scholarly journals Variation in mitochondrial minichromosome composition among Hoplopleura lice (Phthiraptera: Hoplopleuridae) from rats

2020 ◽  
Author(s):  
Yi-Tian Fu ◽  
Yu Nie ◽  
De-Yong Duan ◽  
Guo-Hua Liu
Keyword(s):  
Phylogenetic Analyses ◽  
Amino Acid Sequences ◽  
Coding Region ◽  
Illumina Hiseq ◽  
Protein Coding ◽  
Blood Sucking ◽  
The Family ◽  
Sucking Lice ◽  
Illumina Hiseq Platform ◽  
Mt Genome

Abstract Background The family Hoplopleuridae contains at least 183 species of blood-sucking lice, which widely parasitize both mice and rats. Fragmented mitochondrial (mt) genomes have been reported in two rat lice ( Hoplopleura kitti and H. akanezumi ) from this family, but some minichromosomes were unidentified in their mt genomes. Methods We sequenced the mt genome of rat louse Hoplopleura sp. with an Illumina Hiseq platform and compared its mt genome organization with H. kitti and H. akanezumi . Results Fragmented mt genome of the rat louse Hoplopleura sp. contains 37 genes which are on 12 circular mt minichromosomes. Each mt minichromosome is 1.8-2.7 kb long, which contains 1-5 genes and one large non-coding region. The gene content and arrangement of three mt minichromosomes of Hoplopleura sp. and H. kitti are different from that of the three mt minichromosomes of H. akanezumi . Phylogenetic analyses based on the deduced amino acid sequences of the eight protein-coding genes showed that the Hoplopleura sp. was more closely related to H. akanezumi than to H. kitti , and then they form a monophyletic group. Conclusions Comparison among the three rat lice revealed variation in the composition of mt minichromosomes within the genus Hoplopleura . Hoplopleura sp. is the first species from the family Hoplopleuridae for which a complete fragmented mt genome has been sequenced. The new data provides useful genetic markers for studying the population genetics, molecular systematics and phylogenetics of blood-sucking lice.

scholarly journals Variation in mitochondrial minichromosome composition among Hoplopleura lice (Phthiraptera: Hoplopleuridae) from rats

2020 ◽  
Author(s):  
Yi-Tian Fu ◽  
Yu Nie ◽  
De-Yong Duan ◽  
Guo-Hua Liu
Keyword(s):  
Phylogenetic Analyses ◽  
Amino Acid Sequences ◽  
Coding Region ◽  
Illumina Hiseq ◽  
Protein Coding ◽  
Blood Sucking ◽  
The Family ◽  
Sucking Lice ◽  
Illumina Hiseq Platform ◽  
Mt Genome

Abstract Background The family Hoplopleuridae contains at least 183 species of blood-sucking lice, which widely parasitize both mice and rats. Fragmented mitochondrial (mt) genomes have been reported in two rat lice (Hoplopleura kitti and H. akanezumi) from this family, but some minichromosomes were unidentified in their mt genomes. Methods We sequenced the mt genome of rat louse Hoplopleura sp. with an Illumina Hiseq platform and compared its mt genome organization with H. kitti and H. akanezumi. Results Fragmented mt genome of the rat louse Hoplopleura sp. contains 37 genes which are on 12 circular mt minichromosomes. Each mt minichromosome is 1.8–2.7 kb long, which contains 1–5 genes and one large non-coding region. The gene content and arrangement of three mt minichromosomes of Hoplopleura sp. and H. kitti are different from that of the three mt minichromosomes of H. akanezumi. Phylogenetic analyses based on the deduced amino acid sequences of the eight protein-coding genes showed that the Hoplopleura sp. was more closely related to H. akanezumi than to H. kitti, and then they form a monophyletic group. Conclusions Comparison among the three rat lice revealed variation in the composition of mt minichromosomes within the genus Hoplopleura. Hoplopleura sp. is the first species from the family Hoplopleuridae for which a complete fragmented mt genome has been sequenced. The new data provides useful genetic markers for studying the population genetics, molecular systematics and phylogenetics of blood-sucking lice.

scholarly journals Variation in mitochondrial minichromosome composition among Hoplopleura lice (Phthiraptera: Hoplopleuridae) from rats

2020 ◽  
Author(s):  
Yi-Tian Fu ◽  
Yu Nie ◽  
De-Yong Duan ◽  
Guo-Hua Liu
Keyword(s):  
Phylogenetic Analyses ◽  
Amino Acid Sequences ◽  
Coding Region ◽  
Illumina Hiseq ◽  
Protein Coding ◽  
Blood Sucking ◽  
The Family ◽  
Sucking Lice ◽  
Illumina Hiseq Platform ◽  
Mt Genome

Abstract Background The family Hoplopleuridae contains at least 183 species of blood-sucking lice, which widely parasitize both mice and rats. Fragmented mitochondrial (mt) genomes have been reported in two rat lice ( Hoplopleura kitti and H. akanezumi ) from this family, but some minichromosomes were unidentified in their mt genomes. Methods We sequenced the mt genome of rat louse Hoplopleura sp. with an Illumina Hiseq platform and compared its mt genome organization with H. kitti and H. akanezumi . Results Fragmented mt genome of the rat louse Hoplopleura sp. contains 37 genes which are on 12 circular mt minichromosomes. Each mt minichromosome is 1.8-2.7 kb long, which contains 1-5 genes and one large non-coding region. The gene content and arrangement of three mt minichromosomes of Hoplopleura sp. and H. kitti are different from that of the three mt minichromosomes of H. akanezumi . Phylogenetic analyses based on the deduced amino acid sequences of the eight protein-coding genes showed that the Hoplopleura sp. was more closely related to H. akanezumi than to H. kitti , and then they form a monophyletic group. Conclusions Comparison among the three rat lice revealed variation in the composition of mt minichromosomes within the genus Hoplopleura . Hoplopleura sp. is the first species from the family Hoplopleuridae for which a complete fragmented mt genome has been sequenced. The new data provides useful genetic markers for studying the population genetics, molecular systematics and phylogenetics of blood-sucking lice.

scholarly journals Variation of mitochondrial minichromosome composition in Hoplopleura lice (Phthiraptera: Hoplopleuridae) from rats

2020 ◽  
Author(s):  
Yi-Tian Fu ◽  
Yu Nie ◽  
De-Yong Duan ◽  
Guo-Hua Liu
Keyword(s):  
Phylogenetic Analyses ◽  
Amino Acid Sequences ◽  
Coding Region ◽  
Illumina Platform ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Blood Sucking ◽  
The Family ◽  
Sucking Lice ◽  
Mt Genome

Abstract Background: The family Hoplopleuridae contains at least 183 species of blood-sucking lice, which widely parasitize both mice and rats. Fragmented mitochondrial (mt) genomes have been reported in two rat lice (Hoplopleura kitti and H. akanezumi) from this family, but some minichromosomes were unidentified in their mt genomes.Methods: We sequenced the mt genome of the rat louse Hoplopleura sp. with an Illumina platform and compared its mt genome organization with H. kitti and H. akanezumi.Results: Fragmented mt genome of the rat louse Hoplopleura sp. contains 37 genes which are on 12 circular mt minichromosomes. Each mt minichromosome is 1.8–2.7 kb long and contains 1–5 genes and one large non-coding region. The gene content and arrangement of mt minichromosomes of Hoplopleura sp. (n = 3) and H. kitti (n = 3) are different from those in H. akanezumi (n = 3). Phylogenetic analyses based on the deduced amino acid sequences of the eight protein-coding genes showed that the Hoplopleura sp. was more closely related to H. akanezumi than to H. kitti, and then they formed a monophyletic group.Conclusions: Comparison among the three rat lice revealed variation in the composition of mt minichromosomes within the genus Hoplopleura. Hoplopleura sp. is the first species from the family Hoplopleuridae for which a complete fragmented mt genome has been sequenced. The new data provide useful genetic markers for studying the population genetics, molecular systematics and phylogenetics of blood-sucking lice.

scholarly journals Variation in mitochondrial minichromosome composition among Hoplopleura lice (Phthiraptera: Hoplopleuridae) from rats

2020 ◽  
Author(s):  
Yi-Tian Fu ◽  
Yu Nie ◽  
De-Yong Duan ◽  
Guo-Hua Liu
Keyword(s):  
Phylogenetic Analyses ◽  
Amino Acid Sequences ◽  
Coding Region ◽  
Illumina Platform ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Blood Sucking ◽  
The Family ◽  
Sucking Lice ◽  
Mt Genome

Abstract Background: The family Hoplopleuridae contains at least 183 species of blood-sucking lice, which widely parasitize both mice and rats. Fragmented mitochondrial (mt) genomes have been reported in two rat lice (Hoplopleura kitti and Hoplopleura akanezumi) from this family, but some minichromosomes were unidentified in their mt genomes.Methods: We sequenced the mt genome of rat louse Hoplopleura sp. with an Illumina platform and compared its mt genome organization with Hoplopleura kitti and Hoplopleura akanezumi. Results: Fragmented mt genome of the rat louse Hoplopleura sp. contains 37 genes which are on 12 circular mt minichromosomes. Each mt minichromosome is 1.8-2.7 kb long, which contains 1-5 genes and one large non-coding region. The gene content and arrangement of three mt minichromosomes of Hoplopleura sp. and Hoplopleura kitti are different from that of the three mt minichromosomes of Hoplopleura akanezumi. Phylogenetic analyses based on the deduced amino acid sequences of the eight protein-coding genes showed that the Hoplopleura sp. was more closely related to Hoplopleura akanezumi than to Hoplopleura kitti, and then they formed a monophyletic group. Conclusions: Comparison among the three rat lice revealed variation in the composition of mt minichromosomes within the genus Hoplopleura. Hoplopleura sp. is the first species from the family Hoplopleuridae for which a complete fragmented mt genome has been sequenced. The new data provides useful genetic markers for studying the population genetics, molecular systematics and phylogenetics of blood-sucking lice.

scholarly journals Variation of mitochondrial minichromosome composition in Hoplopleura lice (Phthiraptera: Hoplopleuridae) from rats

2020 ◽  
Vol 13 (1) ◽  
Author(s):  
Yi-Tian Fu ◽  
Yu Nie ◽  
De-Yong Duan ◽  
Guo-Hua Liu
Keyword(s):  
Phylogenetic Analyses ◽  
Amino Acid Sequences ◽  
Coding Region ◽  
Illumina Platform ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Blood Sucking ◽  
The Family ◽  
Sucking Lice ◽  
Mt Genome

Abstract Background The family Hoplopleuridae contains at least 183 species of blood-sucking lice, which widely parasitize both mice and rats. Fragmented mitochondrial (mt) genomes have been reported in two rat lice (Hoplopleura kitti and H. akanezumi) from this family, but some minichromosomes were unidentified in their mt genomes. Methods We sequenced the mt genome of the rat louse Hoplopleura sp. with an Illumina platform and compared its mt genome organization with H. kitti and H. akanezumi. Results Fragmented mt genome of the rat louse Hoplopleura sp. contains 37 genes which are on 12 circular mt minichromosomes. Each mt minichromosome is 1.8–2.7 kb long and contains 1–5 genes and one large non-coding region. The gene content and arrangement of mt minichromosomes of Hoplopleura sp. (n = 3) and H. kitti (n = 3) are different from those in H. akanezumi (n = 3). Phylogenetic analyses based on the deduced amino acid sequences of the eight protein-coding genes showed that the Hoplopleura sp. was more closely related to H. akanezumi than to H. kitti, and then they formed a monophyletic group. Conclusions Comparison among the three rat lice revealed variation in the composition of mt minichromosomes within the genus Hoplopleura. Hoplopleura sp. is the first species from the family Hoplopleuridae for which a complete fragmented mt genome has been sequenced. The new data provide useful genetic markers for studying the population genetics, molecular systematics and phylogenetics of blood-sucking lice.

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.

scholarly journals First detection and molecular characterization of kobuvirus from a dog in Turkey

2019 ◽  
Vol 75 (05) ◽  
pp. 6248-2019
Author(s):  
ZEYNEP AKKUTAY-YOLDAR ◽  
TAYLAN KOÇ B. ◽  
ÇIĞDEM OĞUZOĞLU T.
Keyword(s):  
Molecular Characterization ◽  
Rectal Swab ◽  
Clinical Symptoms ◽  
Phylogenetic Analyses ◽  
Amino Acid Sequences ◽  
Coding Region ◽  
Gastrointestinal Infections ◽  
Protein Coding ◽  
Pcr Product ◽  
Domestic Carnivores

Canine kobuvirus (CaKVs) is a newly emerging virus detected in dogs in several countries. However, kobuvirus infection has not yet been described in domestic carnivores in Turkey. In this study, we tested blood and rectal swab samples to determine the presence of kobuvirus in a dog with clinical symptoms by reverse transcription-polymerase chain reaction (RT-PCR), using 3D (RNA polymerase) region primers of canine kobuviruses. To provide molecular characterization data, the Maximum Likelihood (ML) method was used for the phylogenetic analyses. The PCR product of the partial protein-coding region of the 3D protein gene from the rectal swab was amplified, purified, and sequenced. Phylogenetic analysis of amino acid sequences suggests that our CaKV strain was closely related to US-CaKVs,and placed on a monophyletic clade as a sister branch localized in the CaKV cluster. These results indicate that CaKV exists in dogs in Turkey. With a similarity of 94.2–96.1%, it is like other CaKVs. To our knowledge, this is the first report of CaKV infection of a dog by in Turkey. Further studies are needed to determine its role in dog gastrointestinal infections.

scholarly journals Highly rearranged mitochondrial genome in Falcolipeurus lice (Phthiraptera: Philopteridae) from endangered eagles

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Yu Nie ◽  
Yi-Tian Fu ◽  
Yu Zhang ◽  
Yuan-Ping Deng ◽  
Wei Wang ◽  
...  
Keyword(s):  
Phylogenetic Analyses ◽  
Phylogenetic Position ◽  
Gene Rearrangements ◽  
Posterior Probabilities ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
The Family ◽  
Louse Species ◽  
Mt Genome ◽  
Rna Genes

Abstract Background Fragmented mitochondrial (mt) genomes and extensive mt gene rearrangements have been frequently reported from parasitic lice (Insecta: Phthiraptera). However, relatively little is known about the mt genomes from the family Philopteridae, the most species-rich family within the suborder Ischnocera. Methods Herein, we use next-generation sequencing to decode the mt genome of Falcolipeurus suturalis and compare it with the mt genome of F. quadripustulatus. Phylogenetic relationships within the family Philopteridae were inferred from the concatenated 13 protein-coding genes of the two Falcolipeurus lice and members of the family Philopteridae using Bayesian inference (BI) and maximum likelihood (ML) methods. Results The complete mt genome of F. suturalis is a circular, double-stranded DNA molecule 16,659 bp in size that contains 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and three non-coding regions. The gene order of the F. suturalis mt genome is rearranged relative to that of F. quadripustulatus, and is radically different from both other louse species and the putative ancestral insect. Phylogenetic analyses revealed clear genetic distinctiveness between F. suturalis and F. quadripustulatus (Bayesian posterior probabilities = 1.0 and bootstrapping frequencies = 100), and that the genus Falcolipeurus is sister to the genus Ibidoecus (Bayesian posterior probabilities = 1.0 and bootstrapping frequencies = 100). Conclusions These datasets help to better understand gene rearrangements in lice and the phylogenetic position of Falcolipeurus and provide useful genetic markers for systematic studies of bird lice. Graphic abstract

scholarly journals Highly Rearranged Mitochondrial Genome in Falcolipeurus lice (Phthiraptera: Philopteridae) from Endangered Eagles

2021 ◽  
Author(s):  
Yu Nie ◽  
Yi-Tian Fu ◽  
Yu Zhang ◽  
Yuan-Ping Deng ◽  
Ya Tu ◽  
...  
Keyword(s):  
Phylogenetic Analyses ◽  
Phylogenetic Position ◽  
Gene Rearrangements ◽  
Posterior Probabilities ◽  
Genome Sequences ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
The Family ◽  
Mt Genome ◽  
Rna Genes

Abstract Background: Fragmented mitochondrial (mt) genomes and extensive mt gene rearrangements have been frequently reported from parasitic lice (Insecta: Phthiraptera). However, relatively little is available about the mt genomes from the family Philopteridae that is the most species-rich family within the suborder Ischnocera. Methods: Herein, we use next-generation sequencing to decode the mt genome sequences of Falcolipeurus suturalis and compared it with the mt genome sequences of F. quadripustulatus. Phylogenetic relationship of the concatenated amino acid sequence data for 13 protein-coding genes of the two Falcolipeurus lice and selected members of the family Philopteridae was evaluated using Bayesian inference (BI).Results: The complete mt genome of F. suturalis is a circular double-stranded DNA molecule of 16,659 bp, and contains 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes, as well as three putative non-coding regions. The gene order in F. suturalis mt genome was rearranged compared with that of F. quadripustulatus, and they were radical different from other louse species and the ancestral insect. Phylogenetic analyses revealed that the clear genetic distinctiveness between F. suturalis and F. quadripustulatus (Bayesian posterior probabilities=1.0), and the genus Falcolipeurus is more closely related to the genus Ibidoecus than to other genera (Bayesian posterior probabilities=1.0). Conclusions: These novel datasets will help to better understand the gene rearrangements and phylogenetic position of Falcolipeurus and provide useful genetic markers for systematics and phylogenetic studies of bird lice.

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. 

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