scholarly journals Characterization of the Complete Mitochondrial Genome of a Whipworm Trichuris skrjabini (Nematoda: Trichuridae)

Genes ◽  
2019 ◽  
Vol 10 (6) ◽  
pp. 438
Author(s):  
Awais Ali Ahmad ◽  
Muhammad Abu Bakr Shabbir ◽  
Yang Xin ◽  
Muhammad Ikram ◽  
Mian Abdul Hafeez ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Complete Mitochondrial Genome ◽  
Distinct Species ◽  
Molecular Data ◽  
Amino Acid Sequences ◽  
Rrna Genes ◽  
Gene Arrangement ◽  
Protein Coding ◽  
Coding Regions ◽  
Mt Genome

The complete mitochondrial (mt) genome of Trichuris skrjabini has been determined in the current study and subsequently compared with closely related species by phylogenetic analysis based on concatenated datasets of mt amino acid sequences. The whole mt genome of T. skrjabini is circular and 14,011 bp in length. It consists of a total of 37 genes including 13 protein coding genes (PCGs), two ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNAs) genes, and two non-coding regions. The gene arrangement and contents were consistent with other members of the Trichuridae family including Trichuris suis, Trichuris trichiura, Trichuris ovis, and Trichuris discolor. Phylogenetic analysis based on concatenated datasets of amino acids of the 12 PCGs predicted the distinctiveness of Trichuris skrjabini as compared to other members of the Trichuridae family. Overall, our study supports the hypothesis that T. skrjabini is a distinct species. The provision of molecular data of whole mt genome of T. skrjabini delivers novel genetic markers for future studies of diagnostics, systematics, population genetics, and molecular epidemiology of T. skrjabini.

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.

The mitochondrial genome of Gyrodactylus salaris (Platyhelminthes: Monogenea), a pathogen of Atlantic salmon (Salmo salar)

Parasitology ◽  
2006 ◽  
Vol 134 (5) ◽  
pp. 739-747 ◽  
Author(s):  
T. HUYSE ◽  
L. PLAISANCE ◽  
B. L. WEBSTER ◽  
T. A. MO ◽  
T. A. BAKKE ◽  
...  
Keyword(s):  
Atlantic Salmon ◽  
Ribosomal Rna ◽  
Trna Gene ◽  
Rrna Genes ◽  
Gene Arrangement ◽  
Mitochondrial Genomes ◽  
Trna Genes ◽  
Protein Coding ◽  
Coding Regions ◽  
Mt Genome

SUMMARYIn the present study, we describe the complete mitochondrial (mt) genome of the Atlantic salmon parasite Gyrodactylus salaris, the first for any monogenean species. The circular genome is 14 790 bp in size. All of the 35 genes recognized from other flatworm mitochondrial genomes were identified, and they are transcribed from the same strand. The protein-coding and ribosomal RNA (rRNA) genes share the same gene arrangement as those published previously for neodermatan mt genomes (representing cestodes and digeneans only), and the genome has an overall A+T content of 65%. Three transfer RNA (tRNA) genes overlap with other genes, whereas the secondary structure of 3 tRNA genes lack the DHU arm and 1 tRNA gene lacks the TΨC arm. Eighteen regions of non-coding DNA ranging from 4 to 112 bp in length, totalling 278 bp, were identified as well as 2 large non-coding regions (799 bp and 768 bp) that were almost identical to each other. The completion of the mt genome offers the opportunity of defining new molecular markers for studying evolutionary relationships within and among gyrodactylid species.

scholarly journals Characterization of the Complete Mitochondrial Genome of Ostertagia trifurcata of Small Ruminants and its Phylogenetic Associations for the Trichostrongyloidea Superfamily

Genes ◽  
2019 ◽  
Vol 10 (2) ◽  
pp. 107 ◽  
Author(s):  
Awais Ahmad ◽  
Xin Yang ◽  
Ting Zhang ◽  
Chunqun Wang ◽  
Caixian Zhou ◽  
...  
Keyword(s):  
Amino Acid ◽  
Complete Mitochondrial Genome ◽  
Small Ruminants ◽  
Complete Characterization ◽  
Amino Acid Sequences ◽  
Trna Genes ◽  
Protein Coding ◽  
Coding Regions ◽  
Mtdna Sequence ◽  
Mt Genome

The complete mitochondrial (mt) genome of Ostertagia trifurcata, a parasitic nematode of small ruminants, has been sequenced and its phylogenetic relationship with selected members from the superfamily Trichostrongyloidea was investigated on the basis of deduced datasets of mt amino acid sequences. The entire mt genome of Ostertagia trifurcata is circular and 14,151 bp in length. It consists of a total of 36 genes comprising 12 genes coding for proteins (PCGs), 2 genes for ribosomal RNA (rRNA), 22 transfer RNA (tRNA) genes and 2 non-coding regions, since all genes are transcribed in the same direction. The phylogenetic analysis based on the concatenated datasets of predicted amino acid sequences of the 12 protein coding genes supported monophylies of the Haemonchidae, Dictyocaulidae and Molineidae families, but rejected monophylies of the Trichostrongylidae family. The complete characterization and provision of the mtDNA sequence of Ostertagia trifurcata provides novel genetic markers for molecular epidemiological investigations, systematics, diagnostics and population genetics of Ostertagia trifurcata and its correspondents.

scholarly journals The Complete Mitochondrial Genome Sequence Variation and Phylogenetic Analysis of Mulberry

2021 ◽  
Author(s):  
Guo Liangliang ◽  
Shi Yisu ◽  
Wu Mengmeng ◽  
Michael Ackah ◽  
Guo Peng ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Sequence Variation ◽  
Complete Mitochondrial Genome ◽  
Taxonomic Status ◽  
Rrna Genes ◽  
Trna Genes ◽  
Protein Coding ◽  
And Migration ◽  
Mt Genome ◽  
Development Prospects

Abstract Mulberry is admired for its landscaping and possesses high development prospects and scientific research value. Mitochondria are the plants' powerhouse that produces energy to carry out life processes. In this study, the mt genome of Morus L(M. atropurpurea and M. multicaulis)were annotated and assembled. The circular mt genome of M. multicaulis has a length of 361,546bp, contains 54 genes, including 31 protein-coding genes, 20 tRNA genes, and 3 rRNA genes and composition of A(27.38%), T (27.20%), C (22.63%) and G (22.79%). The sequence repeats, RNA editing gene and migration from cp to mt and was observed in M. multicaulis mt genome. Phylogenetic analysis based on the complete mt genomes of Morus and other 28 species reflects an exact evolutionary and taxonomic status. Furthermore, we investigation on mt genome size, organization, and plastomes at the global level and pi analysis of Morus genome was investigated and compared to other land plants. The results indicate that the exist mt genome's variation in plants. We reported the mt genome assembly and annotation of a halophytic model plant, M. multicaulis, and subsequent analysis, which provided us with a comprehensive understanding of the Morus mt genome.

The mitochondrial genome and phylogenetic analysis of the tick Haemaphysalis qinghaiensis Teng, 1980 (Acari:Ixodidae)

2022 ◽  
Author(s):  
Tianhong Wang ◽  
Zihao Wang ◽  
Ruwei Bai ◽  
Zhijun Yu ◽  
Jingze Liu
Keyword(s):  
Phylogenetic Analysis ◽  
Mitochondrial Genome ◽  
Complete Mitochondrial Genome ◽  
Rrna Genes ◽  
Trna Genes ◽  
Illumina Hiseq ◽  
Protein Coding ◽  
Haemaphysalis Qinghaiensis ◽  
Mitogenome Sequence ◽  
Illumina Hiseq Platform

Haemaphysalis qinghaiensis is an endemic species and mainly inhabiting in the northwestern plateau of China, which can transmit many zoonotic pathogens and cause great harm to animals. In this study, the complete mitochondrial genome (mitogenome) of H. qinghaiensis was assembled through the Illumina HiSeq platform. The mitogenome was 14,533 bp in length, consisting of 13 protein-coding genes (PCGs), 22 tRNA genes, 2 rRNA genes and 3 noncoding regions (NCRs). The bias towards a high A+T content with 77.65% in mitogenome of H. qinghaiensis. The rearrangement of mitochondrial genes in H. qinghaiensis was consistent with other hard ticks. The phylogenetic analysis based on the concatenation of 13 PCGs from 65 tick mitogenomes showed that the H. qinghaiensis was clustered into a well-supported clade within the Haemaphysalis genus. This is the first complete mitogenome sequence of H. qinghaiensis, which provides a useful reference for understanding of the taxonomic and genetics of ticks.

scholarly journals Assembly and comparative analysis of the complete mitochondrial genome of Suaeda glauca

2020 ◽  
Author(s):  
Yan Cheng ◽  
Xiaoxue He ◽  
S. V. G. N. Priyadarshani ◽  
Yu Wang ◽  
Li Ye ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Complete Mitochondrial Genome ◽  
Sandy Beaches ◽  
Rrna Genes ◽  
Trna Genes ◽  
Protein Coding ◽  
Landscape Plant ◽  
Suaeda Glauca ◽  
Mt Genome ◽  
Mitochondria Genome

Abstract Background Suaeda glauca is a halophyte widely distributed in saline and sandy beaches, with strong saline-alkali tolerance. It is also a beautiful landscape plant with high development prospects and scientific research value. The S. glauca chloroplast genome has recently been reported; however, the mitochondria genome is still unexplored. Results This study assembled the mitochondria genome and annotated the mitochondrial genes of S. glauca based on the Pacbio long reads. The circular mitochondrial genome of S. glauca has a length of 474,330 bp. The base composition of the S. glauca mt genome showed A (27.96%), T (28.01%), C (21.64%), G (21.64%). S. glauca mt genome has 51 genes, including 26 protein-coding genes, 22 tRNA genes, and 3 rRNA genes. Phylogenetic analysis with common genes of 28 species resulted in similar morphological classification. Conclusions As a Chenopodiaceae species, S. glauca mt genome will provide insights into the missing pieces in the evolution of sex determination and improve genomic breeding in the future.

Characterisation of the complete mitochondrial genome of the insect-parasitic nematode Heterorhabditis bacteriophora: an idiosyncratic gene order and the presence of multiple long non-coding regions

Nematology ◽  
2021 ◽  
pp. 1-18
Author(s):  
Sassia Omar Regeai ◽  
David A. Fitzpatrick ◽  
Ann M. Burnell ◽  
Thomais Kakouli-Duarte
Keyword(s):  
Control Region ◽  
Insect Pests ◽  
Biological Control Agent ◽  
Complete Mitochondrial Genome ◽  
Heterorhabditis Bacteriophora ◽  
Rrna Genes ◽  
Gene Arrangement ◽  
Trna Genes ◽  
Entire Genome ◽  
Coding Regions

Summary We present here the complete mtDNA genome (mitogenome) of Heterorhabditis bacteriophora, an important biological control agent of soil-dwelling insect pests in agriculture and horticulture. This is the first description of a mitogenome for a member of the family Heterorhabditidae. The genome contains the typical chromadorean complement of 12 protein-coding genes, 22 tRNA genes and two rRNA genes. All genes are transcribed in the same direction and have a nucleotide composition high in A and T. For the entire genome, the nucleotide contents are 47.02% (T), 28.81% (A), 16.10% (G), 8.08% (C) and 75.83% (AT). Heterorhabditis bacteriophora has a unique, idiosyncratic gene arrangement. It differs from that of Caenorhabditis elegans in having a block of seven genes: trnQ-trnF-cytb-trnL1-cox3-trnT-nad4 translocated to a position between nad3 and nad5, as well as having a change in the position of the four tRNA block gene cluster, trnC-trnM-trnD-trnG, where trnC and trnM have switched places and trnD and trnG have translocated between nad4 and nad5 genes. The H. bacteriophora mitogenome is 18 128 bp long, and thus is ca 4 kb larger than the mitogenomes of most chromadoreans. This relatively large genome is due to the presence of five non-coding regions (NCR): NCR1 (114 bp), NCR2 (159 bp), NCR3 (498 bp), NCR4 (1917 bp) and NCR5 (2154 bp), which make up 26.7% of the genome. The NCR5 had the highest A + T content of 83.47% indicating that this region is the likely AT-rich control region. The complete 498 bp NCR3 sequence is duplicated in NCR4 and in NCR5 (the putative AT-rich control region). Such an organisation has not been reported previously in nematode mtDNA.

The symbiotic mites of some Appalachian Xystodesmidae (Diplopoda:Polydesmida) and the complete mitochondrial genome sequence of the mite Stylochyrus rarior (Berlese) (Acari:Mesostigmata:Ologamasidae)

2009 ◽  
Vol 23 (5) ◽  
pp. 445 ◽  
Author(s):  
Lynn Swafford ◽  
Jason E. Bond
Keyword(s):  
Mitochondrial Genome ◽  
Complete Mitochondrial Genome ◽  
Mite Species ◽  
Gene Arrangement ◽  
Trna Genes ◽  
Rrna Gene ◽  
Protein Coding ◽  
Coding Regions ◽  
The Family ◽  
Coding Control

Millipedes of the family Xystodesmidae (Polydesmida) are often host to several symbiotic mite species, but very little work has been done to identify these acarines or to understand their relationship to the millipedes. In an attempt to better understand these associations, mites found on xystodesmid millipedes, a group for which a species phylogeny has been proposed, were collected in the Appalachian Mountains of Kentucky, Virginia, Tennessee and North Carolina. Mites in the genera Stylochyrus Canestrini & Canestrini, 1882 (Mesostigmata: Ologamasidae) and Schwiebea Oudemans, 1916 (Sarcoptiformes: Acaridae) were prevalent among millipedes in the genera Apheloria Chamberlin, 1921, Appalachioria Marek & Bond, 2006, Boraria Chamberlin, 1943, Brachoria Chamberlin, 1939, Dixioria Chamberlin, 1947, Nannaria Chamberlin, 1918, Pleuroloma Rafinesque, 1820, Prionogonus Shelley, 1982, Rudiloria Causey, 1955 and Sigmoria Chamberlin, 1939. Of the mite taxa collected, the species Stylochyrus rarior (Berlese, 1916) was found on the greatest number of sampled millipede taxa. To enhance future coevolutionary studies of xystodesmid millipedes and their mite symbionts, the complete mitochondrial genome of S. rarior associated with the millipede genus Apheloria (Polydesmida: Xystodesmidae) was sequenced. The genome is 14 899 nucleotides in length, has all the typical genes of an arthropod mitochondrion, differs in gene arrangement from that of the ancestral arthropod, and has a gene order that is unique among mites and ticks. The major difference in S. rarior is the placement of the protein-coding gene nad1, which is positioned between the rRNA gene 12S and the protein-coding gene nad2 (tRNA genes and non-coding regions excluded). There are also two non-coding control regions within this mitochondrial genome.

The complete mitochondrial genome of the flat bug Aradacanthia heissi (Hemiptera: Aradidae)

Zootaxa ◽  
2012 ◽  
Vol 3238 (1) ◽  
pp. 23 ◽  
Author(s):  
AIMIN SHI ◽  
HU LI ◽  
XIAOSHUAN BAI ◽  
XUN DAI ◽  
JIAN CHANG ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Phylogenetic Analyses ◽  
Complete Mitochondrial Genome ◽  
Nucleotide Composition ◽  
Gene Arrangement ◽  
Entire Genome ◽  
Protein Coding ◽  
Simple Loop ◽  
Secondary Structure Models ◽  
Mt Genome

The 15528 bp long complete mitochondrial genome (mt-genome) of a flat bug, Aradacanthia heissi Bai, Zhang & Cai,was determined. The entire genome contains typical 37 genes with an A+T content of 74.7%. The gene arrangement dif-fers from that of Drosophila yakuba Burla which is considered the representative ground pattern for insect mt-genomes,as the results of inversion of tRNAIle - tRNAGln and tRNACys - tRNATrp . All protein-coding genes (PCGs) use standard initia-tion codons (methionine and isoleucine), except COI which starts with TTG. Three of the 13 PCGs harbor the incompletetermination codon. Meanwhile, opposite CG-skew tendency occurs on the nucleotide composition and codon usage andthis tendency is also reflected on the J-strand and N-strand of PCGs. All tRNAs can fold into classic clover-leaf structure,whereas the dihydrouridine (DHU) arm of tRNASer(AGN) forms a simple loop. Secondary structure models of the ribosomalRNA genes of A. heissi are predicted and similar to those proposed for other insects. The control region is located betweensrRNA and tRNAGln with 81.5% A+T content, which was the most A+T-rich region of the mt-genome and four 68 bp tan-dem repeat units were found in this region. Phylogenetic analyses of available species of Pentatomomorpha showed Ara-doidea and the Trichophora are sister groups that bolstered the mainstream hypothesis, and provide the evidence for the feasibility of mt-genome data to resolve relationships at the subfamily level in Aradidae.

scholarly journals Complete mitochondrial genome of the freshwater fish Onychostoma lepturum (Teleostei, Cyprinidae): genome characterization and phylogenetic analysis

ZooKeys ◽  
2020 ◽  
Vol 1005 ◽  
pp. 57-72
Author(s):  
I-Chen Wang ◽  
Hung-Du Lin ◽  
Chih-Ming Liang ◽  
Chi-Chun Huang ◽  
Rong-Da Wang ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Mitochondrial Genome ◽  
Phylogenetic Trees ◽  
Complete Mitochondrial Genome ◽  
Genomic Variation ◽  
Rrna Genes ◽  
Valid Species ◽  
Trna Genes ◽  
Protein Coding ◽  
Protein Coding Genes

The cyprinid genus Onychostoma Günther, 1896 consists of 24 valid species distributed in Southeast Asia, including Taiwan, Hainan, mainland China and the Indochina region. In the present study, we determined the complete mitochondrial genome of O. lepturum, which is 16,598 bp in length, containing 13 protein-coding genes, two rRNA genes, 22 tRNA genes and a typical control region (D-loop). To verify the molecular phylogeny of the subfamily Acrossocheilinae, we provide new insights to better understand the taxonomic status of Acrossocheilus, Onychostoma and Folifer brevifilis. The phylogenetic trees presented three major clades based on the 13 protein-coding genes from 28 Acrossocheilinae species. Clades I and II represent the Onychostoma and Acrossocheilus groups, respectively. Species of Acrossocheilus, Onychostoma and F. brevifilis are included in Clade III, which is considered as an ancestral group. This work provides genomic variation information and improves our understanding of the Acrossocheilinae mitogenome, which will be most valuable in providing new insights for phylogenetic analysis and population genetics research.

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