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.

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.

Complete mitogenome of Parum colligata (Lepidoptera: Sphingidae) and its phylogenetic position within the Sphingidae

Zootaxa ◽  
2019 ◽  
Vol 4652 (1) ◽  
pp. 126-134 ◽  
Author(s):  
JUN LI ◽  
KUNJIE HU ◽  
YAQI ZHAO ◽  
RUIRUI LIN ◽  
YAOYAO ZHANG ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
Ribosomal Rna ◽  
Phylogenetic Analyses ◽  
Transfer Rna ◽  
Phylogenetic Position ◽  
Rich Region ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Complete Mitogenome ◽  
Rna Genes

In this study, the complete mitochondrial DNA sequence of Parum colligata (Lepidoptera: Sphingidae: Smerinthinae) was sequenced firstly. The mitogenome is 15,288 bp in size, containing 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), two ribosomal RNA genes (rRNAs), and an A+T-rich region. In the mitogenome, Ile, Leu2, and Phe are the most frequently used codon families, while codons GCG, TGC, GGC, CTG, AGG, and ACG are absent. The A+T-rich region is 358 bp in length including a motif ‘ATAGA’, an 18 bp poly-T stretch, three copies of a 12 bp ‘TATATATATATA’, and a short poly-A element. The nucleotides sequence of A+T-rich region is closer to Sphinginae than Macroglossinae. Phylogenetic analyses, based on the PCGs by using Maximum Likelihood (ML) and Bayesian Inference (BI) methods, generated consistent results that Smerinthinae was clustered together with Sphinginae to be the sister groups rather than Macroglossinae. 

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.

The complete mitochondrial genome of Pseudanoplocephala crawfordi and a comparison with closely related cestode species

2015 ◽  
Vol 90 (5) ◽  
pp. 588-595 ◽  
Author(s):  
G.H. Zhao ◽  
H.B. Wang ◽  
Y.Q. Jia ◽  
W. Zhao ◽  
X.F. Hu ◽  
...  
Keyword(s):  
Complete Mitochondrial Genome ◽  
Taxonomic Status ◽  
Amino Acid Sequences ◽  
Health Concern ◽  
Phylogenetic Position ◽  
Protein Coding ◽  
Economic Significance ◽  
The Family ◽  
Mt Genome ◽  
Rna Genes

AbstractPseudanoplocephala crawfordi is an important zoonotic cestode of economic significance and public health concern. In spite of its significance as a pathogen, the systematics, genetics, epidemiology and biology of this parasite remain poorly understood. In the present study, we sequenced and characterized the complete mitochondrial (mt) genome of P. crawfordi, which is 14,192 bp long and encodes 36 genes, including 12 protein-coding genes, 22 transfer RNA genes and two ribosomal RNA genes. Phylogenetic analysis of the concatenated amino acid sequences using the Bayesian inference (BI) method showed that P. crawfordi was closely related to the family Hymenolepididae. Considering that the taxonomic status of P. crawfordi has been controversial when based only on morphological features, the mt genome obtained here will provide novel molecular markers to ascertain the phylogenetic position of this parasite accurately.

The complete mitochondrial genome of Orthocoelium streptocoelium (Digenea: Paramphistomidae) for comparison with other digeneans

2016 ◽  
Vol 91 (2) ◽  
pp. 255-261 ◽  
Author(s):  
Y.Y. Zhao ◽  
X. Yang ◽  
H.M. Chen ◽  
L.X. Wang ◽  
H.L. Feng ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Phylogenetic Analyses ◽  
Complete Mitochondrial Genome ◽  
Small Ruminants ◽  
Amino Acid Sequences ◽  
Population Variation ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Mt Genome ◽  
Rna Genes

AbstractOrthocoelium streptocoelium is a common paramphistome species parasitizing the rumen and/or reticulum of small ruminants, leading to significant losses. This study first determined the complete mitochondrial (mt) genome of O. streptocoelium. The complete mt genome of O. streptocoelium was amplified, sequenced, assembled, analysed and then compared with those of other digeneans. The entire mt genome of O. streptocoelium is 13,800 bp in length, which is smaller than those of other digeneans except for Opisthorchis viverrini. This mt genome contains 12 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes and two non-coding regions. The arrangement of the O. streptocoelium mt genome is the same as those of other digeneans except for Schistosoma haematobium and Schistosoma spindale. Phylogenetic analyses based on concatenated amino acid sequences of the 12 protein-coding genes representing 16 digeneans were conducted to assess the relationship of O. streptocoelium with other digeneans. The result indicated that O. streptocoelium is closely related to Paramphistomum cervi and Fischoederius elongates, which is in accordance with their relationships by taxonomy. This complete mt genome of O. streptocoelium enriched the mitochondrial genome data of paramphistomes and provided important molecular markers for diagnostics and studies of population variation, epidemiology, ecology and evolution of O. streptocoelium and other digeneans.

scholarly journals Phylogenetic relationships and taxonomic position of genus Hyperacrius (Rodentia: Arvicolinae) from Kashmir based on evidences from analysis of mitochondrial genome and study of skull morphology

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e10364
Author(s):  
Natalia I. Abramson ◽  
Fedor N. Golenishchev ◽  
Semen Yu. Bodrov ◽  
Olga V. Bondareva ◽  
Evgeny A. Genelt-Yanovskiy ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
De Novo ◽  
Phylogenetic Analyses ◽  
Complete Mitochondrial Genome ◽  
Morphological Characters ◽  
Molecular Data ◽  
Phylogenetic Position ◽  
Skull Morphology ◽  
Protein Coding ◽  
Protein Coding Genes

In this article, we present the nearly complete mitochondrial genome of the Subalpine Kashmir vole Hyperacrius fertilis (Arvicolinae, Cricetidae, Rodentia), assembled using data from Illumina next-generation sequencing (NGS) of the DNA from a century-old museum specimen. De novo assembly consisted of 16,341 bp and included all mitogenome protein-coding genes as well as 12S and 16S RNAs, tRNAs and D-loop. Using the alignment of protein-coding genes of 14 previously published Arvicolini tribe mitogenomes, seven Clethrionomyini mitogenomes, and also Ondatra and Dicrostonyx outgroups, we conducted phylogenetic reconstructions based on a dataset of 13 protein-coding genes (PCGs) under maximum likelihood and Bayesian inference. Phylogenetic analyses robustly supported the phylogenetic position of this species within the tribe Arvicolini. Among the Arvicolini, Hyperacrius represents one of the early-diverged lineages. This result of phylogenetic analysis altered the conventional view on phylogenetic relatedness between Hyperacrius and Alticola and prompted the revision of morphological characters underlying the former assumption. Morphological analysis performed here confirmed molecular data and provided additional evidence for taxonomic replacement of the genus Hyperacrius from the tribe Clethrionomyini to the tribe Arvicolini.

scholarly journals Phylogenetic placement of Paratrichaptum and reconsideration of Gloeophyllales

2020 ◽  
Vol 5 (1) ◽  
pp. 119-130 ◽  
Author(s):  
C.-C. Chen ◽  
B. Cao ◽  
T. Hattori ◽  
B.-K. Cui ◽  
C.-Y. Chen ◽  
...  
Keyword(s):  
Phylogenetic Analyses ◽  
Strong Support ◽  
Brown Rot ◽  
Phylogenetic Position ◽  
Nuclear Rdna ◽  
Protein Coding ◽  
Phylogenetic Placement ◽  
The Family ◽  
Ancestral States ◽  
Relic Species

Paratrichaptum accuratum is a large conspicuous polypore fungus growing on dead or living angiosperm trees in subtropical-boreal areas of China, Indonesia, Japan, and Taiwan. The present study places P. accuratum in the family Gloeophyllaceae that belongs to the order Gloeophyllales within Agaricomycetes (Basidiomycota), based on evidence derived from morphological and ecological characteristics, and phylogenetic analyses of sequences of nuclear rDNA regions (5.8S, nuc 18S, nuc 28S) and protein-coding genes (rpb1, rpb2, and tef1). The analyses presented in this study also give strong support for including Jaapia in Gloeophyllaceae and Gloeophyllales. Thus, the names Jaapiaceae and Jaapiales are considered here as synonyms of Gloeophyllaceae and Gloeophyllales. Since Paratrichaptum represents the earliest diverging lineage in Gloeophyllales, pileate basidiocarps and brown rot appear to be ancestral states of Gloeophyllales. Paratrichaptum accuratum may represent a relic species, according to its phylogenetic position, peculiar distribution pattern and rare occurrence.

Mitochondrial DNA dataset suggest that the genus Sphaerirostris Golvan, 1956 is a synonym of the genus Centrorhynchus Lühe, 1911

Parasitology ◽  
2020 ◽  
Vol 147 (10) ◽  
pp. 1149-1157 ◽  
Author(s):  
Nehaz Muhammad ◽  
Suleman ◽  
Munawar Saleem Ahmad ◽  
Liang Li ◽  
Qing Zhao ◽  
...  
Keyword(s):  
Phylogenetic Analyses ◽  
Systematic Position ◽  
Likelihood Methods ◽  
Sister Relationship ◽  
Protein Coding ◽  
Maximum Likelihood Methods ◽  
Relationship Of ◽  
First Time ◽  
Mt Genome ◽  
Rna Genes

AbstractOur present genetic data of Acanthocephala, especially the mitochondrial (mt) genomes, remains very limited. In the present study, the nearly complete mt genome sequences of Sphaerirostris lanceoides (Petrochenko, 1949) was sequenced and determined for the first time based on specimens collected from the Indian pond heron Ardeola grayii (Sykes) (Ciconiiformes: Ardeidae) in Pakistan. The mt genome of S. lanceoides is 13 478 bp in size and contains 36 genes, including 12 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs) and two ribosomal RNA genes (rRNAs). Moreover, in order to clarify the phylogenetic relationship of the genera Centrorhynchus and Sphaerirostris, and to test the systematic position of S. lanceoides in the Centrorhynchidae, the phylogenetic analyses were performed using Bayesian inference and maximum likelihood methods, based on concatenated nucleotide sequences of 12 PCGs, rRNAs and tRNAs. The phylogenetic results further confirmed the monophyly of the order Polymorphida and the paraphyly of the order Echinorhynchida in the class Palaeacanthocephala. Our results also challenged the validity of the genus Sphaerirostris (Polymorphida: Centrorhynchidae) and showed a sister relationship between S. lanceoides and S. picae (Rudolphi, 1819).

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