scholarly journals Characterisation of the Complete Mitochondrial Genome of Critically Endangered Mustela lutreola (Carnivora: Mustelidae) and Its Phylogenetic and Conservation Implications

Genes ◽  
2022 ◽  
Vol 13 (1) ◽  
pp. 125
Author(s):  
Jakub Skorupski
Keyword(s):  
Mitochondrial Genome ◽  
Complete Mitochondrial Genome ◽  
Critically Endangered ◽  
Mustela Lutreola ◽  
Single Nucleotide Variants ◽  
Protein Coding ◽  
European Mink ◽  
Protein Coding Genes ◽  
Close Phylogenetic Relationship ◽  
Rna Genes

In this paper, a complete mitochondrial genome of the critically endangered European mink Mustela lutreola L., 1761 is reported. The mitogenome was 16,504 bp in length and encoded the typical 13 protein-coding genes, two ribosomal RNA genes and 22 transfer RNA genes, and harboured a putative control region. The A+T content of the entire genome was 60.06% (A > T > C > G), and the AT-skew and GC-skew were 0.093 and −0.308, respectively. The encoding-strand identity of genes and their order were consistent with a collinear gene order characteristic for vertebrate mitogenomes. The start codons of all protein-coding genes were the typical ATN. In eight cases, they were ended by complete stop codons, while five had incomplete termination codons (TA or T). All tRNAs had a typical cloverleaf secondary structure, except tRNASer(AGC) and tRNALys, which lacked the DHU stem and had reduced DHU loop, respectively. Both rRNAs were capable of folding into complex secondary structures, containing unmatched base pairs. Eighty-one single nucleotide variants (substitutions and indels) were identified. Comparative interspecies analyses confirmed the close phylogenetic relationship of the European mink to the so-called ferret group, clustering the European polecat, the steppe polecat and the black-footed ferret. The obtained results are expected to provide useful molecular data, informing and supporting effective conservation measures to save M. lutreola.

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.

scholarly journals The complete mitochondrial genome of stag beetle Lucanus cervus (Coleoptera: Lucanidae) and phylogenetic analysis

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e8274 ◽  
Author(s):  
Dan Chen ◽  
Jing Liu ◽  
Luca Bartolozzi ◽  
Xia Wan
Keyword(s):  
Mitochondrial Genome ◽  
Bayesian Methods ◽  
Phylogenetic Relationships ◽  
Phylogenetic Analyses ◽  
Complete Mitochondrial Genome ◽  
Illumina Platform ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Rna Genes ◽  
Generation Sequencing

Background The stag beetle Lucanus cervus (Coleoptera: Lucanidae) is widely distributed in Europe. Habitat loss and fragmentation has led to significant reductions in numbers of this species. In this study, we sequenced the complete mitochondrial genome of L. cervus and reconstructed phylogenetic relationships among Lucanidae using complete mitochondrial genome sequences. Methods Raw data sequences were generated by the next generation sequencing using Illumina platform from genomic DNA of L. cervus. The mitochondrial genome was assembled by IDBA and annotated by MITOS. The aligned sequences of mitochondrial genes were partitioned using PartitionFinder 2. Phylogenetic relationships among 19 stag beetle species were constructed using Maximum Likelihood (ML) method implemented in IQ-TREE web server and Bayesian method implemented in PhyloBayes MPI 1.5a. Three scarab beetles were used as outgroups. Results The complete mitochondrial genome of L. cervus is 20,109 bp in length, comprising 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNAs and a control region. The A + T content is 69.93% for the majority strand. All protein-coding genes start with the typical ATN initiation codons except for cox1, which uses AAT. Phylogenetic analyses based on ML and Bayesian methods shown consistent topologies among Lucanidae.

scholarly journals First mitochondrial genome from Yponomeutidae (Lepidoptera, Yponomeutoidea) and the phylogenetic analysis for Lepidoptera

ZooKeys ◽  
2019 ◽  
Vol 879 ◽  
pp. 137-156
Author(s):  
Mingsheng Yang ◽  
Bingyi Hu ◽  
Lin Zhou ◽  
Xiaomeng Liu ◽  
Yuxia Shi ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Phylogenetic Analyses ◽  
Complete Mitochondrial Genome ◽  
Start Codon ◽  
Length Variation ◽  
Protein Coding ◽  
Conserved Sequence ◽  
Protein Coding Genes ◽  
The One ◽  
Rna Genes

The complete mitochondrial genome (mitogenome) of Yponomeuta montanatus is sequenced and compared with other published yponomeutoid mitogenomes. The mitogenome is circular, 15,349 bp long, and includes the typical metazoan mitochondrial genes (13 protein-coding genes, two ribosomal RNA genes, and 22 transfer RNA genes) and an A + T-rich region. All 13 protein-coding genes use a typical start codon ATN, the one exception being cox1, which uses CGA across yponomeutoid mitogenomes. Comparative analyses further show that the secondary structures of tRNAs are conserved, including loss of the Dihydorouidine (DHU) arm in trnS1 (AGN), but remarkable nucleotide variation has occurred mainly in the DHU arms and pseudouridine (TψC) loops. A + T-rich regions exhibit substantial length variation among yponomeutoid mitogenomes, and conserved sequence blocks are recognized but some of them are not present in all species. Multiple phylogenetic analyses confirm the position of Y. montanatus in Yponomeutoidea. However, the superfamily-level relationships in the Macroheterocera clade in Lepidoptera recovered herein show considerable difference with that recovered in previous mitogenomic studies, raising the necessity of extensive phylogenetic investigation when more mitogenomes become available for this clade.

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 Pentatoma rufipes (Hemiptera, Pentatomidae) and its phylogenetic implications

ZooKeys ◽  
2021 ◽  
Vol 1042 ◽  
pp. 51-72
Author(s):  
Ling Zhao ◽  
Jiufeng Wei ◽  
Wanqing Zhao ◽  
Chao Chen ◽  
Xiaoyun Gao ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Phylogenetic Trees ◽  
Complete Mitochondrial Genome ◽  
Genome Structure ◽  
Nucleotide Composition ◽  
Genome Database ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Phylogenetic Implications ◽  
Rna Genes

Pentatoma rufipes (Linnaeus, 1758) is an important agroforestry pest widely distributed in the Palaearctic region. In this study, we sequence and annotate the complete mitochondrial genome of P. rufipes and reconstruct the phylogenetic trees for Pentatomoidea using existing data for eight families published in the National Center for Biotechnology Information database. The mitogenome of P. rufipes is 15,887-bp-long, comprising 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and a control region, with an A+T content of 77.7%. The genome structure, gene order, nucleotide composition, and codon usage of the mitogenome of P. rufipes were consistent with those of typical Hemiptera insects. Among the protein-coding genes of Pentatomoidea, the evolutionary rate of ATP8 was the fastest, and COX1 was found to be the most conservative gene in the superfamily. Substitution saturation assessment indicated that neither transition nor transversion substitutions were saturated in the analyzed datasets. Phylogenetic analysis using the Bayesian inference method showed that P. rufipes belonged to Pentatomidae. The node support values based on the dataset concatenated from protein-coding and RNA genes were the highest. Our results enrich the mitochondrial genome database of Pentatomoidea and provide a reference for further studies of phylogenetic systematics.

scholarly journals The mitochondrial genome of Faughnia haani (Stomatopoda): novel organization of the control region and phylogenetic position of the superfamily Parasquilloidea

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Hee-seung Hwang ◽  
Jongwoo Jung ◽  
Juan Antonio Baeza
Keyword(s):  
Mitochondrial Genome ◽  
Control Region ◽  
Complete Mitochondrial Genome ◽  
Mitochondrial Protein ◽  
Phylogenetic Position ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Marine Predators ◽  
Hairpin Structures ◽  
Rna Genes

Abstract Background Stomatopod crustaceans are aggressive marine predators featuring complex compound eyes and powerful raptorial appendages used for “smashing” or “spearing” prey and/or competitors. Among them, parasquilloids (superfamily Parasquilloidea) possess eyes with 2-3 midband rows of hexagonal ommatidia and spearing appendages. Here, we assembled and analyzed the complete mitochondrial genome of the parasquilloid Faughnia haani and explored family- and superfamily-level phylogenetic relationships within the Stomatopoda based on mitochondrial protein coding genes (PCGs). Results The mitochondrial genome of F. haani is 16,089 bp in length and encodes 13 protein coding genes (PCGs), 22 transfer RNA genes, 2 ribosomal RNA genes, and a control region that is relatively well organized, containing 2 GA-blocks, 4 poly-T stretches, various [TA(A)]n-blocks, and 2 hairpin structures. This organized control region is likely a synapomorphic characteristic in the Stomatopoda. Comparison of the control region among superfamilies shows that parasquilloid species are more similar to gonodactyloids than to squilloids and lysiosquilloids given the presence of various  poly-T stretches between the hairpin structures and [TA(A)]n-blocks. Synteny is identical to that reported for other stomatopods and corresponds to the Pancrustacea ground pattern. A maximum-likelihood phylogenetic tree based on PCGs revealed that Parasquilloidea is sister to Lysiosquilloidea and Gonodactyloidea and not to Squilloidea, contradicting previous phylogenetic studies. Conclusions The novel phylogenetic position of Parasquilloidea revealed by our study indicates that ‘spearing’ raptorial appendages are plesiomorphic and that the ‘smashing’ type is either derived (as reported in previous studies) or apomorphic. Our results raise the possibility that the spearing raptorial claw may have independently evolved twice. The superfamily Parasquilloidea exhibits a closer relationship with other stomatopod superfamilies with a different raptorial claw type and with dissimilar numbers of midband rows of hexagonal ommatidia. Additional studies focusing on the assembly of mitochondrial genomes from species belonging to different genera, families, and superfamilies within the order Stomatopoda are warranted to reach a robust conclusion regarding the evolutionary history of this iconic clade based on mitochondrial PCGs.

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 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.

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 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.

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