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Schizothorax argentatus that only distributes in the Ili River basin in Xinjiang is one of the rare and endangered species of schizothorax in China, thus has high scientific and economic values. In this study, the complete mitochondrial genome sequence of S. argenteus with a length of 16 580 bp was obtained by high-throughput sequencing. The gene compositions and arrangement were similar to those of typical vertebrates. It contained 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and a non-coding region (D-loop). The nucleotide compositions were A (30.25%), G (17.28%), C (27.20%), and T (25.27%), respectively, showing obvious AT bias and anti-G bias. Among the tRNA genes, only tRNA-Ser(GCU) could not form a typical cloverleaf structure due to the lack of dihydrouracil arm. The AT-skew and GC-skew values of the ND6 gene were fluctuating the most, suggesting that the gene may experience different selection and mutation pressures from other genes. The mitochondrial control region of S. argenteus contained three different domains, i.e., termination sequence region (ETAS), central conserved region (CSB-F, CSB-E, CSB-D, and CSB-B), and conserved sequence region (CSB1, CSB2, and CSB3). The conserved sequence fragment TT (AT) nGTG, which was ubiquitous in Cypriniformes, was identified at about 50 bp downstream CSB3. Phylogenetic relationships based on the complete mitochondrial genome sequence of 28 Schizothorax species showed that S. argenteus had differentiated earlier and had a distant relationship with other species, which may be closely related to the geographical location and the hydrological environment where it lives.
Subject(s)
Animals , Genome, Mitochondrial/genetics , Phylogeny , Sequence Analysis, DNA , Cyprinidae/genetics , RNA, Transfer/genetics , DNA, Mitochondrial/genetics , Genes, MitochondrialABSTRACT
ABSTRACT Megaloptera is a small holometabolous insect order that includes two genera and three species of Corydalidae in Pakistan. Here we sequenced the complete mitochondrial genomes of these three Pakistani corydalids: Nevromus intimus (McLachlan, 1869) (16,614 bp), Protohermes motuoensis Liu & Yang, 2006 (16,238 bp), and Protohermes walkeri Navás, 1929 (16,514 bp). It also represents the first set of complete mitogenomes sequenced for Neuropterida in Pakistan. The gene order was found to be similar to other published dobsonfly mitogenomes except the variable length of the non-coding region in each species. The phylogenetic analysis using 13 protein-coding genes by Maximum likelihood and Bayesian inference yielded largely consistent topologies, in which the phylogenetic positions of the three species herein studied are recovered.
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Mitochondria play a key role in cell metabolism. In addition to synthesizing ATP, they also participate in many physiological and pathological processes, including apoptosis, inflammation, oxidative stress, neuronal disease, tumor development, and aging. Most gene transcription of mitochondrial proteins occurs in the nucleus, so the biogenesis of mitochondria and the maintenance of mitochondrial homeostasis mainly depend on the expression of nuclear genes (nDNA) and mitochondria-nucleus interactions. Conversely, mitochondria can affect the expression of nuclear genes through nuclear transcription factors, a process called mitochondrial retrograde signaling. This review summarizes the research progress on mitochondria-nucleus retrograde signaling and its regulation, including the ways by which mitochondria regulate nuclear genes and affect biological processes, and discusses new strategies for the treatment of diseases that involve mitochondrial retrograde signaling in disease pathology.
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Objective To compare the complete mitochondrial genome sequences of two phenotypes of Paragonimus westermani isolated from Fujian Province with different sizes of metacercariae, and perform a phylogenetic analysis of various geographical isolates of P. westermani from Asia, so as to identify the possible genetic characteristics associated with the P. westermani phenotypes. Methods P. westermani metacercariae with different sizes (large metacercariae, 380–420 μm in diameter; small metacercariae, 320–340 μm) isolated from freshwater crabs were used to infect dogs, and the eggs and adult worms of P. westermani were collected from the dog stool samples and lung tissues. Then, the egg size and morphology were compared. In addition, genomic DNA was extracted from the adult worms of the two phenotypes of P. westermani and used for the PCR amplification to yield the complete mitochondrial genome sequence. Sequence structure and phylogenetic analyses were performed based on the complete mitochondrial genome of P. westermani. Results Following infection with large and small P. westermani metacercariae, the adult worms recovered from the dog lung had a thick body, and had oral and ventral suckers. The ventral sucker was located slightly in front of the midline of the body, and testes, ovary and vitelline gland were seen in the adult worms. Following fixation, the adults appeared oval, with an approximately 1.7∶1 of the length-width ratio. The length and width of the eggs isolated from the fecal samples of dogs infected with large and small P. westermani metacercariae varied significantly, and the large metacercariae produced bigger eggs than the smaller metacercariae. Based on the morphological features of adults and eggs and the ITS2 sequences, both phenotypes were identified as P. westermani. The complete mitochondrial genome sequence analysis of adults showed almost consistent sequences in the protein-coding region of the mitochondrial genome of adult worms derived from large and small metacercariae, with a major variation seen in the former non-coding region. Sliding window analysis revealed the most polymorphic region within the ND4 gene across the mitochondrial genome from various geographical isolates of P. westermani, and phylogenetic analysis showed that both phenotypes were clustered into the Chinese branch of P. westermani, which was close to the Japanese branch and distinct from the South/Southeast Asian branch. Conclusions The genetic distance between the phenotypes of P. westermani isolated from Fujian Province is near at a mitochondrial genome level, with no remarkable genetic differentiation seen; however, the mutation and structural changes in the non-coding region may result in the phenotypic variations. In addition, there is a distinct variation of the evolutionary rate in the mitochondrial coding genes, suggesting the selection of appropriate molecular markers during the phylogenic researches.
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@#Keratoconus is a corneal disease characterized by corneal ectasia, progressive corneal thinning, conical protrusion and irregular astigmatism. Several studies have indicated that keratoconus is a complex disease with genetic heterogeneity. Genetic studies on keratoconus involving nuclear genome, mitochondrial genome and epigenetics were increasing. This article reviews the recent progress in genetic research on keratoconus.
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This study was undertaken to determine the complete mitochondrial DNA sequence and structure of the mitochondrial genome of Spirometra ranarum, and to compare it with those of S. erinaceieuropaei and S. decipiens. The aim of this study was to provide information of the species level taxonomy of Spirometra spp. using the mitochondrial genomes of 3 Spirometra tapeworms. The S. ranarum isolate originated from Myanmar. The mitochondrial genome sequence of S. ranarum was compared with that of S. erinaceieuropaei (GenBank no. KJ599680) and S. decipiens (Gen-Bank no. KJ599679). The complete mtDNA sequence of S. ranarum comprised 13,644 bp. The S. ranarum mt genome contained 36 genes comprising 12 protein-coding genes, 22 tRNAs and 2 rRNAs. The mt genome lacked the atp8 gene, as found for other cestodes. All genes in the S. ranarum mitochondrial genome are transcribed in the same direction and arranged in the same relative position with respect to gene loci as found for S. erinaceieuropaei and S. decipiens mt genomes. The overall nucleotide sequence divergence of 12 protein-coding genes between S. ranarum and S. decipiens differed by 1.5%, and 100% sequence similarity was found in the cox2 and nad6 genes, while the DNA sequence divergence of the cox1, nad1, and nad4 genes of S. ranarum and S. decipiens was 2.2%, 2.1%, and 2.6%, respectively.
Subject(s)
Base Sequence , Cestoda , Classification , DNA, Mitochondrial , Genes, vif , Genome , Genome, Mitochondrial , Myanmar , RNA, Transfer , SpirometraABSTRACT
Abstract Leigh syndrome is a devastating neurodegenerative disease, typically manifesting in infancy or early childhood. Hallmarks of the disease are symmetrical lesions in the basal ganglia or brain stem on MRI, and a clinical course with rapid deterioration of cognitive and motor functions. It is genetically heterogeneous, causative mutations have been disclosed in mitochondrial DNA and nuclear genes involved in the process of energy production in the mitochondria .We investigated the whole mitochondrial DNA in three Brazilian patients with LS, based on their clinical and biochemical data, with the aim to identify the disease-causing mutations. In two of the patients, with complex I deficiency, a novel heteroplasmic variant m.4142G>T (p.R279L) in MT-ND1 and a recurrent homoplasmic mutation m.10197G>A (p.A47T) in MT-ND3 were identified. In the remaining patient, with complex IV deficiency, a de novo heteroplasmic variant in MT-CO1 m.6547T>C (p.L215P) was found. The molecular investigation in mitochondrial diseases have shifted their focus from mitochondrial DNA to nuclear DNA, however, mtDNA protein-coding genes are one of the important genetic causes of mitochondrial disorders for Leigh syndrome. This study expands the molecular and clinical spectrum associated with this disease.
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Triatoma rubrofasciata is a wide-spread vector of Chagas disease in Americas. In this study, we completed the mitochondrial genome sequencing of T. rubrofasciata. The total length of T. rubrofasciata mitochondrial genome was 17,150 bp with the base composition of 40.4% A, 11.6% G, 29.4% T and 18.6% C. It included 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes and one control region. We constructed a phylogenetic tree on the 13 protein-coding genes of T. rubrofasciata and other 13 closely related species to show their phylogenic relationship. The determination of T. rubrofasciata mitogenome would play an important role in understanding the genetic diversity and evolution of triatomine bugs.
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Americas , Base Composition , Chagas Disease , Genes, rRNA , Genetic Variation , Genome, Mitochondrial , Phylogeny , RNA, Transfer , Trees , TriatomaABSTRACT
BACKGROUND: Mitochondrial DNA (mtDNA) mutations may regulate the progression and chemosensitivity of leukemia. Few studies regarding mitochondrial aberrations and haplogroups in acute myeloid leukemia (AML) and their clinical impacts have been reported. Therefore, we focused on the mtDNA length heteroplasmies minisatellite instability (MSI), copy number alterations, and distribution of mitochondrial haplogroups in Korean patients with AML. METHODS: This study investigated 74 adult patients with AML and 70 controls to evaluate mtDNA sequence alterations, MSI, mtDNA copy number, haplogroups, and their clinical implications. The hypervariable (HV) control regions (HV1 and HV2), tRNA(leu1)gene, and cytochrome b gene of mtDNA were analyzed. Two mtDNA minisatellite markers, 16189 poly-C (¹⁶¹⁸⁴CCCCCTCCCC¹⁶¹⁹³, 5CT4C) and 303 poly-C (³⁰³CCCCCCCTCCCCC³¹⁵, 7CT5C), were used to examine the mtDNA MSI. RESULTS: In AML, most mtDNA sequence variants were single nucleotide substitutions, but there were no significant differences compared to those in controls. The number of mtMSI patterns increased in AML. The mean mtDNA copy number of AML patients increased approximately 9-fold compared to that of controls (P < 0.0001). Haplogroup D4 was found in AML with a higher frequency compared to that in controls (31.0% vs. 15.7%, P=0.046). None of the aforementioned factors showed significant impacts on the outcomes. CONCLUSION: AML cells disclosed more heterogeneous patterns with the mtMSI markers and had increased mtDNA copy numbers. These findings implicate mitochondrial genome instability in primary AML cells. Therefore, mtDNA haplogroup D4 might be associated with AML risk among Koreans.
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Adult , Humans , Cytochromes b , DNA, Mitochondrial , Genome, Mitochondrial , Leukemia , Leukemia, Myeloid, Acute , Minisatellite RepeatsABSTRACT
Abstract Engyodontium album is a widespread pathogen that causes different kinds of dermatoses and respiratory tract diseases in humans and animals. In spite of its perniciousness, the basic genetic and molecular background of this species remains poorly understood. In this study, the mitochondrial genome sequence of E. album was determined using a high-throughput sequencing platform. The circular mitogenome was found to be 28,081 nucleotides in length and comprised of 17 protein-coding genes, 24 tRNA genes, and 2 rRNA genes. The nucleotide composition of the genome was A+T-biased (74.13%). Group-II introns were found in the nad1, nad5, and cob genes. The most frequently used codon of protein-coding genes was UAU. Isoleucine was identified as the most common amino acid, while proline was the least common amino acid in protein-coding genes. The gene-arrangement order is nearly the same when compared with other Ascomycota mitogenomes. Phylogenetic relationships based on the shared protein-coding genes revealed that E. album is closely related to the Cordycipitaceae family, with a high-confidence support value (100%). The availability of the mitogenome of E. album will shed light on the molecular systematic and genetic differentiation of this species.
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Abstract The mitochondrial genome (mitogenome) characteristics of the monotypic Lasiocampoidea are largely unknown, because only limited number of mitogenomes is available from this superfamily. In this study, we sequenced the complete mitogenome of the lappet moth, Kunugia undans (Lepidoptera: Lasiocampidae) and compared it to those of Lasiocampoidea and macroheteroceran superfamilies (59 species in six superfamilies). The 15,570-bp K. undans genome had one additional trnR that was located between trnA and trnN loci and this feature was unique in Macroheterocera, including Lasiocampoidea. Considering that the two trnR copies are located in tandem with proper secondary structures and identical anticodons, a gene duplication event might be responsible for the presence of the two tRNAs. Nearly all macroheteroceran species, excluding Lasiocampoidea, have a spacer sequence (1-34 bp) at the trnS2 and ND1 junction, but most lasiocampid species, including K. undans, have an overlap at the trnS2 and ND1 junction, which represents a different genomic feature in Lasiocampoidea. Nevertheless, a TTAGTAT motif, which is typically detected in Macroheterocera at the trnS2 and ND1 junction, was also detected in all Lasiocampoidea. In summary, the general mitogenome characteristics of Lasiocampoidea did not differ greatly from the remaining macroheteroceran superfamilies, but it did exhibit some unique features.
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Objective To optimize the extraction methods of mitochondrial genome DNA(mtDNA)of Oncomelania hupen-sis. Methods The pyrolysis,protein K variable-temperature digestion and high-concentration potassium acetate purification were applied to optimize the high-concentration-salt precipitation method,and then the optimized method was compared with two common extraction methods,the sucrose density gradient centrifugation method and traditional high-concentration-salt pre-cipitation method. The mtDNA samples were identified by using spectrophotometry,agarose gel electrophoresis and the amplifi-cation products of COX1. The nuclear DNA contamination was tested by the amplification products of ITS. Results The concen-tration and yield of the improved method was significantly higher than those of the traditional method(F=3032.65,10185.00, both P<0.01). The mtDNA samples extracted were essentially free of nuclear DNA and protein,meeting PCR,sequence analy-sis and other molecular biology research requirements. Conclusions The improved high-concentration-salt precipitation meth-od for isolating mtDNA is simple,and it has high yield and low cost. The extracted mtDNA can meet relevant analysis require-ments.
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Mitochondrion is an organelle containing its own genome in eukaryotic cells , which encodes 37 genes involved in mitochondrial functions .Mitoepigenetic regulation is a major form of mitochondrial genome-encoded genes that regulates the expression levels without altering the sequences of the genes .The mitoepigenetic regulation is involved in the occurrence and development of various diseases .This paper reviews the progress of mitoepigenetic regulation and Alzhe-imer disease.
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Mitochondrion is an organelle containing its own genome in eukaryotic cells , which encodes 37 genes involved in mitochondrial functions .Mitoepigenetic regulation is a major form of mitochondrial genome-encoded genes that regulates the expression levels without altering the sequences of the genes .The mitoepigenetic regulation is involved in the occurrence and development of various diseases .This paper reviews the progress of mitoepigenetic regulation and Alzhe-imer disease.
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Chinese hamster is an important laboratory animal in medical and biological researches,but the molecular genetic markers research was rarely reported.In our study the base composition,gene structure,genetic evolution and other characteristics of mitochondrial genome of Chinese hamster were analyzed using the methods of bioinformatics and comparative genomics,genetic quality detection system of Chinese hamster were also established.These results would supply genome data for animal models of human diseases,and lay the foundation for scientific evaluation and reasonable utilization.
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Toxascaris leonina is a common parasitic nematode of wild mammals and has significant impacts on the protection of rare wild animals. To analyze population genetic characteristics of T. leonina from South China tiger, its mitochondrial (mt) genome was sequenced. Its complete circular mt genome was 14,277 bp in length, including 12 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and 2 non-coding regions. The nucleotide composition was biased toward A and T. The most common start codon and stop codon were TTG and TAG, and 4 genes ended with an incomplete stop codon. There were 13 intergenic regions ranging 1 to 10 bp in size. Phylogenetically, T. leonina from a South China tiger was close to canine T. leonina. This study reports for the first time a complete mt genome sequence of T. leonina from the South China tiger, and provides a scientific basis for studying the genetic diversity of nematodes between different hosts.
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Animals , Animals, Wild , Bias , China , Codon, Initiator , Codon, Terminator , DNA, Intergenic , Genes, rRNA , Genetic Variation , Genome , Genome, Mitochondrial , Mammals , Phylogeny , RNA, Transfer , Sequence Analysis , Tigers , ToxascarisABSTRACT
Armillifer agkistrodontis (Ichthyostraca: Pantastomida) is a parasitic pathogen, only reported in China, which can cause a zoonotic disease, pentastomiasis. A complete mitochondrial (mt) genome was 16,521 bp comprising 13 protein-coding genes (PCGs), 22 tRNA genes, 2 rRNA genes, and 1 non-coding region (NCR). A phylogenetic tree drawn with the concatenated amino acid sequences of the 6 conserved PCGs (atp6, cox1-3, and nad2) showed that A. agkistrodontis and Armillifer armillatus constituted a clade Pentastomida which was a sister group of the Branchiura. The complete mt genome sequence of A. agkistrodontis provides important genetic markers for both phylogenetic and epidemiological studies of pentastomids.
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Humans , Amino Acid Sequence , China , Epidemiologic Studies , Genes, rRNA , Genetic Markers , Genome , Genome, Mitochondrial , Pentastomida , RNA, Transfer , Siblings , Tongue , Trees , ZoonosesABSTRACT
The 2 species of the genus Anoplocephala (Anoplocephalidae), A. perfoliata and A. magna, are among the most important equine cestode parasites. However, there is little information about their differences at the molecular level. The present study revealed that the mitochondrial (mt) genome of A. magna was 13,759 bp in size and 700 bp shorter than that of A. perfoliata. The 2 species includes 2 rRNA, 22 tRNA, and 12 protein-coding genes each. The size of each of the 36 genes was the same as that of A. perfoliata, except for cox1, rrnL, trnC, trnS2(UCN), trnG, trnH, trnQ, and trnP. In the full mitochondrial genome, the sequence similarity was 87.1%. The divergence in the nucleotide and amino acid sequences of individual protein-coding genes ranged from 11.1% to 16% and 6.8% to 16.4%, respectively. The 2 noncoding regions of the mt genome of A. magna were 199 bp and 271 bp in length, while the equivalent regions in A. perfoliata were 875 bp and 276 bp, respectively. The results of this study support the proposal that A. magna and A. perfoliata are separate species, consistent with previous morphological analyses.
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Amino Acid Sequence , Cestoda , Genome , Genome, Mitochondrial , Parasites , RNA, TransferABSTRACT
Background The classification of diversity in germplasm collections is important for plant breeding. The repetitive element palindromic-polymerase chain reaction (rep-PCR) technique was used to investigate inter-specific diversity within 17 species from the Euphorbiaceae family using REP and BOX primers. Results The agglomerative cluster analysis was used to evaluate the scoring data. BOX and REP gave amplification with polymorphism of 98.84% and 100% respectively. REP marker demarcated between the subgenus peltatae. Both markers confirmed Jatropha tanjorensis as a natural hybrid between Jatropha gossypifolia and Jatropha curcas. Five random sequences from the rep-PCR gels were chosen, cloned and sequenced. The blast results demonstrated that the amplified products were from the mitochondrial genomes. Conclusion The rep-PCR molecular tool can be used to characterize diversity in plants as they are suitable for distinguishing eukaryotic genomes effectively.
Subject(s)
Genetic Variation , Polymerase Chain Reaction/methods , Euphorbiaceae/genetics , Jatropha/genetics , Genome, MitochondrialABSTRACT
Objective Assembly whole mitochondrial genome sequence of Rongshui miniature pig ( RMP ) breed and analysis the structure of mitochondrion based on the next-generation sequecing method.Comparison of phylogenetic relationship and genetic diversity among different pig breeds.Methods We collected peripheral venous blood sample from RMP and constructed two paired-end sequencing libraries.A whole-genome shotgun sequencing strategy and Illumina Genome Analyser sequencing technology were used in our study.Results The mitochondrial genome of RMP consists of 13 protein coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes and the length of pig is 16888 bp.The GC content of this pig mitochondrial genome is about 44 %.Based on phlogenetic analysis, population genetic analysis, our findings confirmed that the ancestral cluster in East Asia mainly occurred among Diannan 7#pig, Hainan wild boar, Lanyu and RMP.Conclusion RMP, a typical miniature pig breed in China, is an earlier ancestor than Lanyu pig breed.