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.

The complete mitochondrial genome of Plodia interpunctella (Lepidoptera: Pyralidae) and comparison with other Pyraloidea insects

Genome ◽  
2016 ◽  
Vol 59 (1) ◽  
pp. 37-49 ◽  
Author(s):  
Qiu-Ning Liu ◽  
Xin-Yue Chai ◽  
Dan-Dan Bian ◽  
Chun-Lin Zhou ◽  
Bo-Ping Tang
Keyword(s):  
Control Region ◽  
Complete Mitochondrial Genome ◽  
Plodia Interpunctella ◽  
Rrna Genes ◽  
Likelihood Method ◽  
Trna Genes ◽  
Cox1 Gene ◽  
Stem Loop ◽  
Lepidoptera Pyralidae ◽  
Mt Genome

The mitochondrial (mt) genome can provide important information for the understanding of phylogenetic relationships. The complete mt genome of Plodia interpunctella (Lepidoptera: Pyralidae) has been sequenced. The circular genome is 15 287 bp in size, encoding 13 protein-coding genes (PCGs), 2 rRNA genes, 22 tRNA genes, and a control region. The AT skew of this mt genome is slightly negative, and the nucleotide composition is biased toward A+T nucleotides (80.15%). All PCGs start with the typical ATN (ATA, ATC, ATG, and ATT) codons, except for the cox1 gene which may start with the CGA codon. Four of the 13 PCGs harbor the incomplete termination codon T or TA. All the tRNA genes are folded into the typical clover-leaf structure of mitochondrial tRNA, except for trnS1 (AGN) in which the DHU arm fails to form a stable stem–loop structure. The overlapping sequences are 35 bp in total and are found in seven different locations. A total of 240 bp of intergenic spacers are scattered in 16 regions. The control region of the mt genome is 327 bp in length and consisted of several features common to the sequenced lepidopteran insects. Phylogenetic analysis based on 13 PCGs using the Maximum Likelihood method shows that the placement of P. interpunctella was within the Pyralidae.

scholarly journals Insights into molecular structure, genome evolution and phylogenetic implication through mitochondrial genome sequence of Gleditsia sinensis

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Hongxia Yang ◽  
Wenhui Li ◽  
Xiaolei Yu ◽  
Xiaoying Zhang ◽  
Zhongyi Zhang ◽  
...  
Keyword(s):  
Phylogenetic Relationships ◽  
Rrna Genes ◽  
Trna Genes ◽  
Ribosomal Protein Genes ◽  
Protein Coding ◽  
Medicinal Value ◽  
The Family ◽  
Gleditsia Sinensis ◽  
Mt Genome ◽  
Insight Into

AbstractGleditsia sinensis is an endemic species widely distributed in China with high economic and medicinal value. To explore the genomic evolution and phylogenetic relationships of G. sinensis, the complete mitochondrial (mt) genome of G. sinensis was sequenced and assembled, which was firstly reported in Gleditsia. The mt genome was circular and 594,121 bp in length, including 37 protein-coding genes (PCGs), 19 transfer RNA (tRNA) genes and 3 ribosomal RNA (rRNA) genes. The overall base composition of the G. sinensis mt genome was 27.4% for A, 27.4% for T, 22.6% for G, 22.7% for C. The comparative analysis of PCGs in Fabaceae species showed that most of the ribosomal protein genes and succinate dehydrogenase genes were lost. In addition, we found that the rps4 gene was only lost in G. sinensis, whereas it was retained in other Fabaceae species. The phylogenetic analysis based on shared PCGs of 24 species (22 Fabaceae and 2 Solanaceae) showed that G. sinensis is evolutionarily closer to Senna species. In general, this research will provide valuable information for the evolution of G. sinensis and provide insight into the phylogenetic relationships within the family Fabaceae.

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. 

Mitogenomic features of Pteronarcys sachalina (Plecoptera: Pteronarcyidae), the only salmonfly known from China

Zootaxa ◽  
2020 ◽  
Vol 4860 (3) ◽  
pp. 401-412
Author(s):  
ZHI-TENG CHEN
Keyword(s):  
Mitochondrial Genome ◽  
Control Region ◽  
Tandem Repeats ◽  
Evolutionary Rate ◽  
Complete Mitochondrial Genome ◽  
Rrna Genes ◽  
Long Control Region ◽  
Trna Genes ◽  
Stem Loop ◽  
First Time

The complete mitochondrial genome (mitogenome) of Pteronarcys sachalina Klapálek was sequenced and compared with those of two other salmonflies for the first time. The mitogenome of P. sachalina was 16,180 bp in length, with an A+T content of 70.6%. The uniform set of 37 genes (13 PCGs, 22 tRNA genes and two rRNA genes) and a long control region (1431 bp) were all annotated. Most PCGs had standard ATN start codons and TAN stop codons. COX1 exhibited the highest evolutionary rate among the 13 PCGs of sequenced species of Pteronarcyidae. ND2 was truncated at the 3′ end when compared with congeners. Most tRNA genes had typical cloverleaf secondary structures, whereas the dihydrouridine (DHU) arm of trnS1 was reduced. Tandem repeats and stem-loop (SL) structures were predicted in the control region of P. sachalina. Conserved sequences were found in control regions of the three already sequenced salmonflies, P. sachalina, Pteronarcys princeps Banks, and Pteronarcella badia (Hagen). 

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.

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.

Aleksey Peshkov as an editor of Samarskaya Gazeta

2020 ◽  
pp. 128-138
Author(s):  
A. S. Bik-Bulatov
Keyword(s):  
Local History ◽  
Organizational Skills ◽  
First Time ◽  
New Evidence ◽  
Insight Into ◽  
Shed Light

The article uses little known letters of M. Gorky, many of which were published for the first time in 1997, as well as findings of Samara-based experts in local history to shed light on the writer’s work as editor-in-chief of the Samarskaya Gazeta newspaper in 1895. The researcher introduces hitherto unstudied reminiscences of the journalist D. Linyov (Dalin) about this period, which reference a letter by Gorky, now lost. The paper details a newly discovered episode of Gorky’s professional biography as a journalist: it concerns his campaign against a Samara ‘she-wolf,’ the madam of a local brothel A. Neucheva. Linyov’s reminiscences turn out to be an important and interesting source, offering an insight into the daily grind of the young editor Gorky, providing new evidence of his excellent organizational skills, and describing his moral and social stance. The author presents his work in the context of a recently initiated broader discussion about the need to map out all Russian periodicals for the period until 1917, as well as all research devoted to individual publications.

An Insight into Oligopeptide Transporter 3 (OPT3) family proteins

2020 ◽  
Vol 27 ◽  
Author(s):  
Fırat Kurt
Keyword(s):  
Stress Responses ◽  
Chelating Agent ◽  
Biological Processes ◽  
Biotic And Abiotic Stress ◽  
Oligopeptide Transporter ◽  
Binding Residues ◽  
Fe Homeostasis ◽  
Proteins Interactions ◽  
Insight Into ◽  
Selection Of

: Oligopeptide transporter 3 (OPT3) proteins are one of the subsets of OPT clade, yet little is known about these transporters. Therefore, homolog OPT3 proteins in several plant species were investigated and characterized using bioinformatical tools. Motif and co-expression analyses showed that OPT3 proteins may be involved in both biotic and abiotic stress responses as well as growth and developmental processes. AtOPT3 usually seemed to take part in Fe homeostasis whereas ZmOPT3 putatively interacted with proteins involved in various biological processes from plant defense system to stress responses. Glutathione (GSH), as a putative alternative chelating agent, was used in the AtOPT3 and ZmOPT3 docking analyses to identify their putative binding residues. The information given in this study will contribute to the understanding of OPT3 proteins’ interactions in various pathways and to the selection of potential ligands for OPT3s.

scholarly journals Comparative Study of Chemical Compositions and Antioxidant Capacities of Oils Obtained from 15 Macadamia (Macadamia integrifolia) Cultivars in China

Foods ◽  
2021 ◽  
Vol 10 (5) ◽  
pp. 1031
Author(s):  
Xixiang Shuai ◽  
Taotao Dai ◽  
Mingshun Chen ◽  
Ruihong Liang ◽  
Liqing Du ◽  
...  
Keyword(s):  
Palmitoleic Acid ◽  
Linear Regression Analysis ◽  
Monounsaturated Fatty Acids ◽  
Multiple Linear Regression Analysis ◽  
Chemical Compositions ◽  
Macadamia Integrifolia ◽  
Antioxidant Capacities ◽  
Squalene Content ◽  
First Time ◽  
Insight Into

The planting area of macadamia in China accounted for more than one third of the world’s planted area. The lipid compositions, minor components, and antioxidant capacities of fifteen varieties of macadamia oil (MO) in China were comparatively investigated. All varieties of MO were rich in monounsaturated fatty acids, mainly including oleic acid (61.74–66.47%) and palmitoleic acid (13.22–17.63%). The main triacylglycerols of MO were first time reported, including 19.2–26.1% of triolein, 16.4–18.2% of 1-palmitoyl-2,3-dioleoyl-glycerol, and 11.9–13.7% of 1-palmitoleoyl-2-oleoyl-3-stearoyl-glycerol, etc. The polyphenol, α-tocotrienol and squalene content varied among the cultivars, while Fuji (791) contained the highest polyphenols and squalene content. Multiple linear regression analysis indicated the polyphenols and squalene content positively correlated with the antioxidant capacity. This study can provide a crucial directive for the breeding of macadamia and offer an insight into industrial application of MO in China.

scholarly journals Frequent tRNA gene translocation towards the boundaries with control regions contributes to the highly dynamic mitochondrial genome organization of the parasitic lice of mammals

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Wen-Ge Dong ◽  
Yalun Dong ◽  
Xian-Guo Guo ◽  
Renfu Shao
Keyword(s):  
Mitochondrial Genome ◽  
Control Region ◽  
Genome Organization ◽  
Trna Gene ◽  
Trna Genes ◽  
Single Chromosome ◽  
Gene Translocation ◽  
Sucking Lice ◽  
Different Types ◽  
Mt Genome

Abstract Background The typical single-chromosome mitochondrial (mt) genome of animals has fragmented into multiple minichromosomes in the lineage Mitodivisia, which contains most of the parasitic lice of eutherian mammals. These parasitic lice differ from each other even among congeneric species in mt karyotype, i.e. the number of minichromosomes, and the gene content and gene order in each minichromosome, which is in stark contrast to the extremely conserved single-chromosome mt genomes across most animal lineages. How fragmented mt genomes evolved is still poorly understood. We use Polyplax sucking lice as a model to investigate how tRNA gene translocation shapes the dynamic mt karyotypes. Results We sequenced the full mt genome of the Asian grey shrew louse, Polyplax reclinata. We then inferred the ancestral mt karyotype for Polyplax lice and compared it with the mt karyotypes of the three Polyplax species sequenced to date. We found that tRNA genes were entirely responsible for mt karyotype variation among these three species of Polyplax lice. Furthermore, tRNA gene translocation observed in Polyplax lice was only between different types of minichromosomes and towards the boundaries with the control region. A similar pattern of tRNA gene translocation can also been seen in other sucking lice with fragmented mt genomes. Conclusions We conclude that inter-minichromosomal tRNA gene translocation orientated towards the boundaries with the control region is a major contributing factor to the highly dynamic mitochondrial genome organization in the parasitic lice of mammals.

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