Zootaxa ◽  
2019 ◽  
Vol 4671 (4) ◽  
pp. 571-580 ◽  
Author(s):  
YUE SHEN ◽  
YU-ZHOU DU
Keyword(s):  
Mitochondrial Genome ◽  
Phylogenetic Analyses ◽  
Complete Mitochondrial Genome ◽  
Mitochondrial Gene ◽  
Gene Arrangement ◽  
Likelihood Methods ◽  
Protein Coding ◽  
Maximum Likelihood Methods ◽  
Rna Genes ◽  
Drosophila Yakuba

The nearly complete mitochondrial genome (mitogenome) of Leuctra sp. (Plecoptera: Leuctridae) was sequenced. The 14,585-bp long mitogenome of L. sp. contained 37 genes including 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), two ribosomal RNA genes (rRNAs), and a control region (CR). The mitochondrial gene arrangement of L. sp. was identical with other stoneflies and the putative ancestral mitogenome of Drosophila yakuba Burla. Most PCGs used standard ATN start codons and TAN termination codons. Twenty-one of the 22 tRNAs in each mitogenome exhibited the cloverleaf secondary structures, while the dihydrouridine (DHU) arm of trnSer (AGN) was reduced. Phylogenetic analyses using our new Leuctra sp. genome and all other publicly available genomes for Plecoptera and Bayesian inference (BI) and maximum likelihood methods (ML) generated identical topologies, both supporting the monophyly of all stonefly families for which tests were possible and the infraorder Systellognatha. Scopuridae and Gripopterygidae were grouped with the infraorder Euholognatha. The final relationships within Plecoptera were recovered as (((((Perlodidae + Chloroperlidae) + Perlidae) + Pteronarcyidae) + Peltoperlidae) + Styloperlidae) + (((((Capniidae + Taeniopterygidae) + Nemouridae) + Scopuridae) + Leuctridae) + Gripopterygidae). 

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