Complete mitochondrial genome of the Western Capercaillie Tetrao urogallus (Phasianidae, Tetraoninae)

Zootaxa ◽  
2019 ◽  
Vol 4550 (4) ◽  
pp. 585
Author(s):  
GAËL ALEIX-MATA ◽  
FRANCISCO J. RUIZ-RUANO ◽  
JESÚS M. PÉREZ ◽  
MATHIEU SARASA ◽  
ANTONIO SÁNCHEZ
Keyword(s):  
Mitochondrial Genome ◽  
Control Region ◽  
Sequence Data ◽  
Complete Mitochondrial Genome ◽  
Tetrao Urogallus ◽  
Protein Coding ◽  
Mitogenome Sequence ◽  
Putative Origin ◽  
Fragmented Population ◽  
Galliform Bird

The Western Capercaillie (Tetrao urogallus) is a galliform bird of boreal climax forests from Scandinavia to eastern Siberia, with a fragmented population in southwestern Europe. We extracted the DNA of T. urogallus aquitanicus and obtained the complete mitochondrial genome (mitogenome) sequence by combining Illumina and Sanger sequencing sequence data. The mitochondrial genome of T. urogallus is 16,683 bp long and is very similar to that of Lyrurus tetrix (16,677 bp). The T. urogallus mitogenome contains the normal 13 protein-coding genes (PCGs), 22 transfer RNAs, 2 ribosomal RNAs, and the control region. The number, order, and orientation of the mitochondrial genes are the same as in L. tetrix and in other species of the same and other bird families. The three domains of the control region contained conserved sequences (ETAS; CSBs), boxes (F, E, D, C, B, BS box), the putative origin of replication of the H-strand (OH) and bidirectional promoters of translation (LSP/HSP). 

The mitochondrial genome and phylogenetic analysis of the tick Haemaphysalis qinghaiensis Teng, 1980 (Acari:Ixodidae)

2022 ◽  
Author(s):  
Tianhong Wang ◽  
Zihao Wang ◽  
Ruwei Bai ◽  
Zhijun Yu ◽  
Jingze Liu
Keyword(s):  
Phylogenetic Analysis ◽  
Mitochondrial Genome ◽  
Complete Mitochondrial Genome ◽  
Rrna Genes ◽  
Trna Genes ◽  
Illumina Hiseq ◽  
Protein Coding ◽  
Haemaphysalis Qinghaiensis ◽  
Mitogenome Sequence ◽  
Illumina Hiseq Platform

Haemaphysalis qinghaiensis is an endemic species and mainly inhabiting in the northwestern plateau of China, which can transmit many zoonotic pathogens and cause great harm to animals. In this study, the complete mitochondrial genome (mitogenome) of H. qinghaiensis was assembled through the Illumina HiSeq platform. The mitogenome was 14,533 bp in length, consisting of 13 protein-coding genes (PCGs), 22 tRNA genes, 2 rRNA genes and 3 noncoding regions (NCRs). The bias towards a high A+T content with 77.65% in mitogenome of H. qinghaiensis. The rearrangement of mitochondrial genes in H. qinghaiensis was consistent with other hard ticks. The phylogenetic analysis based on the concatenation of 13 PCGs from 65 tick mitogenomes showed that the H. qinghaiensis was clustered into a well-supported clade within the Haemaphysalis genus. This is the first complete mitogenome sequence of H. qinghaiensis, which provides a useful reference for understanding of the taxonomic and genetics of ticks.

An additional record of Fejervarya manoharani Garg and Biju from the Western Ghats with a description of its complete mitochondrial genome

Zootaxa ◽  
2017 ◽  
Vol 4277 (4) ◽  
pp. 491 ◽  
Author(s):  
S. KUMAR KIRAN ◽  
V. S. ANOOP ◽  
K. C. SIVAKUMAR ◽  
RAGHUNATHAN DINESH ◽  
J. P. MANO ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Control Region ◽  
Complete Mitochondrial Genome ◽  
Gene Organization ◽  
Morphological Data ◽  
12S Rrna ◽  
Trna Genes ◽  
Protein Coding ◽  
Its Gene ◽  
Nd5 Gene

An additional sighting of newly described frog species, Fejervarya manoharani Garg and Biju, outside of the type locality along with their morphological data is reported herewith. We are also providing the whole DNA sequence of the mitochondrial genome with its gene organization as additional data to distinguish this species from its congeners. The mitogenome of F. manoharani was 17,654 bp in length. It contains 38 genes including two rRNAs, 23 tRNAs, 13 protein-coding genes and a control region. Similar to other dicroglossid frogs, a tandem duplication of tRNAMet was found. The ND5 gene was located at the 3' end of the control region like in three other Fejervarya species for which mitogenomic data are available. A rearrangement of four tRNA genes, namely Leucine, Threonine, Proline, and Phenylalanine, between ND5 and 12S rRNA, differing from other Fejervarya species, was also observed. 

scholarly journals Complete mitochondrial genome sequences of the northern spotted owl (Strix occidentalis caurina) and the barred owl (Strix varia; Aves: Strigiformes: Strigidae) confirm the presence of a duplicated control region

2017 ◽  
Author(s):  
Zachary R Hanna ◽  
James B Henderson ◽  
Anna B Sellas ◽  
Jérôme Fuchs ◽  
Rauri C. K. Bowie ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Control Region ◽  
Sequence Data ◽  
Complete Mitochondrial Genome ◽  
Nuclear Genome ◽  
Genome Sequences ◽  
Spotted Owl ◽  
Strix Occidentalis ◽  
Northern Spotted Owl ◽  
Strix Occidentalis Caurina

We report here the successful assembly of the complete mitochondrial genomes of the northern spotted owl (Strix occidentalis caurina) and the barred owl (S. varia). We utilized sequence data from two sequencing methodologies, Illumina paired-end sequence data with insert lengths ranging from approximately 250 nucleotides (nt) to 9,600 nt and read lengths from 100-375 nt and Sanger sequences. We employed multiple assemblers and alignment methods to generate the final assemblies. The circular genomes of S. o. caurina and S. varia are comprised of 19,948 nt and 18,975 nt, respectively. Both code for two rRNAs, twenty-two tRNAs, and thirteen polypeptides. They both have duplicated control region sequences with complex repeat structures. These are the first complete mitochondrial genome sequences of owls (Aves: Strigiformes) possessing duplicated control regions. We searched the nuclear genome of S. o. caurina for copies of mitochondrial genes and found at least nine separate stretches of nuclear copies of gene sequences originating in the mitochondrial genome (Numts).

scholarly journals The complete mitochondrial genome sequence of Oryctes rhinoceros (Coleoptera: Scarabaeidae) based on long-read nanopore sequencing

2020 ◽  
Author(s):  
Igor Filipović ◽  
James P. Hereward ◽  
Gordana Rašić ◽  
Gregor J. Devine ◽  
Michael J. Furlong ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Control Region ◽  
Complete Mitochondrial Genome ◽  
Rrna Genes ◽  
Invasive Pest ◽  
Long Control Region ◽  
Trna Genes ◽  
Oryctes Rhinoceros ◽  
Mitogenome Sequence ◽  
Long Read

AbstractThe coconut rhinoceros beetle (CRB, Oryctes rhinoceros) is a severe and invasive pest of coconut and other palms throughout Asia and the Pacific. The biocontrol agent, Oryctes rhinoceros nudivirus (OrNV), has successfully suppressed O. rhinoceros populations for decades but new CRB invasions started appearing after 2007. A single-SNP variant within the mitochondrial cox1 gene is used to distinguish the recently-invading CRB-G lineage from other haplotypes, but the lack of mitogenome sequence for this species hinders further development of a molecular toolset for biosecurity and management programmes against CRB. Here we report the complete circular sequence and annotation for CRB mitogenome, generated to support such efforts.Sequencing data were generated using long-read Nanopore technology from genomic DNA isolated from a CRB-G female. The mitochondrial genome was assembled with Flye v.2.5, using the short-read Illumina sequences to remove homopolymers with Pilon, and annotated with MITOS. Independently-generated transcriptome data were used to assess the O. rhinoceros mitogenome annotation and transcription. The aligned sequences of 13 protein-coding genes (PCGs) (with degenerate third codon position) from O. rhinoceros, 13 other Scarabaeidae taxa and two outgroup taxa were used for the phylogenetic reconstruction with the Maximum likelihood (ML) approach in IQ-TREE and Bayesian (BI) approach in MrBayes.The complete circular mitochondrial genome of O. rhinoceros is 20,898 bp-long, with a gene content canonical for insects (13 PCGs, 2 rRNA genes, and 22 tRNA genes), as well as one structural variation (rearrangement of trnQ and trnI) and a long control region (6,204 bp). Transcription was detected across all 37 genes, and interestingly, within three domains in the control region. ML and BI phylogenies had the same topology, correctly grouping O. rhinoceros with one other Dynastinae taxon, and recovering the previously reported relationship among lineages in the Scarabaeidae. In silico PCR-RFLP analysis recovered the correct fragment set that is diagnostic for the CRB-G haplogroup. These results validate the high-quality of the CRB mitogenome sequence and annotation.

scholarly journals The phylogeny of the Anderson’s White-bellied Rat (Niviventer andersoni) based on complete mitochondrial genomes provides insight into its evolutionary history

2021 ◽  
Author(s):  
Shujing Liu ◽  
Lili Fu ◽  
Jihua Zhou ◽  
Jizhou Lv ◽  
Zhongyang Tan ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Phylogenetic Analyses ◽  
Complete Mitochondrial Genome ◽  
Gene Tree ◽  
Sister Group ◽  
Protein Coding ◽  
Mitogenome Sequence ◽  
D Loop ◽  
Coding Control ◽  
Rna Genes

Anderson’s White-bellied Rat, Niviventer andersoni (Thomas, 1911) (Muridae, Niviventer) is an species endemic to China. In the present study, we have sequenced the first complete mitochondrial genome of N. andersoni using next-generation sequencing. The 16,291 bp mitochondrial genome consists of 22 transfer RNA genes, 13 protein-coding genes (PCGs), two ribosomal RNA genes, and one non-coding control region (D-Loop). Phylogenetic analyses of the nucleotide sequences of all 13 PCGs, PCGs minus ND6 and the entire mitogenome sequence except for the D-loop, produce nearly identical, well-resolved topologies. Our results support that N. andersoni clustered with N. excelsior and form a sister group with N. confucianus, and they statistically reject the hypothesis from one cytochrome b (cytb) gene tree that N. confucianus is sister to N. fulvescens. Our research may be helpful to further reconsideration of clearer taxonomy and improve our understanding of mitogenomic evolution in the genus Niviventer.

Characterization of Clarias gariepinus mitochondrial genome sequence and a comparative analysis with other catfishes

Biologia ◽  
2015 ◽  
Vol 70 (9) ◽  
pp. 1245-1253
Author(s):  
Chong Han ◽  
Qiang Li ◽  
Junqiu Xu ◽  
Xiufeng Li ◽  
Jianrong Huang
Keyword(s):  
Mitochondrial Genome ◽  
Control Region ◽  
Genome Sequence ◽  
Complete Mitochondrial Genome ◽  
Clarias Gariepinus ◽  
African Catfish ◽  
Protein Coding ◽  
Mitochondrial Genome Sequence ◽  
Complete Mitochondrial Genome Sequence

Abstract Clarias gariepinus is an economically important fish belonging to Siluriformes. In order to understand the characterization of catfishes, the complete mitochondrial genome sequence of the African catfish C. gariepinus was determined using 17 pairs of primers. The complete mitogenome is 16,508 bp in length and contains 37 mitochondrial genes (13 protein-coding, two rRNA, and 22 tRNA genes) and a control region as in most other fishes. Moreover, a comparison of C. gariepinus with Clarias batrachus, Clarias fuscus and Clarias sp. NM-2010 indicated that the four mitogenomics were similar in length, total nucleotide compositions and codon usage patterns, but different in 13 protein-coding genes, control region and other aspects. The complete mitochondrial genome sequence of C. gariepinus would contribute to better understanding of population genetics, conservation, biogeography and evolution of this species.

The complete mitochondrial genome of a tessaratomid bug, Eusthenes cupreus (Hemiptera: Heteroptera: Pentatomomorpha: Tessaratomidae)

Zootaxa ◽  
2013 ◽  
Vol 3620 (2) ◽  
pp. 260-272 ◽  
Author(s):  
WEN SONG ◽  
HU LI ◽  
FAN SONG ◽  
LI LIU ◽  
PEI WANG ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Control Region ◽  
Complete Mitochondrial Genome ◽  
Repetitive Sequences ◽  
Rrna Genes ◽  
Gene Arrangement ◽  
Trna Genes ◽  
Protein Coding ◽  
Simple Loop ◽  
Complete Mitogenome

The 16, 299 bp long mitochondrial genome (mitogenome) of a tessaratomid bug, Eusthenes cupreus (Westwood), is reported and analyzed. The mitogenome represents the first sequenced complete mitogenome of the heteropteran family Tessaratomidae. The mitogenome of E. cuopreus is a typical circular DNA molecule with a total AT content of 74.1%, and contains 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes, and a control region. The gene arrangement is identical with the most common type in insects. Most PCGs start with the typical ATN codon, except that the initiation codon for COI is TTG. All tRNAs possess the typical clover-leaf structure, except tRNASer (AGN), in which the dihydrouridine (DHU) arm forms a simple loop. Six domains with 45 helices and three domains with 27 helices are predicted in the secondary structures of rrnL and rrnS, respectively. The control region is located between rrnS and tRNAIle, including some short microsatellite repeat sequences. In addition, three different repetitive sequences are found in the control region and the tRNAIle-tRNAGln-tRNAMet-ND2 gene cluster. One of the unusual features of this mitogenome is the presence of one tRNAGln-like sequence in the control region. This extra tRNAGln-like sequence is 73 bp long, and the anticodon arm is identical to that of the regular tRNAGln.

scholarly journals Complete mitochondrial genome of Echinophyllia aspera (Scleractinia, Lobophylliidae): Mitogenome characterization and phylogenetic positioning

ZooKeys ◽  
2018 ◽  
Vol 793 ◽  
pp. 1-14
Author(s):  
Wentao Niu ◽  
Shuangen Yu ◽  
Peng Tian ◽  
Jiaguang Xiao
Keyword(s):  
Mitochondrial Genome ◽  
Complete Mitochondrial Genome ◽  
Molecular Data ◽  
Start Codon ◽  
Gene Arrangement ◽  
Protein Coding ◽  
Genome Data ◽  
Mitogenome Sequence ◽  
Complete Mitogenome ◽  
First Time

Lack of mitochondrial genome data of Scleractinia is hampering progress across genetic, systematic, phylogenetic, and evolutionary studies concerning this taxon. Therefore, in this study, the complete mitogenome sequence of the stony coralEchinophylliaaspera(Ellis & Solander, 1786), has been decoded for the first time by next generation sequencing and genome assembly. The assembled mitogenome is 17,697 bp in length, containing 13 protein coding genes (PCGs), two transfer RNAs and two ribosomal RNAs. It has the same gene content and gene arrangement as in other Scleractinia. All genes are encoded on the same strand. Most of the PCGs use ATG as the start codon except for ND2, which uses ATT as the start codon. The A+T content of the mitochondrial genome is 65.92% (25.35% A, 40.57% T, 20.65% G, and 13.43% for C). Bayesian and maximum likelihood phylogenetic analysis have been performed using PCGs, and the result shows thatE.asperaclustered closely withSclerophylliamaxima(Sheppard & Salm, 1988), both of which belong to Lobophylliidae, when compared with species belonging to Merulinidae and other scleractinian taxa used as outgroups. The complete mitogenome ofE.asperaprovides essential and important DNA molecular data for further phylogenetic and evolutionary analyses of corals.

scholarly journals Complete mitochondrial genome sequences of the northern spotted owl (Strix occidentalis caurina) and the barred owl (Strix varia; Aves: Strigiformes: Strigidae) confirm the presence of a duplicated control region

2017 ◽  
Author(s):  
Zachary R Hanna ◽  
James B Henderson ◽  
Anna B Sellas ◽  
Jérôme Fuchs ◽  
Rauri C. K. Bowie ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Control Region ◽  
Sequence Data ◽  
Complete Mitochondrial Genome ◽  
Nuclear Genome ◽  
Genome Sequences ◽  
Spotted Owl ◽  
Strix Occidentalis ◽  
Northern Spotted Owl ◽  
Strix Occidentalis Caurina

We report here the successful assembly of the complete mitochondrial genomes of the northern spotted owl (Strix occidentalis caurina) and the barred owl (S. varia). We utilized sequence data from two sequencing methodologies, Illumina paired-end sequence data with insert lengths ranging from approximately 250 nucleotides (nt) to 9,600 nt and read lengths from 100-375 nt and Sanger sequences. We employed multiple assemblers and alignment methods to generate the final assemblies. The circular genomes of S. o. caurina and S. varia are comprised of 19,948 nt and 18,975 nt, respectively. Both code for two rRNAs, twenty-two tRNAs, and thirteen polypeptides. They both have duplicated control region sequences with complex repeat structures. These are the first complete mitochondrial genome sequences of owls (Aves: Strigiformes) possessing duplicated control regions. We searched the nuclear genome of S. o. caurina for copies of mitochondrial genes and found at least nine separate stretches of nuclear copies of gene sequences originating in the mitochondrial genome (Numts).

Characterization of the complete mitochondrial genome of a coconut crab, Birgus latro (Linnaeus, 1767) (Decapoda: Anomura: Coenobitidae), from Okinawa, Japan

2020 ◽  
Vol 40 (4) ◽  
pp. 390-400 ◽  
Author(s):  
Werner P Veldsman ◽  
Yaqin Wang ◽  
Jiaojiao Niu ◽  
J Antonio Baeza ◽  
Ka Hou Chu
Keyword(s):  
Indian Ocean ◽  
Mitochondrial Genome ◽  
Control Region ◽  
Complete Mitochondrial Genome ◽  
Gc Content ◽  
Gene Families ◽  
Full Description ◽  
Population Divergence ◽  
Protein Coding ◽  
Protein Coding Genes

Abstract We present a full description and analysis of the complete mitochondrial genome of a Pacific Ocean specimen of the coconut crab Birgus latro (Linnaeus, 1767), the largest extant terrestrial arthropod in the world. Our de novo-assembled mitogenome has a massive 16,161 times organelle read coverage, a length of 16,411 bp, contains 22 tDNAs (20 unique), 13 protein-coding genes, two rDNAs, and a putative control region of length 1,381 bp. The control region contains three microsatellites and two pairs of inverted repeats. Contrary to the mitochondrial sentinel gene concept, two-dimensional nucleotide analysis reveals higher GC-content in cox gene families than in nadh gene families. Moreover, cox gene families are more conserved than nadh gene families among the species of Coenobitidae selected for comparison. Secondary structure prediction of the 22 tDNAs shows major deviations from the cloverleaf pattern, which points to a relatively high rate of mutation in these genes. We also present a repertoire of mitochondrial variation between our male Okinawan coconut crab and an Indian Ocean specimen that consists of one insertion, one deletion, 135 SNPs, three MNPs and nine complex polymorphisms. We provide confirmatory evidence that the superfamily Paguroidea, to which the coconut crab belongs, is polyphyletic, that all the protein-coding genes of B. latro are under purifying selection, and that a Pacific versus Indian Ocean coconut crab population divergence occurred during the Pleistocene.

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