scholarly journals The complete mitochondrial genome and description of a new cryptic species of Benedenia Diesing, 1858 (Monogenea: Capsalidae), a major pathogen infecting the yellowtail kingfish Seriola lalandi Valenciennes in the South-East Pacific

2019 ◽  
Vol 12 (1) ◽  
Author(s):  
J. Antonio Baeza ◽  
Fabiola A. Sepúlveda ◽  
M. Teresa González
Keyword(s):  
Mitochondrial Genome ◽  
Ribosomal Rna ◽  
Complete Mitochondrial Genome ◽  
Transfer Rna ◽  
The South ◽  
Protein Coding ◽  
East Pacific ◽  
Yellowtail Kingfish ◽  
Seriola Lalandi ◽  
Rna Genes

Abstract Background The monogenean Benedenia seriolae parasitizes fishes belonging to the genus Seriola, represents a species complex, and causes substantial impact on fish welfare in aquaculture systems worldwide. This study reports, for the first time, the complete mitochondrial genome of B. humboldti n. sp., a new cryptic species from the South-East Pacific (SEP). Methods The mitogenome of B. humboldti n. sp. was assembled from short Illumina 150 bp pair-end reads. The phylogenetic position of B. humboldti n. sp. among other closely related congeneric and confamiliar capsalids was examined using mitochondrial protein-coding genes (PCGs). Morphology of B. humboldti n. sp. was examined based on fixed and stained specimens. Results The AT-rich mitochondrial genome of B. humboldti is 13,455 bp in length and comprises 12 PCGs (atp8 was absent as in other monogenean genomes), 2 ribosomal RNA genes, and 22 transfer RNA genes. All protein-coding, ribosomal RNA, and transfer RNA genes are encoded on the H-strand. The gene order observed in the mitochondrial genome of B. humboldti n. sp. was identical to that of B. seriolae from Japan but different from that of B. seriolae from Australia. The genetic distance between B. humboldti n. sp. and B. seriolae from Japan was high. Minor but reliable differences in the shape of the penis were observed between Benedenia humboldti n. sp. and congeneric species. Conclusions Phylogenetic analyses based on PCGs in association with differences in the shape of the penis permitted us to conclude that the material from the South-East Pacific represents a new species of Benedenia infecting S. lalandi off the coast of Chile. The discovery of this parasite represents the first step to improving our understanding of infestation dynamics and to develop control strategies for this pathogen infecting the farmed yellowtail kingfish, Seriola lalandi, in the South-East Pacific.

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.

scholarly journals The complete mitochondrial genome of Dermacentor (Indocentor) auratus (Acari, Ixodidae)

Parasite ◽  
2021 ◽  
Vol 28 ◽  
pp. 6
Author(s):  
Jean-Marc Chavatte ◽  
Sophie Octavia
Keyword(s):  
Mitochondrial Genome ◽  
Ribosomal Rna ◽  
Complete Mitochondrial Genome ◽  
Illumina Miseq ◽  
Mitochondrial Genomes ◽  
Protein Coding ◽  
Veterinary Importance ◽  
Long Range Pcr ◽  
Coding Control ◽  
Rna Genes

Dermacentor (Indocentor) auratus Supino, 1897 is a prominent ixodid vector of numerous pathogens of public health and veterinary importance. Using long-range PCR of two overlapping regions sequenced on an Illumina MiSeq machine, the complete mitochondrial genome of D. auratus is reported here. The resulting contigs were able to be assembled into a complete and circularised genome which had the general organisation of the mitochondrial genomes of the Metastriates. It had a total length of 14,766 bp and contained 37 genes, including 13 protein-coding genes, 22 transfer RNA genes, and 2 ribosomal RNA genes, as well as 2 non-coding control regions and 3 tick-boxes. The phylogenetic analysis on the whole mitogenome confirmed the position of D. auratus within the Dermacentor clade.

First complete mitochondrial genome of Rhodinia species (Lepidoptera: Saturniidae): genome description and phylogenetic implication

2021 ◽  
pp. 1-10
Author(s):  
Dong-Bin Chen ◽  
Ru-Song Zhang ◽  
Xiang-Dong Jin ◽  
Jian Yang ◽  
Peng Li ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Ribosomal Rna ◽  
Complete Mitochondrial Genome ◽  
Repeat Sequence ◽  
Rich Region ◽  
Protein Coding ◽  
Repeat Elements ◽  
The Family ◽  
Circular Molecule ◽  
Rna Genes

Abstract To explore the characteristics of the mitochondrial genome (mitogenome) of the squeaking silkmoths Rhodinia, a genus of wild silkmoths in the family Saturniidae of Lepidoptera, and reveal phylogenetic relationships, the mitogenome of Rhodinia fugax Butler was determined. This wild silkmoth spins a green cocoon that has potential significance in sericulture, and exhibits a unique feature that its larvae can squeak loudly when touched. The mitogenome of R. fugax is a circular molecule of 15,334 bp long and comprises 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes, and an A + T-rich region, consistent with previous observations of Saturniidae species. The 370-bp A + T-rich region of R. fugax contains no tandem repeat elements and harbors several features common to the Bombycidea insects, but microsatellite AT repeat sequence preceded by the ATTTA motif is not present. Mitogenome-based phylogenetic analysis shows that R. fugax belongs to Attacini, instead of Saturniini. This study presents the first mitogenome for Rhodinia genus.

scholarly journals The first complete mitochondrial genome of marigold pest thrips,Neohydatothrips samayunkur(Sericothripinae) and comparative analysis

2018 ◽  
Author(s):  
Vikas Kumar ◽  
Kaomud Tyagi ◽  
Shantanu Kundu ◽  
Rajasree Chakraborty ◽  
Devkant Singha ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Ribosomal Rna ◽  
Complete Mitochondrial Genome ◽  
Hierarchical Level ◽  
Evolutionary Relationships ◽  
Protein Coding ◽  
Intergenic Spacers ◽  
Protein Coding Genes ◽  
Scirtothrips Dorsalis ◽  
Rna Genes

AbstractThe complete mitogenomes in order Thysanoptera is limited to subfamily Thripinae heretofore. In the present study, we sequenced the first mitochondrial genome ofNeohydatothrips samayunkur(15,295 bp), a member of subfamily Sericothripinae. The genome was characterized by 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), two ribosomal RNA genes (rRNAs) and three control regions (CRs). This mitogenome had two overlapping regions of 4 bp and twenty four intergenic spacers accounting for 165 bp. All the tRNA had typical cloverleaf secondary structures, except fortrnV and trnSwhich lacked DHU stem and loop. The mitogenomes ofN. samayunkurwas highly rearranged with many unique features as compared to other thrips mitogenomes,atp6andnad1were terminated with TAG and TGA stop codons respectively; location oftrnL2,trnA,trnC, andtrnVwas rearranged; and the first control region (CR1) was upstream ofnad6.The phylogenetic analysis of 13 PCGs implementing maximum likelihood and Bayesian inference showed the clustering ofN. samayunkurwithScirtothrips dorsalissupporting theScirtothripsgenus-group and Sericothripinae morphology based relationships. Generation of more mitogenomes from different hierarchical level in the order Thysanoptera is required to understand the gene rearrangements, phylogeny and evolutionary relationships.

scholarly journals The Complete Mitochondrial Genome of endemic giant tarantula, Lyrognathus crotalus (Araneae: Theraphosidae) and comparative analysis

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Vikas Kumar ◽  
Kaomud Tyagi ◽  
Rajasree Chakraborty ◽  
Priya Prasad ◽  
Shantanu Kundu ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Complete Mitochondrial Genome ◽  
Start Codon ◽  
Gene Arrangement ◽  
Sister Relationship ◽  
Protein Coding ◽  
Relationship Of ◽  
Rna Genes ◽  
Boundary Mapping ◽  
Cloverleaf Structure

AbstractThe complete mitochondrial genome of Lyrognathus crotalus is sequenced, annotated and compared with other spider mitogenomes. It is 13,865 bp long and featured by 22 transfer RNA genes (tRNAs), and two ribosomal RNA genes (rRNAs), 13 protein-coding genes (PCGs), and a control region (CR). Most of the PCGs used ATN start codon except cox3, and nad4 with TTG. Comparative studies indicated the use of TTG, TTA, TTT, GTG, CTG, CTA as start codons by few PCGs. Most of the tRNAs were truncated and do not fold into the typical cloverleaf structure. Further, the motif (CATATA) was detected in CR of nine species including L. crotalus. The gene arrangement of L. crotalus compared with ancestral arthropod showed the transposition of five tRNAs and one tandem duplication random loss (TDRL) event. Five plesiomophic gene blocks (A-E) were identified, of which, four (A, B, D, E) retained in all taxa except family Salticidae. However, block C was retained in Mygalomorphae and two families of Araneomorphae (Hypochilidae and Pholcidae). Out of 146 derived gene boundaries in all taxa, 15 synapomorphic gene boundaries were identified. TreeREx analysis also revealed the transposition of trnI, which makes three derived boundaries and congruent with the result of the gene boundary mapping. Maximum likelihood and Bayesian inference showed similar topologies and congruent with morphology, and previously reported multi-gene phylogeny. However, the Gene-Order based phylogeny showed sister relationship of L. crotalus with two Araneomorphae family members (Hypochilidae and Pholcidae) and other Mygalomorphae species.

The complete mitochondrial genome of the jumping grasshopper Sinopodisma pieli (Orthoptera: Acrididae) and the phylogenetic analysis of Melanoplinae

Zootaxa ◽  
2017 ◽  
Vol 4363 (4) ◽  
pp. 506
Author(s):  
HUAXUAN LIU ◽  
LIYUN YAN ◽  
GUOFANG JIANG
Keyword(s):  
Phylogenetic Analysis ◽  
Mitochondrial Genome ◽  
Ribosomal Rna ◽  
Complete Mitochondrial Genome ◽  
Taxonomic Status ◽  
Polymerase Chain Reaction Method ◽  
Ribosomal Rna Genes ◽  
Start Codon ◽  
Trna Genes ◽  
Rna Genes

In this study, we reported the complete mitochondrial genome (mitogenome) of Sinopodisma pieli by polymerase chain reaction method for the first time, the type species of the genus Sinopodisma. Its mitogenome was a circular DNA molecule of 15,625 bp in length, with 76.0% A+T, and contained 13 protein-coding genes, 22 transfer RNA genes and two ribosomal RNA genes and one A+T control region. The overall base composition of the S. pieli mitogenome was 42.8% for A, 33.2% for T, 13.5% for C, and 10.5% for G, respectively. All 13 mitochondrial PCGs shared the start codon ATN. Twelve of the PCGs ended with termination codon TAA and TAG, while cytochrome coxidase subunit 1 (COI) utilized an incomplete T as terminator codon. All tRNA genes could be folded into the typical cloverleaf secondary structure, except trnS(AGN) lacking of dihydrouridine arm. The sizes of the large and small ribosomal RNA genes were 1379 bp and 794 bp, respectively. The A+T rich region was 798 bp in length and contained 88.5% AT content. A phylogenetic analysis based on 13 PCGs by using Bayesian inference (BI) and maximum likelihood (ML) revealed that Sinopodisma is not monophyletic group. We think that the name and taxonomic status of S. tsinlingensis are right, and it should not be moved into the genus Pedopodisma. These data will provide important information for a better understanding of the population genetics and species identification for Sinopodisma. 

The mitochondrial genome of Leuctra sp. (Plecoptera: Leuctridae) and its performance in phylogenetic analyses

Zootaxa ◽  
2019 ◽  
Vol 4671 (4) ◽  
pp. 571-580 ◽  
Author(s):  
YUE SHEN ◽  
YU-ZHOU DU
Keyword(s):  
Mitochondrial Genome ◽  
Phylogenetic Analyses ◽  
Complete Mitochondrial Genome ◽  
Mitochondrial Gene ◽  
Gene Arrangement ◽  
Likelihood Methods ◽  
Protein Coding ◽  
Maximum Likelihood Methods ◽  
Rna Genes ◽  
Drosophila Yakuba

The nearly complete mitochondrial genome (mitogenome) of Leuctra sp. (Plecoptera: Leuctridae) was sequenced. The 14,585-bp long mitogenome of L. sp. contained 37 genes including 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), two ribosomal RNA genes (rRNAs), and a control region (CR). The mitochondrial gene arrangement of L. sp. was identical with other stoneflies and the putative ancestral mitogenome of Drosophila yakuba Burla. Most PCGs used standard ATN start codons and TAN termination codons. Twenty-one of the 22 tRNAs in each mitogenome exhibited the cloverleaf secondary structures, while the dihydrouridine (DHU) arm of trnSer (AGN) was reduced. Phylogenetic analyses using our new Leuctra sp. genome and all other publicly available genomes for Plecoptera and Bayesian inference (BI) and maximum likelihood methods (ML) generated identical topologies, both supporting the monophyly of all stonefly families for which tests were possible and the infraorder Systellognatha. Scopuridae and Gripopterygidae were grouped with the infraorder Euholognatha. The final relationships within Plecoptera were recovered as (((((Perlodidae + Chloroperlidae) + Perlidae) + Pteronarcyidae) + Peltoperlidae) + Styloperlidae) + (((((Capniidae + Taeniopterygidae) + Nemouridae) + Scopuridae) + Leuctridae) + Gripopterygidae). 

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 Flavoperla biocellata Chu, 1929 (Plecoptera: Perlidae) and the phylogenetic analyses of Plecoptera

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e8762
Author(s):  
Yue Shen ◽  
Yu-Zhou Du
Keyword(s):  
Mitochondrial Genome ◽  
Northern Hemisphere ◽  
Phylogenetic Analyses ◽  
Complete Mitochondrial Genome ◽  
Gene Arrangement ◽  
Trna Genes ◽  
Protein Coding ◽  
The Family ◽  
Maximum Likelihood Methods ◽  
Rna Genes

Of the roughly 400 species of Perlidae in the world, most species are widely distributed in the northern hemisphere, but a few can be found in South Africa and South America. There are only five species in the genus Flavoperla of the family Perlidae in China. To gain a better understanding of the architecture and evolution of mitochondrial genome in Flavoperla, the entire mitochondrial genome (mitogenome) of a Chinese Flavoperla biocellata Chu, 1929 from family Perlidae (Insecta: Plecoptera) was sequenced. The 15,805-bp long mitochondrial genome of F. biocellata contained 37 genes, including 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), two ribosomal RNA genes (rRNAs) and a putative control region (CR). The gene arrangement of F. biocellata was identical with that of other stoneflies and with the fly Drosophila yakuba. Most PCGs of F. biocellata used the standard ATN start codons and complete TAN termination codons. Twenty-one of the 22 tRNA genes exhibited cloverleaf secondary structures, but the dihydrouridine (DHU) arm of trnSer (AGN) was completely reduced. Phylogenetic analyses with both Bayesian inference (BI) and maximum likelihood methods (ML) generated similar topology, both supporting the monophyly of all stonefly families and the infraorder Systellognatha. The phylogenetic analysis based on mitochondrial genomic data from 30 stonefly species recovered a well-supported tree resolving higher-level relationships within Plecoptera. The northern hemisphere suborder Arctoperlaria divided into two groups, Euholognatha and Systellognatha. The southern hemisphere suborder Antarctoperlaria formed two clades: Eustheniidae+Diamphipnoidae and Austroperlidae+ Gripopterygidae; consistent with relationships proposed based on morphology. The final relationships within Plecoptera were recovered as (((Perlidae+(Perlodidae+Chloroperlidae))+(Pteronarcyidae+(Peltoperlidae+Styloperlidae))) +(Taeniopterygidae+(Capniidae+(Nemouridae+Notonemouridae))))+ (Gripopterygoidae+Eusthenioidae).

scholarly journals Characterization and comparative analysis of the complete mitochondrial genome of Azygia hwangtsiyui Tsin, 1933 (Digenea), the first for a member of the family Azygiidae

ZooKeys ◽  
2020 ◽  
Vol 945 ◽  
pp. 1-16
Author(s):  
Yuan-An Wu ◽  
Jin-Wei Gao ◽  
Xiao-Fei Cheng ◽  
Min Xie ◽  
Xi-Ping Yuan ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Complete Mitochondrial Genome ◽  
Nucleotide Composition ◽  
Amino Acid Sequences ◽  
Phylogenetic Study ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
The Family ◽  
Close Relationship ◽  
Rna Genes

Azygia hwangtsiyui (Trematoda, Azygiidae), a neglected parasite of predatory fishes, is little-known in terms of its molecular epidemiology, population ecology and phylogenetic study. In the present study, the complete mitochondrial genome of A. hwangtsiyui was sequenced and characterized: it is a 13,973 bp circular DNA molecule and encodes 36 genes (12 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes) as well as two non-coding regions. The A+T content of the A. hwangtsiyui mitogenome is 59.6% and displays a remarkable bias in nucleotide composition with a negative AT skew (–0.437) and a positive GC skew (0.408). Phylogenetic analysis based on concatenated amino acid sequences of twelve protein-coding genes reveals that A. hwangtsiyui is placed in a separate clade, suggesting that it has no close relationship with any other trematode family. This is the first characterization of the A. hwangtsiyui mitogenome, and the first reported mitogenome of the family Azygiidae. These novel datasets of the A. hwangtsiyui mt genome represent a meaningful resource for the development of mitochondrial markers for the identification, diagnostics, taxonomy, homology and phylogenetic relationships of trematodes.

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