scholarly journals The Mitochondrial Genome of a Freshwater Pelagic Amphipod Macrohectopus branickii Is among the Longest in Metazoa

Genes ◽  
2021 ◽  
Vol 12 (12) ◽  
pp. 2030
Author(s):  
Elena V. Romanova ◽  
Yurij S. Bukin ◽  
Kirill V. Mikhailov ◽  
Maria D. Logacheva ◽  
Vladimir V. Aleoshin ◽  
...  
Keyword(s):  
Trna Genes ◽  
Amphipod Species ◽  
Genome Length ◽  
Coding Region ◽  
Coding Regions ◽  
Animal Phyla ◽  
Baikalian Amphipod ◽  
Length Changes ◽  
Mt Genome ◽  
Rna Genes

There are more than 350 species of amphipods (Crustacea) in Lake Baikal, which have emerged predominantly through the course of endemic radiation. This group represents a remarkable model for studying various aspects of evolution, one of which is the evolution of mitochondrial (mt) genome architectures. We sequenced and assembled the mt genome of a pelagic Baikalian amphipod species Macrohectopus branickii. The mt genome is revealed to have an extraordinary length (42,256 bp), deviating significantly from the genomes of other amphipod species and the majority of animals. The mt genome of M. branickii has a unique gene order within amphipods, duplications of the four tRNA genes and Cox2, and a long non-coding region, that makes up about two thirds of the genome’s size. The extension of the mt genome was most likely caused by multiple duplications and inversions of regions harboring ribosomal RNA genes. In this study, we analyzed the patterns of mt genome length changes in amphipods and other animal phyla. Through a statistical analysis, we demonstrated that the variability in the mt genome length may be a characteristic of certain phyla and is primarily conferred by expansions of non-coding regions.

Mitochondrial genomes of Vanhornia eucnemidarum (Apocrita: Vanhorniidae) and Primeuchroeus spp. (Aculeata: Chrysididae): evidence of rearranged mitochondrial genomes within the Apocrita (Insecta: Hymenoptera)

Genome ◽  
2006 ◽  
Vol 49 (7) ◽  
pp. 752-766 ◽  
Author(s):  
Lyda Raquel Castro ◽  
Kalani Ruberu ◽  
Mark Dowton
Keyword(s):  
Molecular Evolution ◽  
Gene Duplication ◽  
Ribosomal Rna ◽  
Nucleotide Composition ◽  
Gene Organization ◽  
Mitochondrial Genomes ◽  
Trna Genes ◽  
Noncoding Regions ◽  
Mt Genome ◽  
Rna Genes

We sequenced most of the mitochondrial (mt) genomes of 2 apocritan taxa: Vanhornia eucnemidarum and Primeuchroeus spp. These mt genomes have similar nucleotide composition and codon usage to those of mt genomes reported for other Hymenoptera, with a total A + T content of 80.1% and 78.2%, respectively. Gene content corresponds to that of other metazoan mt genomes, but gene organization is not conserved. There are a total of 6 tRNA genes rearranged in V. eucnemidarum and 9 in Primeuchroeus spp. Additionally, several noncoding regions were found in the mt genome of V. eucnemidarum, as well as evidence of a sustained gene duplication involving 3 tRNA genes. We also report an inversion of the large and small ribosomal RNA genes in Primeuchroeus spp. mt genome. However, none of the rearrangements reported are phylogenetically informative with respect to the current taxon sample.Key words: mitochondrial genomes, molecular evolution, hymenoptera.

scholarly journals The Whole Genome Assembly and Comparative Genomic Research ofThellungiella parvula(Extremophile Crucifer) Mitochondrion

2016 ◽  
Vol 2016 ◽  
pp. 1-13 ◽  
Author(s):  
Xuelin Wang ◽  
Changwei Bi ◽  
Yiqing Xu ◽  
Suyun Wei ◽  
Xiaogang Dai ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Tandem Repeats ◽  
Genomic Research ◽  
Comparative Genomic ◽  
Trna Genes ◽  
Protein Coding ◽  
Ssr Analysis ◽  
Brassicaceae Species ◽  
Mt Genome ◽  
Rna Genes

The complete nucleotide sequences of the mitochondrial (mt) genome of an extremophile speciesThellungiella parvula(T. parvula) have been determined with the lengths of 255,773 bp.T. parvulamt genome is a circular sequence and contains 32 protein-coding genes, 19 tRNA genes, and three ribosomal RNA genes with a 11.5% coding sequence. The base composition of 27.5% A, 27.5% T, 22.7% C, and 22.3% G in descending order shows a slight bias of 55% AT. Fifty-three repeats were identified in the mitochondrial genome ofT. parvula, including 24 direct repeats, 28 tandem repeats (TRs), and one palindromic repeat. Furthermore, a total of 199 perfect microsatellites have been mined with a high A/T content (83.1%) through simple sequence repeat (SSR) analysis and they were distributed unevenly within this mitochondrial genome. We also analyzed other plant mitochondrial genomes’ evolution in general, providing clues for the understanding of the evolution of organelles genomes in plants. Comparing with other Brassicaceae species,T. parvulais related toArabidopsis thalianawhose characters of low temperature resistance have been well documented. This study will provide important genetic tools for other Brassicaceae species research and improve yields of economically important plants.

According to mitochondrial DNA evidence, Parascaris equorum and Parascaris univalens may represent the same species

2018 ◽  
Vol 93 (3) ◽  
pp. 383-388 ◽  
Author(s):  
J.F. Gao ◽  
X.X. Zhang ◽  
X.X. Wang ◽  
Q. Li ◽  
Y. Li ◽  
...  
Keyword(s):  
Severe Illness ◽  
Total Amino Acid ◽  
Parasitic Infections ◽  
Trna Genes ◽  
Protein Coding ◽  
Parascaris Equorum ◽  
Protein Coding Genes ◽  
Mt Genome ◽  
Rna Genes ◽  
Complete Mtdna

AbstractParascarosis is caused mainly by parasitic infections with Parascaris equorum and Parascaris univalens, the most common ascarid nematodes, in the small intestine of equines. Parascarosis often causes severe illness and even death in foals and yearlings. In this study, we obtained the complete sequence of the P. equorum mitochondrial (mt) genome and compared its organization and structure with that of P. equorum Japan isolate (nearly complete), and the complete mtDNA sequences of P. univalens Switzerland and USA isolates. The complete mtDNA genome of P. equorum China isolate is 13,899 base pairs (bp), making it the smallest of the four genomes. All four Parascaris mt genomes are circular, and all genes are transcribed in the same direction. The P. equorum mtDNA genome consists of 12 protein-coding genes, two ribosomal RNA genes, 22 transfer (t) RNA genes and one non-coding region, which is consistent with P. equorum Japan isolate and P. univalens Switzerland isolate but distinct from P. univalens USA isolate, which has 20 tRNA genes. Differences in nucleotide sequences of the four entire mt genomes range from 0.1–0.9%, and differences in total amino acid sequences of protein-coding genes are 0.2–2.1%. Phylogenetic analyses showed that the four Parascaris species clustered in a clade, indicating that P. equorum and P. univalens are very closely related. These mt genome datasets provide genetic evidence that P. equorum and P. univalens may represent the same species, which will be of use in further studies of the taxonomy, systematics and population genetics of ascarids and other nematodes.

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 Mitochondrial Genome Sequence of Echinostoma revolutum from Red-Crowned Crane (Grus japonensis)

2020 ◽  
Vol 58 (1) ◽  
pp. 73-79
Author(s):  
Rongkun Ran ◽  
Qi Zhao ◽  
Asmaa M. I. Abuzeid ◽  
Yue Huang ◽  
Yunqiu Liu ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Phylogenetic Trees ◽  
Mitochondrial Gene ◽  
Intestinal Bleeding ◽  
Trna Genes ◽  
Genetic Characteristics ◽  
Grus Japonensis ◽  
Echinostoma Revolutum ◽  
Mt Genome ◽  
Rna Genes

<i>Echinostoma revolutum</i> is a zoonotic food-borne intestinal trematode that can cause intestinal bleeding, enteritis, and diarrhea in human and birds. To identify a suspected <i>E. revolutum</i> trematode from a red-crowned crane (<i>Grus japonensis</i>) and to reveal the genetic characteristics of its mitochondrial (mt) genome, the internal transcribed spacer (ITS) and complete mt genome sequence of this trematode were amplified. The results identified the trematode as <i>E. revolutum</i>. Its entire mt genome sequence was 15,714 bp in length, including 12 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes and one non-coding region (NCR), with 61.73% A+T base content and a significant AT preference. The length of the 22 tRNA genes ranged from 59 bp to 70 bp, and their secondary structure showed the typical cloverleaf and D-loop structure. The length of the large subunit of rRNA (<i>rrn</i>L) and the small subunit of rRNA (<i>rrn</i>S) gene was 1,011 bp and 742 bp, respectively. Phylogenetic trees showed that <i>E. revolutum</i> and <i>E. miyagawai</i> clustered together, belonging to Echinostomatidae with <i>Hypoderaeum conoideum</i>. This study may enrich the mitochondrial gene database of <i>Echinostoma</i> trematodes and provide valuable data for studying the molecular identification and phylogeny of some digenean trematodes.

The complete mitochondrial genome of the styloperlid stonefly species Styloperla spinicercia Wu (Insecta: Plecoptera) with family-level phylogenetic analyses of the Pteronarcyoidea

Zootaxa ◽  
2017 ◽  
Vol 4243 (1) ◽  
pp. 125 ◽  
Author(s):  
YING WANG ◽  
JINJUN CAO ◽  
WEIHAI LI
Keyword(s):  
Tandem Repeats ◽  
Phylogenetic Analyses ◽  
Complete Mitochondrial Genome ◽  
Trna Genes ◽  
Coding Region ◽  
Protein Coding ◽  
Simple Loop ◽  
Interspecific Divergence ◽  
Family Level ◽  
Mt Genome

We present the complete mitochondrial (mt) genome sequence of the stonefly, Styloperla spinicercia Wu, 1935 (Plecoptera: Styloperlidae), the type species of the genus Styloperla and the first complete mt genome for the family Styloperlidae. The genome is circular, 16,129 base pairs long, has an A+T content of 70.7%, and contains 37 genes including the large and small ribosomal RNA (rRNA) subunits, 13 protein coding genes (PCGs), 22 tRNA genes and a large non-coding region (CR). All of the PCGs use the standard initiation codon ATN except ND1 and ND5, which start with TTG and GTG. Twelve of the PCGs stop with conventional terminal codons TAA and TAG, except ND5 which shows an incomplete terminator signal T. All tRNAs have the classic clover-leaf structures with the dihydrouridine (DHU) arm of tRNASer(AGN) forming a simple loop. Secondary structures of the two ribosomal RNAs are presented with reference to previous models. The structural elements and the variable numbers of tandem repeats are described within the control region. Phylogenetic analyses using both Bayesian (BI) and Maximum Likelihood (ML) methods support the previous hypotheses regarding family level relationships within the Pteronarcyoidea. The genetic distance calculated based on 13 PCGs and two rRNAs between Styloperla sp. and S. spinicercia is provided and interspecific divergence is discussed. 

scholarly journals Characterization of the complete mitochondrial genome sequence of Tracheophilus cymbius (Digenea), the first representative from the family Cyclocoelidae

2019 ◽  
Vol 94 ◽  
Author(s):  
Y. Li ◽  
X.X. Ma ◽  
Q.B. Lv ◽  
Y. Hu ◽  
H.Y. Qiu ◽  
...  
Keyword(s):  
Phylogenetic Analyses ◽  
Complete Mitochondrial Genome ◽  
Trna Genes ◽  
Coding Region ◽  
Closely Related Species ◽  
Protein Coding ◽  
The Family ◽  
Mt Genome ◽  
High Statistical Support

Abstract Tracheophilus cymbius (Trematoda: Cyclocoelidae) is a common tracheal fluke of waterfowl, causing serious loss in the poultry industry. However, taxonomic identification of T. cymbius remains controversial and confused. Mitochondrial (mt) genomes can provide genetic markers for the identification of closely related species. We determined the mt genome of T. cymbius and reconstructed phylogenies with other trematodes. The T. cymbius mt genome is 13,760 bp in size, and contains 12 protein-coding genes (cox 1–3, nad 1–6, nad 4L, cyt b and atp 6), 22 transfer RNA (tRNA) genes, two ribosomal RNA genes and one non-coding region. All are transcribed in the same direction. The A + T content is 62.82%. ATG and TAG are the most common initiation and termination codons, respectively. Phylogenetic analyses of concatenated nucleotide sequences show T. cymbius grouping in suborder Echinostomata, and clustering together, with high statistical support, as a sister taxon with Echinochasmus japonicus (Echinochasmidae), the two forming a distinct branch rooted to the ancestor of all Echinostomatidae and Fasciolidae species. This is the first report of the T. cymbius mt genome, and the first reported mt genome within the family Cyclocoelidae. These data will provide a significant resource of molecular markers for studying the taxonomy, population genetics and systematics of trematodes.

Complete sequence and structure of the mitochondrial genome of the human tapeworm, Taenia asiatica (Platyhelminthes; Cestoda)

Parasitology ◽  
2005 ◽  
Vol 130 (6) ◽  
pp. 717-726 ◽  
Author(s):  
H. K. JEON ◽  
K. H. LEE ◽  
K. H. KIM ◽  
U. W. HWANG ◽  
K. S. EOM
Keyword(s):  
Mitochondrial Genome ◽  
Ribosomal Rna ◽  
Complete Sequence ◽  
Trna Genes ◽  
Coding Region ◽  
Protein Encoding ◽  
Its Gene ◽  
Polymerase Chain ◽  
Rna Genes ◽  
Taenia Asiatica

The complete Taenia asiatica mitochondrial genome was amplified by long extension polymerase chain reaction (long PCR) to yield overlapping fragments that were then completely sequenced. The whole mitochondrial genome was 13703 bp long and contained 12 protein-encoding, 2 ribosomal RNA (small and large subunits), 22 transfer RNA genes and a short non-coding region. Thus, its gene contents are like those typically found in metazoan animal mitochondrial genomes (apart from the absence of atp8). All the genes were transcribed from the same strand. The 3′ end 34 bp region of nad4L overlapped with the 5′ end portion of nad4. The tRNA genes were 61–69 bp long, and the secondary structures of 18 tRNAs had typical clover-leaf shapes with paired DHU arms. However, trnC, trnS1, trnS2 and trnR had unpaired DHU arms that were 7–12 bp in length. The tRNAs that transferred serine lacked a DHU arm, as is also observed in a number of parasitic platyhelminths and metazoans. However, the trematode trnRs have paired DHU arms. The T. asiatica mtDNA non-coding region was like that in other cestodes since it was composed of a short non-coding region of 72 nucleotides and a long non-coding region of 176 nucleotides separated by a trnL1/, trnS2/, trnL2/, trnR/, nad5 gene cluster. The sequences of the cox1 genes between T. asiatica and T. saginata differ by 4·6%, while the T. asiatica cob gene differs by 4·1% and 12·9% from the cob genes of T. saginata and T. solium, respectively. In conclusion, the T. asiatica mitocondrial genome should provide a resource for comparative mitochondrial genomics and systematic studies of parasitic cestodes.

First comparative insight into the architecture ofCOImitochondrial minicircle molecules of dicyemids reveals marked inter-species variation

Parasitology ◽  
2015 ◽  
Vol 142 (8) ◽  
pp. 1066-1079 ◽  
Author(s):  
SARAH R. CATALANO ◽  
IAN D. WHITTINGTON ◽  
STEPHEN C. DONNELLAN ◽  
TERRY BERTOZZI ◽  
BRONWYN M. GILLANDERS
Keyword(s):  
Trna Genes ◽  
Species Variation ◽  
Biological Processes ◽  
Coding Region ◽  
Stem Loop ◽  
Consistent Feature ◽  
Nucleotide Divergence ◽  
First Time ◽  
Mt Genome ◽  
Insight Into

SUMMARYDicyemids, poorly known parasites of benthic cephalopods, are one of the few phyla in which mitochondrial (mt) genome architecture departs from the typical ~16 kb circular metazoan genome. In addition to a putative circular genome, a series of mt minicircles that each comprises the mt encoded units (I–III) of the cytochromecoxidase complex have been reported. Whether the structure of the mt minicircles is a consistent feature among dicyemid species is unknown. Here we analyse the complete cytochromecoxidase subunit I (COI) minicircle molecule, containing theCOIgene and an associated non-coding region (NCR), for ten dicyemid species, allowing for first time comparisons between species of minicircle architecture, NCR function and inferences of minicircle replication. Divergence inCOInucleotide sequences between dicyemid species was high (average net divergence = 31·6%) while within species diversity was lower (average net divergence = 0·2%). The NCR and putative 5′ section of theCOIgene were highly divergent between dicyemid species (average net nucleotide divergence of putative 5′COIsection = 61·1%). No tRNA genes were found in the NCR, although palindrome sequences with the potential to form stem-loop structures were identified in some species, which may play a role in transcription or other biological processes.

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