scholarly journals The complete mitochondrial genome of Corydoras nattereri (Callichthyidae: Corydoradinae)

2016 ◽  
Vol 14 (1) ◽  
Author(s):  
Daniel A. Moreira ◽  
Paulo A. Buckup ◽  
Marcelo R. Britto ◽  
Maithê G. P. Magalhães ◽  
Paula C. C. de Andrade ◽  
...  
Keyword(s):  
Complete Mitochondrial Genome ◽  
Rrna Genes ◽  
Southeastern Brazil ◽  
Trna Genes ◽  
Protein Coding ◽  
Atpase Subunit ◽  
C Subunit ◽  
D Loop ◽  
Mitochondrial Transcripts ◽  
Complete Mitogenome

ABSTRACT The complete mitogenome of Corydoras nattereri , a species of mailed catfishes from southeastern Brazil, was reconstructed using next-generation sequencing techniques. The mitogenome was assembled using mitochondrial transcripts from the liver transcriptomes of three individuals, and produced a circular DNA sequence of 16,557 nucleotides encoding 22 tRNA genes, two rRNA genes, 13 protein-coding genes and two noncoding control regions (D-loop, OrigL). Phylogeographic analysis of closely related sequences of Cytochrome Oxydase C subunit I (COI) demonstrates high diversity among morphologically similar populations of C. nattereri . Corydoras nattereri is nested within a complex of populations currently assigned to C. paleatus and C. ehrhardti . Analysis of mitogenome structure demonstrated that an insertion of 21 nucleotides between the ATPase subunit-6 and COIII genes may represent a phylogenetically informative character associated with the evolution of the Corydoradinae.

scholarly journals The complete mitochondrial genome and phylogeny of the green chromide, Etroplus suratensis (Bloch, 1790) from Vembanad Lake, Kerala, south India

2019 ◽  
Vol 66 (3) ◽  
Author(s):  
Wilson Sebastian ◽  
Sandhya Sukumaran ◽  
Gopalakrishnan A
Keyword(s):  
Complete Mitochondrial Genome ◽  
12S Rrna ◽  
Trna Genes ◽  
Sri Lankan ◽  
Protein Coding ◽  
Cichlid Species ◽  
Etroplus Suratensis ◽  
D Loop ◽  
Complete Mitogenome ◽  
Coding Control

The green chromide Etroplus suratensis (Bloch, 1790), is a cichlid species which forms an economically valuable food fish and a preferred candidate for brackishwater aquaculture in India. The complete mitogenome of E. suratensis collected from Vembanad Lake, Kerala, India has been characterised in the present study. The entire mitogenome was PCR amplified as contiguous, overlapping segments and sequenced. The assembled mitogenome of E. suratensis is 16456 bp circle, contained the 37 mitochondrial structural genes, two ribosomal RNA genes (12S rRNA and 16S rRNA), 22 transfer RNA (tRNA) genes, 13 protein-coding genes and 1 non-coding control region/D-loop, with the gene order identical to vertebrates. In the phylogenetic analysis, E. suratensis is clustered with other Indo-Sri Lankan taxa. Among cichlids, the groups from South America and Africa are monophyletic in origin. The mitogenomic information generated in this study will be valuable for further studies on evolution, taxonomy, conservation, environmental adaptation and selective breeding of this species having aquaculture, ornamental and evolutionary importance.

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.

Comparative analysis the variability of a complete mitochondrial genome of polledness intersexual goat (PIS- -) from China

2015 ◽  
Author(s):  
GuangXin E ◽  
Yong-Fu Huang ◽  
Yong-Ju Zhao ◽  
Ri-Su Na ◽  
Zhong-Quan Zhao ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Complete Mitochondrial Genome ◽  
Reproductive Function ◽  
Reproductive Organs ◽  
Rrna Genes ◽  
Capra Hircus ◽  
Trna Genes ◽  
Protein Coding ◽  
Indigenous Breed ◽  
Complete Mitogenome

The polledness intersexual goat (PIS- -) (Capra hircus), deformed individuals, could have malformed reproductive organs and loss of reproductive function. Here, we first determined the complete mitochondrial genome of Chinese native polledness intersexual goat (PIS- -) is 16,640 nt in length, consisting of 13 protein-coding genes, 22 transfer RNA (tRNA) genes, 2 ribosomal RNA (rRNA) genes and a non-coding control region. As in other mammals and intrastrains, most mitochondrial genes are encoded on the heavy strand, except for ND6 and eight tRNA genes, which are encoded on the light strand. Its overall base composition is A: 33.5%, T: 27.3%, C: 26.1% and G: 13.1%. The complete mitogenome of the Chinese indigenous breed of goat could provide a basic data for further understanding the contribution of mitochondria in the sex-developmental mechanism, tissue and organ cell deformity of polledness intersexual goat via genomic compare.

scholarly journals The First Complete Mitochondrial Genome of Lachninae Species and Comparative Genomics Provide New Insights into the Evolution of Gene Rearrangement and the Repeat Region

Insects ◽  
2021 ◽  
Vol 12 (1) ◽  
pp. 55
Author(s):  
Hui Zhang ◽  
Qian Liu ◽  
Congcong Lu ◽  
Jun Deng ◽  
Xiaolei Huang
Keyword(s):  
Complete Mitochondrial Genome ◽  
Rrna Genes ◽  
Trna Genes ◽  
Repeat Region ◽  
Protein Coding ◽  
Research Fields ◽  
Tandem Repeat Region ◽  
Complete Mitogenome ◽  
Evolutionary Lineages ◽  
Complete Mitochondrial Genomes

Complete mitochondrial genomes are valuable resources for different research fields such as genomics, molecular evolution and phylogenetics. The subfamily Lachninae represents one of the most ancient evolutionary lineages of aphids. To date, however, no complete Lachninae mitogenome is available in public databases. Here we report the Stomaphis sinisalicis mitogenome, representing the first complete mitogenome of Lachninae. The S. sinisalicis mitogenome is consist of 13 protein-coding genes (PCGs), two rRNA genes (rRNAs), 22 tRNA genes (tRNAs), a control region and a large tandem repeat region. Strikingly, the mitogenome exhibits a novel, highly rearranged gene order between trnE and nad1 compared with that of other aphids. The presence of repeat region in the basal Lachninae may further indicate it is probably an ancestral feature of aphid mitogenomes. Collectively, this study provides new insights on mitogenome evolution and valuable data for future comparative studies across different insect lineages.

scholarly journals Complete mitochondrial genome sequence of Lepus yarkandensis Günther, 1875 (Lagomorpha, Leporidae): characterization and phylogenetic analysis

ZooKeys ◽  
2021 ◽  
Vol 1012 ◽  
pp. 135-150
Author(s):  
Wenjuan Shan ◽  
Mayinur Tursun ◽  
Shiyu Zhou ◽  
Yucong Zhang ◽  
Huiying Dai
Keyword(s):  
Control Region ◽  
Complete Mitochondrial Genome ◽  
Genetic Research ◽  
Rrna Genes ◽  
Trna Genes ◽  
Protein Coding ◽  
Conserved Sequence ◽  
Associated Sequences ◽  
Complete Mitogenome ◽  
Hot Environments

Lepus yarkandensis is a national second-class protected animal endemic to China and distributed only in the hot and arid Tarim Basin in Xinjiang. We sequenced and described the complete mitogenome of L. yarkandensis to analyze its characteristics and phylogeny. The species’ DNA is a 17,047 bp circular molecule that includes 13 protein-coding genes (PCGs), two rRNA genes, 22 tRNA genes, and one control region. The overall base composition was as follows: A, 31.50%; T, 29.40%; G, 13.30% and C, 25.80%, with a high A+T bias of 60.9%. In the PCGs, ND6 had deviation ranges for AT skew (–0.303) and GC skew (0.636). The Ka/Ks values of ND1 (1.067) and ND6 (1.352) genes were >1, indicating positive selection, which might play an important role in the adaptation of L. yarkandensis to arid and hot environments. The conserved sequence block, the central conserved domain, and the extended termination-associated sequences of the control region and their features were identified and described. The phylogenetic tree based on the complete mitogenome showed that L. yarkandensis was closely related to the sympatric Lepus tibetanus pamirensis. These novel datasets of L. yarkandensis can supply basic data for phylogenetic studies of Lepus spp., apart from providing essential and important resource for further genetic research and the protection of this species.

scholarly journals The mitochondrial genome of Dipetalonema gracile from a squirrel monkey in China

2018 ◽  
Vol 94 ◽  
Author(s):  
P. Zhang ◽  
R.K. Ran ◽  
A.Y. Abdullahi ◽  
X.L. Shi ◽  
Y. Huang ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Squirrel Monkey ◽  
Complete Mitochondrial Genome ◽  
Mitochondrial Gene ◽  
Rrna Genes ◽  
Saimiri Sciureus ◽  
Trna Genes ◽  
Loop Structure ◽  
Protein Coding ◽  
Protein Coding Genes

AbstractDipetalonema gracile is a common parasite in squirrel monkeys (Saimiri sciureus), which can cause malnutrition and progressive wasting of the host, and lead to death in the case of massive infection. This study aimed to identify a suspected D. gracile worm from a dead squirrel monkey by means of molecular biology, and to amplify its complete mitochondrial genome by polymerase chain reaction (PCR) and sequence analysis. The results identified the worm as D. gracile, and the full length of its complete mitochondrial genome was 13,584 bp, which contained 22 tRNA genes, 12 protein-coding genes, two rRNA genes, one AT-rich region and one small non-coding region. The nucleotide composition included A (16.89%), G (20.19%), T (56.22%) and C (6.70%), among which A + T = 73.11%. The 12 protein-coding genes used TTG and ATT as start codons, and TAG and TAA as stop codons. Among the 22 tRNA genes, only trnS1AGN and trnS2UCN exhibited the TΨC-loop structure, while the other 20 tRNAs showed the TV-loop structure. The rrnL (986 bp) and rrnS (685 bp) genes were single-stranded and conserved in secondary structure. This study has enriched the mitochondrial gene database of Dipetalonema and laid a scientific basis for further study on classification, and genetic and evolutionary relationships of Dipetalonema nematodes.

scholarly journals The complete mitochondrial genome of a cold seep gastropod Phymorhynchus buccinoides (Neogastropoda: Conoidea: Raphitomidae)

PLoS ONE ◽  
2020 ◽  
Vol 15 (11) ◽  
pp. e0242541
Author(s):  
Lvpei Du ◽  
Shanya Cai ◽  
Jun Liu ◽  
Ruoyu Liu ◽  
Haibin Zhang
Keyword(s):  
Mitochondrial Genome ◽  
Complete Mitochondrial Genome ◽  
Cold Seep ◽  
Start Codon ◽  
Rrna Genes ◽  
Trna Genes ◽  
Protein Coding ◽  
Future Studies ◽  
Protein Coding Genes ◽  
High Support

Phymorhynchus is a genus of deep-sea snails that are most distributed in hydrothermal vent or cold seep environments. In this study, we presented the complete mitochondrial genome of P. buccinoides, a cold seep snail from the South China Sea. It is the first mitochondrial genome of a cold seep member of the superfamily Conoidea. The mitochondrial genome is 15,764 bp in length, and contains 13 protein-coding genes (PCGs), 2 rRNA genes, and 22 tRNA genes. These genes are encoded on the positive strand, except for 8 tRNA genes that are encoded on the negative strand. The start codon ATG and 3 types of stop codons, TAA, TAG and the truncated termination codon T, are used in the 13 PCGs. All 13 PCGs in the 26 species of Conoidea share the same gene order, while several tRNA genes have been translocated. Phylogenetic analysis revealed that P. buccinoides clustered with Typhlosyrinx sp., Eubela sp., and Phymorhynchus sp., forming the Raphitomidae clade, with high support values. Positive selection analysis showed that a residue located in atp6 (18 S) was identified as the positively selected site with high posterior probabilities, suggesting potential adaption to the cold seep environment. Overall, our data will provide a useful resource on the evolutionary adaptation of cold seep snails for future studies.

scholarly journals The complete mitochondrial genome of Microphysogobio elongatus (Teleostei, Cyprinidae) and its phylogenetic implications

ZooKeys ◽  
2021 ◽  
Vol 1061 ◽  
pp. 57-73
Author(s):  
Renyi Zhang ◽  
Qian Tang ◽  
Lei Deng
Keyword(s):  
Complete Mitochondrial Genome ◽  
Genetic Material ◽  
Start Codon ◽  
Trna Genes ◽  
Protein Coding ◽  
Simple Loop ◽  
Stop Codons ◽  
Phylogenetic Implications ◽  
Complete Mitogenome ◽  
Rna Genes

Mitochondria are important organelles with independent genetic material of eukaryotic organisms. In this study, we sequenced and analyzed the complete mitogenome of a small cyprinid fish, Microphysogobio elongatus (Yao & Yang, 1977). The mitogenome of M. elongatus is a typical circular molecule of 16,612 bp in length containing 13 protein-coding genes (PCGs), 22 transfer RNA genes, two ribosomal RNA genes, and a 930 bp control region. The base composition of the M. elongatus mitogenome is 30.8% A, 26.1% T, 16.7% G, and 26.4% C. All PCGs used the standard ATG start codon with the exception of COI. Six PCGs terminate with complete stop codons, whereas seven PCGs (ND2, COII, ATPase 6, COIII, ND3, ND4, and Cyt b) terminate with incomplete (T or TA) stop codons. All tRNA genes exhibited typical cloverleaf secondary structures with the exception of tRNASer(AGY), for which the dihydrouridine arm forms a simple loop. The phylogenetic analysis divided the subfamily Gobioninae in three clades with relatively robust support, and that Microphysogobio is not a monophyletic group. The complete mitogenome of M. elongatus provides a valuable resource for future studies about molecular phylogeny and/or population genetics of Microphysogobio.

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.

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. 

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