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.

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.

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 Characterization of the Complete Mitochondrial Genome of Fischoederius elongatus Derived from Cows in Shanghai, China

2020 ◽  
Vol 2020 ◽  
pp. 1-6
Author(s):  
Zhaoqing Han ◽  
Kun Li ◽  
Houqiang Luo ◽  
Muhammad Shahzad ◽  
Khalid Mehmood
Keyword(s):  
Amino Acids ◽  
Mitochondrial Genome ◽  
Ribosomal Rna ◽  
Parasite Species ◽  
Codon Position ◽  
Complete Mitochondrial Genome ◽  
Nucleotide Composition ◽  
Protein Coding ◽  
Rna Genes

A study was conducted to reveal the characterization of the complete mitochondrial genome of Fischoederius elongatus derived from cows in Shanghai, China. Results indicated that the complete mt genome of F. elongatus was 14,288 bp and contained 12 protein-coding genes (cox1-3, nad1-6, nad4L, atp6, and cytb), 22 transfer RNA genes, and two ribosomal RNA genes (l-rRNA and s-rRNA). The overall A + T content of the mt genome was 63.83%, and the nucleotide composition was A (19.83%), C (9.75%), G (26.43%), and T (44.00%). A total of 3284 amino acids were encoded by current F. elongatus isolate mt genome, TTT (Phe) (9.84%) and TTG (Leu) (7.73%) codon were the most frequent amino acids, whereas the ACC (Thr) (0.06%), GCC (Ala) (0.09%), CTC (Leu) (0.09%), and AAC (Asn) (0.09%) codon were the least frequent ones. At the third codon position of F. elongatus mt protein genes, T (50.82%) was observed most frequently and C (5.85%) was the least one. The current results can contribute to epidemiology diagnosis, molecular identification, taxonomy, genetic, and drug development researches about this parasite species in cattle.

The complete mitochondrial genome of the Korean endemic millipede Anaulaciulus koreanus (Verhoeff, 1937), with notes on the gene arrangement of millipede orders

Zootaxa ◽  
2017 ◽  
Vol 4329 (6) ◽  
pp. 574
Author(s):  
HYUNG JIK WOO ◽  
ANH D. NGUYEN ◽  
KUEM HEE JANG ◽  
EUN HWA CHOI ◽  
SHI HYUN RYU ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Complete Mitochondrial Genome ◽  
Mitochondrial Gene ◽  
Gene Arrangement ◽  
12S Rrna ◽  
Coding Region ◽  
Protein Coding ◽  
Close Relationship ◽  
Relationship Of ◽  
Rna Genes

The millipede Anaulaciulus koreanus (Verhoeff, 1937), belonging to the family Julidae, is an endemic species of the Korean fauna. In this study, we sequence and annotate the mitochondrial genome of A. koreanus. The complete mitochondrial genome of this species is 14,916 bp in length and contains 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes (16S and 12S rRNA), and a large non-coding region. The genome has a very high A+T content (71.1%), less than of the species Brachycybe lecontii Wood, 1864 (order Platydesmida; 76.6%) and Sphaerotheriidae sp. (order Sphaerotheriida; 71.2%). In comparison with the mitochondrial gene arrangement of eight other millipede species, the whole mitochondrial gene arrangement of A. koreanus is most similar to the nemasomatid species, Antrokoreana gracilipes Verhoeff, 1938, but differs from those of the other diplopod orders. The absence of tRNACys between the ND2 and COI regions is unique to the order Polydesmida, whereas the translocation of tRNATyr to between ND2 and COI is exclusive to the Sphaerotheriida. It is also shown that the translocation of tRNAThr between ND4L and ND1 may be a synapomorphy to support a close relationship of two orders Spirobolida and Spirostreptida. 

Characterization of the mitochondrial genome of Diphyllobothrium latum (Cestoda: Pseudophyllidea) – implications for the phylogeny of eucestodes

Parasitology ◽  
2006 ◽  
Vol 134 (5) ◽  
pp. 749-759 ◽  
Author(s):  
J.-K. PARK ◽  
K.-H. KIM ◽  
S. KANG ◽  
H. K. JEON ◽  
J.-H. KIM ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Phylogenetic Analyses ◽  
Complete Mitochondrial Genome ◽  
Amino Acid Sequences ◽  
Hymenolepis Diminuta ◽  
Rrna Genes ◽  
Gene Arrangement ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Diphyllobothrium Latum

SUMMARYThe complete nucleotide sequence of the mitochondrial genome was determined for the fish tapeworm Diphyllobothrium latum. This genome is 13 608 bp in length and encodes 12 protein-coding genes (but lacks the atp8), 22 transfer RNA (tRNA) and 2 ribosomal RNA (rRNA) genes, corresponding to the gene complement found thus far in other flatworm mitochondrial (mt) DNAs. The gene arrangement of this pseudophyllidean cestode is the same as the 6 cyclophyllidean cestodes characterized to date, with only minor variation in structure among these other genomes; the relative position of trnS2 and trnL1 is switched in Hymenolepis diminuta. Phylogenetic analyses of the concatenated amino acid sequences for 12 protein-coding genes of all complete cestode mtDNAs confirmed taxonomic and previous phylogenetic assessments, with D. latum being a sister taxon to the cyclophyllideans. High nodal support and phylogenetic congruence between different methods suggest that mt genomes may be of utility in resolving ordinal relationships within the cestodes. All species of Diphyllobothrium infect fish-eating vertebrates, and D. latum commonly infects humans through the ingestion of raw, poorly cooked or pickled fish. The complete mitochondrial genome provides a wealth of genetic markers which could be useful for identifying different life-cycle stages and for investigating their population genetics, ecology and epidemiology.

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

PeerJ ◽  
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).

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.

The first complete mitochondrial genome of Pygopodidae (Aprasia parapulchella Kluge)

2015 ◽  
Vol 63 (2) ◽  
pp. 111 ◽  
Author(s):  
Anna J. MacDonald ◽  
Theresa Knopp ◽  
Mitzy Pepper ◽  
J. Scott Keogh ◽  
Stephen D. Sarre
Keyword(s):  
Mitochondrial Genome ◽  
Gene Order ◽  
Complete Mitochondrial Genome ◽  
Nucleotide Composition ◽  
Rrna Genes ◽  
Trna Genes ◽  
Base Pairs ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Typical Vertebrate

The Pygopodidae comprise an enigmatic group of legless lizards endemic to the Australo-Papuan region. Here we present the first complete mitochondrial genome for a member of this family, Aprasia parapulchella, from Australia. The mitochondrial genome of A. parapulchella is 16 528 base pairs long and contains 13 protein-coding genes, 22 tRNA genes, two rRNA genes and the control region, conforming to the typical vertebrate gene order. The overall mitochondrial nucleotide composition is 31.7% A, 24.5% T, 30.5% C and 13.2% G. This corresponds to a total A+T content of 56.3%, which is similar to that of other squamate lizard genomes.

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 Characterization of the mitochondrial genome ofArge bellaWei & Du sp. nov. (Hymenoptera: Argidae)

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e6131 ◽  
Author(s):  
Shiyu Du ◽  
Gengyun Niu ◽  
Tommi Nyman ◽  
Meicai Wei
Keyword(s):  
Mitochondrial Genome ◽  
High Throughput Sequencing ◽  
Complete Mitochondrial Genome ◽  
Nucleotide Composition ◽  
Sequencing Data ◽  
Protein Coding ◽  
High Throughput Sequencing Data ◽  
Rna Genes ◽  
Ancestral Type

We describeArge bellaWei & Du sp. nov., a large and beautiful species of Argidae from south China, and report its mitochondrial genome based on high-throughput sequencing data. We present the gene order, nucleotide composition of protein-coding genes (PCGs), and the secondary structures of RNA genes. The nearly complete mitochondrial genome ofA. bellahas a length of 15,576 bp and a typical set of 37 genes (22 tRNAs, 13 PCGs, and 2 rRNAs). Three tRNAs are rearranged in theA. bellamitochondrial genome as compared to the ancestral type in insects:trnMandtrnQare shuffled, whiletrnWis translocated from thetrnW-trnC-trnYcluster to a location downstream oftrnI. All PCGs are initiated by ATN codons, and terminated with TAA, TA or T as stop codons. All tRNAs have a typical cloverleaf secondary structure, except fortrnS1. H821 ofrrnSand H976 ofrrnLare redundant. A phylogenetic analysis based on mitochondrial genome sequences ofA. bella, 21 other symphytan species, two apocritan representatives, and four outgroup taxa supports the placement of Argidae as sister to the Pergidae within the symphytan superfamily Tenthredinoidea.

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