The Complete Mitochondrial Genome of Critically Endangered Hangul (Cervus Hanglu Hanglu) and Its Comparison With the Other Red Deer

Abstract Background: Hangul (Cervus hanglu hanglu) or Kashmiri stag belongs to the family Cervidae and is only surviving red deer in the Indian subcontinent. Its complete mitogenome sequence is lacking in the open database for further phylogenetic inferences.Methods and results: We sequenced and characterized the first complete mitogenome of Hangul, which was 16,354 bp in length. It was compared with other red deer subspecies. We observed eight pairs of overlapping genes and 15 intergenic spacers in between the mitochondrial regions. Relative synonymous codon usage (RSCU) for the 13 PCGs of Hangul was consisting of 3597 codons (excluding stop codons). We observed a highest frequency for leucine (11.75%) and the lowest for tryptophan amino acid (1.12%) in 13 PCGs of Hangul. All the tRNA genes showed a typical secondary cloverleaf arrangement, excluding tRNA-Ser in which dihydrouridine arm did not form a stable structure. Conclusions: The Bayesian inference phylogenetic tree indicated that Hangul clustered within the Tarim deer group (C. h. yarkandensis) and closed to C. e. hippelaphus, which formed the western clade. Besides, the subspecies of C. nippon and C. canadensis clustered together and formed an eastern clade. The finding was supported by the mean pairwise genetic distance based on both complete mitogenome and 13 PCGs. The comparative study of the Hangul mitogenome with other red deer provides crucial information for understanding the evolutionary relationships. It offers a valuable resource for conserving this critically endangered cervid with a limited distribution range.

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Characterization of the Complete Mitochondrial Genome of Leucoma salicis (Lepidoptera: Lymantriidae) and Comparison with Other Lepidopteran Insects

Scientific Reports ◽

10.1038/srep39153 ◽

2016 ◽

Vol 6 (1) ◽

Cited By ~ 16

Author(s):

Yu-Xuan Sun ◽

Lei Wang ◽

Guo-Qing Wei ◽

Cen Qian ◽

Li-Shang Dai ◽

...

Keyword(s):

Mitochondrial Genome ◽

Synonymous Codon ◽

Complete Mitochondrial Genome ◽

Synonymous Codon Usage ◽

Trna Genes ◽

Stem Loop ◽

Protein Coding ◽

Distinctive Features ◽

Protein Coding Genes ◽

Stem Loop Structure

Abstract The complete mitochondrial genome (mitogenome) of Leucoma salicis (Lepidoptera: Lymantriidae) was sequenced and annotated. It is a circular molecule of 15,334 bp, containing the 37 genes usually present in insect mitogenomes. All protein-coding genes (PCGs) are initiated by ATN codons, other than cox1, which is initiated by CGA. Three of the 13 PCGs had an incomplete termination codon, T or TA, while the others terminated with TAA. The relative synonymous codon usage of the 13 protein-coding genes (PCGs) was consistent with those of published lepidopteran sequences. All tRNA genes had typical clover-leaf secondary structures, except for the tRNASer(AGN), in which the dihydrouridine (DHU) arm could not form a stable stem-loop structure. The A + T-rich region of 325 bp had several distinctive features, including the motif ‘ATAGA’ followed by an 18 bp poly-T stretch, a microsatellite-like (AT)7 element, and an 11-bp poly-A present immediately upstream of tRNAMet. Relationships among 32 insect species were determined using Maximum Likelihood (ML), Neighbor Joining (NJ) and Bayesian Inference (BI) phylogenetic methods. These analyses confirm that L. salicis belongs to the Lymantriidae; and that Lymantriidae is a member of Noctuoidea, and is a sister taxon to Erebidae, Nolidae and Noctuidae, most closely related to Erebidae.

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Complete Mitogenome of a Leaf-Mining Buprestid Beetle, Trachys auricollis, and Its Phylogenetic Implications

Genes ◽

10.3390/genes10120992 ◽

2019 ◽

Vol 10 (12) ◽

pp. 992

Author(s):

Lifang Xiao ◽

Shengdi Zhang ◽

Chengpeng Long ◽

Qingyun Guo ◽

Jiasheng Xu ◽

...

Keyword(s):

Tandem Repeats ◽

Synonymous Codon ◽

Complete Mitochondrial Genome ◽

Rrna Genes ◽

Common Finding ◽

Trna Genes ◽

Rich Region ◽

Stop Codons ◽

Phylogenetic Implications ◽

Complete Mitogenome

A complete mitogenome of Trachys auricollis is reported, and a mitogenome-based phylogenetic tree of Elateriformia with all protein-coding genes (PCGs), rRNAs, and tRNAs is presented for the first time. The complete mitochondrial genome of T. auricollis is 16,429 bp in size and contains 13 PCGs, two rRNA genes, 22 tRNA genes, and an A + T-rich region. The A + T content of the entire genome is approximately 71.1%, and the AT skew and GC skew are 0.10 and −0.20, respectively. According to the the nonsynonymous substitution rate to synonymous substitution rates (Ka/Ks) of all PCGs, the highest and lowest evolutionary rates were observed for atp8 and cox1, respectively, which is a common finding among animals. The start codons of all PCGs are the typical ATN. Ten PCGs have complete stop codons, but three have incomplete stop codons with T or TA. As calculated based on the relative synonymous codon usage (RSCU) values, UUA(L) is the codon with the highest frequency. Except for trnS1, all 22 tRNA genes exhibit typical cloverleaf structures. The A + T-rich region of T. auricollis is located between rrnS and the trnI-trnG-trnM gene cluster, with six 72-bp tandem repeats. Both maximum likelihood (ML) and Bayesian (BI) trees suggest that Buprestoidea is close to Byrrhoidea and that Buprestoidea and Byrrhoidea are sister groups of Elateroidea, but the position of Psephenidae is undetermined. The inclusion of tRNAs might help to resolve the phylogeny of Coleoptera.

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

ZooKeys ◽

10.3897/zookeys.1061.70176 ◽

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.

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

Systematic and Applied Acarology ◽

10.11158/saa.27.1.9 ◽

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.

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Sequencing, characterization and phylogenomics of the complete mitochondrial genome of Dactylogyrus lamellatus (Monogenea: Dactylogyridae)

Journal of Helminthology ◽

10.1017/s0022149x17000578 ◽

2017 ◽

Vol 92 (4) ◽

pp. 455-466 ◽

Cited By ~ 15

Author(s):

D. Zhang ◽

H. Zou ◽

S.G. Wu ◽

M. Li ◽

I. Jakovlić ◽

...

Keyword(s):

Complete Mitochondrial Genome ◽

Sister Group ◽

Ctenopharyngodon Idella ◽

Rrna Genes ◽

Gene Arrangement ◽

Trna Genes ◽

Coding Region ◽

Worldwide Distribution ◽

Phylogenetic Resolution ◽

Complete Mitogenome

AbstractDespite the worldwide distribution and pathogenicity of monogenean parasites belonging to the largest helminth genus, Dactylogyrus, there are no complete Dactylogyrinae (subfamily) mitogenomes published to date. In order to fill this knowledge gap, we have sequenced and characterized the complete mitogenome of Dactylogyrus lamellatus, a common parasite on the gills of grass carp (Ctenopharyngodon idella). The circular mitogenome is 15,187 bp in size, containing the standard 22 tRNA genes, 2 rRNA genes, 12 protein-encoding genes and a long non-coding region (NCR). There are two highly repetitive regions in the NCR. We have used concatenated nucleotide sequences of all 36 genes to perform the phylogenetic analysis using Bayesian inference and maximum likelihood approaches. As expected, the two dactylogyrids, D. lamellatus (Dactylogyrinae) and Tetrancistrum nebulosi (Ancyrocephalinae), were closely related to each other. These two formed a sister group with Capsalidae, and this cluster finally formed a further sister group with Gyrodactylidae. Phylogenetic affinity between Dactylogyrinae and Ancyrocephalinae was further confirmed by the similarity in their gene arrangement. The sequencing of the first Dactylogyrinae, along with a more suitable selection of outgroups, has enabled us to infer a much better phylogenetic resolution than recent mitogenomic studies. However, as many lineages of the class Monogenea remain underrepresented or not represented at all, a much larger number of mitogenome sequences will have to be available in order to infer the evolutionary relationships among the monogeneans fully, and with certainty.

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Synonymous Codon Usage Analysis of Thirty Two Mycobacteriophage Genomes

Advances in Bioinformatics ◽

10.1155/2009/316936 ◽

2009 ◽

Vol 2009 ◽

pp. 1-11 ◽

Cited By ~ 15

Author(s):

Sameer Hassan ◽

Vasantha Mahalingam ◽

Vanaja Kumar

Keyword(s):

Codon Usage ◽

Synonymous Codon ◽

Nucleotide Composition ◽

Synonymous Codon Usage ◽

Compositional Bias ◽

Trna Genes ◽

Translation Efficiency ◽

Multivariate Statistical ◽

Strong Negative Correlation ◽

Highly Expressed Genes

Synonymous codon usage of protein coding genes of thirty two completely sequenced mycobacteriophage genomes was studied using multivariate statistical analysis. One of the major factors influencing codon usage is identified to be compositional bias. Codons ending with either C or G are preferred in highly expressed genes among which C ending codons are highly preferred over G ending codons. A strong negative correlation between effective number of codons (Nc) and GC3s content was also observed, showing that the codon usage was effected by gene nucleotide composition. Translational selection is also identified to play a role in shaping the codon usage operative at the level of translational accuracy. High level of heterogeneity is seen among and between the genomes. Length of genes is also identified to influence the codon usage in 11 out of 32 phage genomes. Mycobacteriophage Cooper is identified to be the highly biased genome with better translation efficiency comparing well with the host specific tRNA genes.

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

10.1101/2020.04.27.065235 ◽

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.

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The First Complete Mitochondrial Genome of the Flathead Cociella crocodilus (Scorpaeniformes: Platycephalidae) and the Phylogenetic Relationships within Scorpaeniformes Based on Whole Mitogenomes

Genes ◽

10.3390/genes10070533 ◽

2019 ◽

Vol 10 (7) ◽

pp. 533

Author(s):

Lei Cui ◽

Rongbo Cao ◽

Yuelei Dong ◽

Xingchen Gao ◽

Jingyi Cen ◽

...

Keyword(s):

Phylogenetic Relationships ◽

Tandem Repeats ◽

Complete Mitochondrial Genome ◽

Trna Genes ◽

Protein Coding ◽

Conserved Sequence ◽

Complete Mitogenome ◽

First Time ◽

Rna Genes ◽

Complete Mitochondrial Genomes

Complete mitochondrial genomes (mitogenomes) are important molecular markers for understanding the phylogenetics of various species. Although recent studies on the mitogenomes of the Scorpaeniformes species have been greatly advanced, information regarding molecular studies and the taxonomic localization of Platycephalidae is still sparse. To further analyze the phylogeny of Platycephalidae, we sequenced the complete mitogenome of Cociella crocodilus of the Platycephalidae family within Scorpaeniformes for the first time. The mitogenome was 17,314 bp in length, contained two ribosomal RNA genes (rRNAs), 22 transfer RNA genes (tRNAs), 13 protein-coding genes (PCGs), and two typical noncoding control regions (the control region (CR) and origin of the light strand (OL)). All PCGs used standard initiation codons ATG, apart from cox1. The majority of the tRNA genes could be folded into cloverleaf secondary structures, whereas the secondary structure of tRNASer (AGN) lacked a dihydrouridine (DHU) stem. The CR contained several conserved sequence blocks (CSBs) and eight tandem repeats. In addition, the phylogenetic relationship based on the concatenated nucleotides sequences of 13 PCGs indicated that the Platycephalidae species are relatively basal in the phylogenetic relationships of Scorpaeniformes. Our results may not only advance the origin and the evolution of Scorpaeniformes, but also provide information for the genetic evolution and taxonomy of the teleostean species.

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

Neotropical Ichthyology ◽

10.1590/1982-0224-20150167 ◽

2016 ◽

Vol 14 (1) ◽

Cited By ~ 5

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.

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The complete mitogenome sequence of the coral lily (Lilium pumilum) and the Lanzhou lily (Lilium davidii) in China

Open Life Sciences ◽

10.1515/biol-2020-0102 ◽

2020 ◽

Vol 15 (1) ◽

pp. 1060-1067

Author(s):

Xiangying Qi ◽

Kaiqi Wang ◽

Liping Yang ◽

Zhenshan Deng ◽

Zhihong Sun

Keyword(s):

Phylogenetic Tree ◽

Higher Plants ◽

Core Protein ◽

Protein Coding ◽

Reading Frame ◽

Intergenic Spacers ◽

Additional Information ◽

Mitogenome Sequence ◽

Complete Mitogenome ◽

Lilium Davidii

AbstractBackgroundThe mitogenomes of higher plants are conserved. This study was performed to complete the mitogenome of two China Lilium species (Lilium pumilum Redouté and Lilium davidii var. unicolor (Hoog) cotton).MethodsGenomic DNA was separately extracted from the leaves of L. pumilum and L. davidii in triplicate and used for sequencing. The mitogenome of Allium cepa was used as a reference. Genome assembly, annotation and phylogenetic tree were analyzed.ResultsThe mitogenome of L. pumilum and L. davidii was 988,986 bp and 924,401 bp in length, respectively. There were 22 core protein-coding genes (including atp1, atp4, atp6, atp9, ccmB, ccmC, ccmFc, ccmFN1, ccmFN2, cob, cox3, matR, mttB, nad1, nad2, nad3, nad4, nad4L, nad5, nad6, nad7 and nad9), one open reading frame and one ribosomal protein-coding gene (rps12) in the mitogenomes. Compared with the A. cepa mitogenome, the coding sequence of the 24 genes and intergenic spacers in L. pumilum and L. davidii mitogenome contained 1,621 and 1,617 variable sites, respectively. In the phylogenetic tree, L. pumilum and L. davidii were distinct from A. cepa (NC_030100).ConclusionsL. pumilum and L. davidii mitogenomes have far distances from other plants. This study provided additional information on the species resources of China Lilium.

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