scholarly journals The complete mitochondrial genome of Paragonimus ohirai (Paragonimidae: Trematoda: Platyhelminthes) and its comparison with P. westermani congeners and other trematodes

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e7031 ◽  
Author(s):  
Thanh Hoa Le ◽  
Khue Thi Nguyen ◽  
Nga Thi Bich Nguyen ◽  
Huong Thi Thanh Doan ◽  
Takeshi Agatsuma ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Short Tandem Repeats ◽  
Tandem Repeats ◽  
Complete Mitochondrial Genome ◽  
Mitochondrial Protein ◽  
Coding Region ◽  
Protein Coding ◽  
Lung Fluke ◽  
Short Tandem

We present the complete mitochondrial genome of Paragonimus ohirai Miyazaki, 1939 and compare its features with those of previously reported mitochondrial genomes of the pathogenic lung-fluke, Paragonimus westermani, and other members of the genus. The circular mitochondrial DNA molecule of the single fully sequenced individual of P. ohirai was 14,818 bp in length, containing 12 protein-coding, two ribosomal RNA and 22 transfer RNA genes. As is common among trematodes, an atp8 gene was absent from the mitogenome of P. ohirai and the 5′ end of nad4 overlapped with the 3′ end of nad4L by 40 bp. Paragonimusohirai and four forms/strains of P. westermani from South Korea and India, exhibited remarkably different base compositions and hence codon usage in protein-coding genes. In the fully sequenced P. ohirai individual, the non-coding region started with two long identical repeats (292 bp each), separated by tRNAGlu. These were followed by an array of six short tandem repeats (STR), 117 bp each. Numbers of the short tandem repeats varied among P. ohirai individuals. A phylogenetic tree inferred from concatenated mitochondrial protein sequences of 50 strains encompassing 42 species of trematodes belonging to 14 families identified a monophyletic Paragonimidae in the class Trematoda. Characterization of additional mitogenomes in the genus Paragonimus will be useful for biomedical studies and development of molecular tools and mitochondrial markers for diagnostic, identification, hybridization and phylogenetic/epidemiological/evolutionary studies.

scholarly journals Characterization of the complete mitochondrial genome of the New Zealand parasitic blowfly Calliphora vicina (Insecta: Diptera: Calliphoridae)

2020 ◽  
Author(s):  
Nikola Palevich ◽  
Luis Carvalho ◽  
Paul Maclean
Keyword(s):  
New Zealand ◽  
Mitochondrial Genome ◽  
Complete Mitochondrial Genome ◽  
Calliphora Vicina ◽  
Coding Region ◽  
Protein Coding ◽  
Transfer Rnas ◽  
Next Generation Sequencing Technology ◽  
Monophyletic Cluster

ABSTRACTIn the present study, the complete mitochondrial genome of the New Zealand parasitic blowfly Calliphora vicina (blue bottle blowfly) field strain NZ_CalVic_NP was generated using next-generation sequencing technology and annotated. The 16,518 bp mitochondrial genome consists of 13 protein-coding genes, two ribosomal RNAs, 22 transfer RNAs, and a 1,689 bp non-coding region, similar to most metazoan mitochondrial genomes. Phylogenetic analysis showed that C. vicina NZ_CalVic_NP does not form a monophyletic cluster with the remaining three Calliphorinae species. The complete mitochondrial genome sequence of C. vicina NZ_CalVic_NP is a resource to facilitate future species identification research within the Calliphoridae.

scholarly journals Complete mitochondrial genome of Cultellus attenuatus and its phylogenetic implications

2021 ◽  
Author(s):  
Haikun Li ◽  
Ruihai Yu ◽  
Peizhen Ma ◽  
Chunhua Li
Keyword(s):  
Mitochondrial Genome ◽  
Complete Mitochondrial Genome ◽  
Mitochondrial Genes ◽  
Coding Region ◽  
Protein Coding ◽  
Sinonovacula Constricta ◽  
Transfer Rnas ◽  
Phylogenetic Implications ◽  
Solen Grandis ◽  
Relationship Of

Abstract The complete mitochondrial genome of Cultellus attenuates, a new aquaculture species, was sequenced and compared with mitogenomes from seven species of Heterodonta bivalve mollusk in the gene bank. The mitochondrial genome of C. attenuatus is 16888bp in length and contains 36 genes, including 12 protein-coding genes, 2 ribosomal RNAs and 22 transfer RNAs, and all genes are encoded on the same strand. In comparison with C. attenuates, the mitochondrial genes of the Sinonovacula constricta from the same family were not rearranged, but those of six other species from different family were rearranged to different degrees. The largest non-coding region of C. attenuatus is 1173bp in length and with the A + T content of 68.24%, located between nad2 and trnK. The results of phylogenetic analysis show that the C. attenuates and the S. constricta belonging to Cultellidae cluster into one branch while two species of Solenidae ( Solen grandis and Solen strictus) are clustering as their sister taxon. These data not only contribute to the understanding of the phylogenetic relationship of the Heterodonta, but also serve as a resource for the development of the genetic markers in aquaculture.

scholarly journals Link Between Short tandem Repeats and Translation Initiation Site Selection

2018 ◽  
Author(s):  
M Arabfard ◽  
K Kavousi ◽  
A Delbari ◽  
M Ohadi
Keyword(s):  
Amino Acids ◽  
Translation Initiation ◽  
Short Tandem Repeats ◽  
Tandem Repeats ◽  
Initiation Site ◽  
Translation Initiation Site ◽  
Vertebrate Species ◽  
Protein Coding ◽  
Human Specific ◽  
Short Tandem

AbstractRecent work in yeast and humans suggest that evolutionary divergence in cis-regulatory sequences impact translation initiation sites (TISs). Cis-elements can also affect the efficacy and amount of protein synthesis. Despite their vast biological implication, the landscape and relevance of short tandem repeats (STRs)/microsatellites to the human protein-coding gene TISs remain largely unknown. Here we characterized the STR distribution at the 120 bp cDNA sequence upstream of all annotated human protein-coding gene TISs based on the Ensembl database. Furthermore, we performed a comparative genomics study of all annotated orthologous TIS-flanking sequences across 47 vertebrate species (755,956 transcripts), aimed at identifying human-specific STRs in this interval. We also hypothesized that STRs may be used as genetic codes for the initiation of translation. The initial five amino acid sequences (excluding the initial methionine) that were flanked by STRs in human were BLASTed against the initial orthologous five amino acids in other vertebrate species (2,025,817 pair-wise TIS comparisons) in order to compare the number of events in which human-specific and non-specific STRs occurred with homologous and non-homologous TISs (i.e. ≥50% and <50% similarity of the five amino acids). We characterized human-specific STRs and a bias of this compartment in comparison to the overall (human-specific and non-specific) distribution of STRs (Mann Whitney p=1.4 × 10−11). We also found significant enrichment of non-homologous TISs flanked by human-specific STRs (p<0.00001). In conclusion, our data indicate a link between STRs and TIS selection, which is supported by differential evolution of the human-specific STRs in the TIS upstream flanking sequence.AbbreviationscDNAComplementary DNACDSCoding DNA sequenceSTRShort Tandem RepeatTISTranslation Initiation SiteTSSTranscription Start Site

scholarly journals Characterization of the complete mitochondrial genome of the lung fluke, Paragonimus kellicotti

2018 ◽  
Vol 3 (2) ◽  
pp. 715-716 ◽  
Author(s):  
Tao Wang ◽  
Yunfang Wang ◽  
Fengqiang Xu ◽  
Xia Li ◽  
Rui Qu ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Complete Mitochondrial Genome ◽  
Lung Fluke

Characterization of human short tandem repeats (STRs) for individual identification using the Ion Torrent

2015 ◽  
Vol 9 (2) ◽  
pp. 164-172 ◽  
Author(s):  
Seri Lim ◽  
Jong Pil Youn ◽  
Sang Ok Moon ◽  
Youn Hyung Nam ◽  
Seung Bum Hong ◽  
...  
Keyword(s):  
Short Tandem Repeats ◽  
Tandem Repeats ◽  
Individual Identification ◽  
Ion Torrent ◽  
Short Tandem

The complete mitochondrial genome of Zicrona caerulea (Linnaeus) (Hemiptera: Pentatomidae: Asopinae) and its phylogenetic implications

Zootaxa ◽  
2020 ◽  
Vol 4747 (3) ◽  
pp. 547-561
Author(s):  
QING ZHAO ◽  
GERASIMOS CASSIS ◽  
LING ZHAO ◽  
YIFAN HE ◽  
HUFANG ZHANG ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Tandem Repeats ◽  
Complete Mitochondrial Genome ◽  
Rrna Genes ◽  
Trna Genes ◽  
Stink Bug ◽  
Protein Coding ◽  
Simple Loop ◽  
Phylogenetic Implications ◽  
Maximum Likelihood Methods

Zicrona caerulea (Linnaeus, 1758) is a cosmopolitan stink bug species, which belongs to the predatory subfamily Asopinae. In this study, the complete mitochondrial genome of Zicrona caerulea from Shanxi, China was sequenced for the first time, using next generation sequencing. The mitogenome was found to be 15,479 bp in length. It contained 13 protein-coding genes, two rRNA genes, 22 tRNA genes and a typical control region. This research revealed an overall A+T content of 77.14%. All tRNA genes had a clover-leaf structure except for trnS1, which lacks a dihydrouridine (DHU) arm; and for trnV, the DHU arm forms a simple loop. The lengths of rrnS and rrnL were 797 bp and 1,285 bp, respectively. Because of a shortage in tandem repeats, the A+T-rich region was 644 bp in length. Phylogenetic relationships based on these mitogenomes, using Bayesian inference and Maximum likelihood methods, showed that Zicrona caerulea belongs to Asopinae. The monophyly of families of the Pentatomoidea is supported, albeit limited taxon sampling. 

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. 

scholarly journals The complete mitochondrial genome of Orancistrocerus aterrimus aterrimus and comparative analysis in the family Vespidae (Hymenoptera, Vespidae, Eumeninae)

ZooKeys ◽  
2018 ◽  
Vol 790 ◽  
pp. 127-144 ◽  
Author(s):  
Qiao-Hua Zhang ◽  
Pan Huang ◽  
Bin Chen ◽  
Ting-Jing Li
Keyword(s):  
Mitochondrial Genome ◽  
Stop Codon ◽  
Translation Termination ◽  
Complete Mitochondrial Genome ◽  
Rrna Genes ◽  
Trna Genes ◽  
Coding Region ◽  
Protein Coding ◽  
Tandem Repeat Sequences ◽  
The Family

To date, only one mitochondrial genome (mitogenome) in the Eumeninae has been reported in the world and this is the first report in China. The mitogenome ofO.a.aterrimusis 17 972 bp long, and contains 38 genes, including 13 protein coding genes (PCGs), 23 tRNA genes, two rRNA genes, a long non-coding region (NCR), and a control region (CR). The mitogenome has 79.43% A + T content, its 13 PCGs use ATN as the initiation codon except forcox1using TTG, and nine genes used complete translation termination TAA and four genes have incomplete stop codon T (cox2,cox3,nad4, andcytb). Twenty-two of 23 tRNAs can form the typical cloverleaf secondary structure except fortrnS1. The CR is 1 078 bp long with 84.69% A+T content, comprising 28 bp tandem repeat sequences and 13 bp T-strech. There are two gene rearrangements which are an extratrnM2located betweentrnQandnad2and thetrnL2in the upstream ofnad1. Within all rearrangements of these mitogenomes reported in the family Vespidae, the translocation betweentrnS1andtrnEgenes only appears in Vespinae, and the translocation oftrnYin Polistinae and Vespinae. The absent codons of 13 PCGs in Polistinae are more than those both in Vespinae and Eumeninae in the family Vespidae. The study reports the complete mitogenome ofO.a.aterrimus, compares the characteristics and construct phylogenetic relationships of the mitogenomes in the family Vespidae.

scholarly journals The Complete Mitochondrial Genome of the New Zealand Parasitic Blowfly Lucilia sericata (Insecta: Diptera: Calliphoridae)

2020 ◽  
Author(s):  
Nikola Palevich
Keyword(s):  
Phylogenetic Analysis ◽  
New Zealand ◽  
Mitochondrial Genome ◽  
Complete Mitochondrial Genome ◽  
Lucilia Sericata ◽  
Coding Region ◽  
Protein Coding ◽  
Next Generation Sequencing Technology ◽  
Monophyletic Cluster ◽  
Green Bottle

In the present study, the complete mitochondrial genome of the New Zealand parasitic blowfly Lucilia sericata (green bottle blowfly) field strain NZ_LucSer_NP was generated using next-generation sequencing technology. The length of complete the mitochondrial genome is 15,938 bp, with 39.4% A, 13.0% C, 9.3% G, and 38.2% T nucleotide distribution. The complete mitochondrial genome consists of 13 protein-coding genes, two ribosomal RNAs, 22 transfer RNAs, and a and a 1,124 bp non-coding region, similar to most metazoan mitochondrial genomes. Phylogenetic analysis showed that L. sericata NZ_LucSer_NP forms a monophyletic cluster with the remaining six Lucilia species and the Calliphoridae are polyphyletic. This study provides the first complete mitochondrial genome sequence for a L. sericata blowfly species derived from New Zealand to facilitate species identification and phylogenetic analysis.

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