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Liu J, Zhang S, Wen Y, Su Y, Jiang L, Li S, Shen J, Zheng X, Li X, Chen X, Wang Z. Exploring rare differences in mitochondrial genome between MZ twins using Ion Torrent semiconductor sequencing. Forensic Sci Int 2023; 348:111708. [PMID: 37119662 DOI: 10.1016/j.forsciint.2023.111708] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 04/15/2023] [Accepted: 04/24/2023] [Indexed: 05/01/2023]
Abstract
Monozygotic (MZ) twins are considered to be genetically identical in that they have the same genomic DNA sequences in theory, and thus cannot be differentiated using forensic standard STR-based DNA profiling. However, a recent study employed deep sequencing to explore extremely rare mutations in the nuclear genome and reported that the mutation analysis could be applied to differentiate between MZ twins. Compared with the nuclear genome, the mitochondrial DNA (mtDNA) exhibits higher mutation rates due to fewer DNA repair mechanisms in the mitochondrial genome (mtGenome) and the lack of proofreading capability of the mtDNA polymerase. In a previous study, we used Illumina ultra-deep sequencing to describe point heteroplasmy (PHP) and nucleotide variant of the mtGenomes in venous blood samples of MZ twins. In the present study, we characterized minor differences of the mtGenomes in three tissue samples from seven sets of MZ twins using Ion Torrent semiconductor sequencing (Thermo Fisher Ion S5 XL system) and commercialized mtGenome sequencing kit (Precision ID mtDNA Whole Genome Panel). PHP was observed in blood samples from one set of MZ twins and in saliva samples from two sets of twins, but it presented in hair shaft samples from all seven sets of MZ twins. Overall, the coding region of the mtGenome exhibits more PHPs than the control region. The results of this study have further attested the competence of mtGenome sequencing in differentiating between MZ twins, and that among the three kinds of samples tested, hair shaft is more likely to accumulate minor differences in the mtGenomes of MZ twins.
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Affiliation(s)
- Jing Liu
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Shuyuan Zhang
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Yufeng Wen
- School of Life Sciences, Jilin University, Changchun 130012, China
| | - Yonglin Su
- Department of Rehabilitation Medicine, West China Hospital Sichuan University, Chengdu 610041, China
| | - Lirong Jiang
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Suyu Li
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Jian Shen
- Anhui Hopegenerich Biotechnology, Hefei 230031, China
| | - Xinyue Zheng
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Xingrui Li
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Xiacan Chen
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Zheng Wang
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China.
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Zhang X, He C, Zong D. The complete mitochondrial genome of Populus rotundifolia var. duclouxiana. MITOCHONDRIAL DNA PART B-RESOURCES 2021; 6:2858-2859. [PMID: 34514154 PMCID: PMC8425777 DOI: 10.1080/23802359.2021.1972480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The complete sequence of the circular mitochondrial (mt) DNA of Populus rotundifolia var. duclouxiana is presented in this study. The size of the P. rotundifolia var. duclouxiana mt genome was 775,549 bp and the GC content of the genome was 44.8%. The P. rotundifolia var. duclouxiana mt genome encoded 58 genes, including 33 protein-coding genes, 22 tRNA genes, and three rRNA genes. Among the 58 genes, three genes contained one intron, one gene contained three introns, and four genes contained four introns. Phylogenetic analysis using seven complete mt genomes of Salicaceae supported that P. rotundifolia var. duclouxiana is most closely related to P. davidiana.
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Affiliation(s)
- Xiaolin Zhang
- Key Laboratory for Forest Genetic and Tree Improvement and Propagation in Universities of Yunnan Province, Southwest Forestry University, Kunming, China.,Key Laboratory of Biodiversity Conservation in Southwest China, State Forestry Administration, Southwest Forestry University, Kunming, China
| | - Chengzhong He
- Key Laboratory for Forest Genetic and Tree Improvement and Propagation in Universities of Yunnan Province, Southwest Forestry University, Kunming, China.,Key Laboratory of Biodiversity Conservation in Southwest China, State Forestry Administration, Southwest Forestry University, Kunming, China.,Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming, China
| | - Dan Zong
- Key Laboratory for Forest Genetic and Tree Improvement and Propagation in Universities of Yunnan Province, Southwest Forestry University, Kunming, China.,Key Laboratory of Biodiversity Conservation in Southwest China, State Forestry Administration, Southwest Forestry University, Kunming, China
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Al Amir Dache Z, Otandault A, Tanos R, Pastor B, Meddeb R, Sanchez C, Arena G, Lasorsa L, Bennett A, Grange T, El Messaoudi S, Mazard T, Prevostel C, Thierry AR. Blood contains circulating cell-free respiratory competent mitochondria. FASEB J 2020; 34:3616-3630. [PMID: 31957088 DOI: 10.1096/fj.201901917rr] [Citation(s) in RCA: 220] [Impact Index Per Article: 55.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 11/27/2019] [Accepted: 11/29/2019] [Indexed: 11/11/2022]
Abstract
Mitochondria are considered as the power-generating units of the cell due to their key role in energy metabolism and cell signaling. However, mitochondrial components could be found in the extracellular space, as fragments or encapsulated in vesicles. In addition, this intact organelle has been recently reported to be released by platelets exclusively in specific conditions. Here, we demonstrate for the first time, that blood preparation with resting platelets, contains whole functional mitochondria in normal physiological state. Likewise, we show, that normal and tumor cultured cells are able to secrete their mitochondria. Using serial centrifugation or filtration followed by polymerase chain reaction-based methods, and Whole Genome Sequencing, we detect extracellular full-length mitochondrial DNA in particles over 0.22 µm holding specific mitochondrial membrane proteins. We identify these particles as intact cell-free mitochondria using fluorescence-activated cell sorting analysis, fluorescence microscopy, and transmission electron microscopy. Oxygen consumption analysis revealed that these mitochondria are respiratory competent. In view of previously described mitochondrial potential in intercellular transfer, this discovery could greatly widen the scope of cell-cell communication biology. Further steps should be developed to investigate the potential role of mitochondria as a signaling organelle outside the cell and to determine whether these circulating units could be relevant for early detection and prognosis of various diseases.
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Affiliation(s)
- Zahra Al Amir Dache
- IRCM, Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, Université de Montpellier, Institut régional du Cancer de Montpellier, Montpellier, France
| | - Amaëlle Otandault
- IRCM, Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, Université de Montpellier, Institut régional du Cancer de Montpellier, Montpellier, France
| | - Rita Tanos
- IRCM, Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, Université de Montpellier, Institut régional du Cancer de Montpellier, Montpellier, France
| | - Brice Pastor
- IRCM, Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, Université de Montpellier, Institut régional du Cancer de Montpellier, Montpellier, France
| | - Romain Meddeb
- IRCM, Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, Université de Montpellier, Institut régional du Cancer de Montpellier, Montpellier, France
| | - Cynthia Sanchez
- IRCM, Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, Université de Montpellier, Institut régional du Cancer de Montpellier, Montpellier, France
| | - Giuseppe Arena
- Gustave Roussy Cancer Campus, INSERM U1030, Villejuif, 94805, France
| | - Laurence Lasorsa
- IRCM, Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, Université de Montpellier, Institut régional du Cancer de Montpellier, Montpellier, France
| | - Andrew Bennett
- Institut Jacques Monod, Université Paris Diderot, Paris, France
| | - Thierry Grange
- Institut Jacques Monod, Université Paris Diderot, Paris, France
| | - Safia El Messaoudi
- IRCM, Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, Université de Montpellier, Institut régional du Cancer de Montpellier, Montpellier, France
| | - Thibault Mazard
- IRCM, Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, Université de Montpellier, Institut régional du Cancer de Montpellier, Montpellier, France
| | - Corinne Prevostel
- IRCM, Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, Université de Montpellier, Institut régional du Cancer de Montpellier, Montpellier, France
| | - Alain R Thierry
- IRCM, Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, Université de Montpellier, Institut régional du Cancer de Montpellier, Montpellier, France
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Packaging and transfer of mitochondrial DNA via exosomes regulate escape from dormancy in hormonal therapy-resistant breast cancer. Proc Natl Acad Sci U S A 2017; 114:E9066-E9075. [PMID: 29073103 PMCID: PMC5664494 DOI: 10.1073/pnas.1704862114] [Citation(s) in RCA: 449] [Impact Index Per Article: 64.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Increasing evidence suggests that extracellular vesicles (EVs) can transfer genetic material to recipient cells. However, the mechanism and role of this phenomenon are largely unknown. Here we have made a remarkable discovery: EVs can harbor the full mitochondrial genome. These extracellular vesicles can in turn transfer their mtDNA to cells with impaired metabolism, leading to restoration of metabolic activity. We determined that hormonal therapy induces oxidative phosphorylation-deficient breast cancer cells, which can be rescued via the transfer of mtDNA-laden extracellular vesicles. Horizontal transfer of mtDNA occurred in cancer stem-like cells and was associated with increased self-renewal potential of these cells, leading to resistance to hormonal therapy. We propose that mtDNA transfer occurs in human cancer via EVs. The horizontal transfer of mtDNA and its role in mediating resistance to therapy and an exit from dormancy have never been investigated. Here we identified the full mitochondrial genome in circulating extracellular vesicles (EVs) from patients with hormonal therapy-resistant (HTR) metastatic breast cancer. We generated xenograft models of HTR metastatic disease characterized by EVs in the peripheral circulation containing mtDNA. Moreover, these human HTR cells had acquired host-derived (murine) mtDNA promoting estrogen receptor-independent oxidative phosphorylation (OXPHOS). Functional studies identified cancer-associated fibroblast (CAF)-derived EVs (from patients and xenograft models) laden with whole genomic mtDNA as a mediator of this phenotype. Specifically, the treatment of hormone therapy (HT)-naive cells or HT-treated metabolically dormant populations with CAF-derived mtDNAhi EVs promoted an escape from metabolic quiescence and HTR disease both in vitro and in vivo. Moreover, this phenotype was associated with the acquisition of EV mtDNA, especially in cancer stem-like cells, expression of EV mtRNA, and restoration of OXPHOS. In summary, we have demonstrated that the horizontal transfer of mtDNA from EVs acts as an oncogenic signal promoting an exit from dormancy of therapy-induced cancer stem-like cells and leading to endocrine therapy resistance in OXPHOS-dependent breast cancer.
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Wang C, Liang C, Feng W, Xia X, Chen F, Qiao E, Zhang X, Chen D, Ling Z, Yang H. ICT1 knockdown inhibits breast cancer cell growth via induction of cell cycle arrest and apoptosis. Int J Mol Med 2017; 39:1037-1045. [PMID: 28290601 DOI: 10.3892/ijmm.2017.2913] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Accepted: 01/23/2017] [Indexed: 11/05/2022] Open
Abstract
The protein encoded by immature colon carcinoma transcript 1 (ICT1) is a component of the human mitochondrial ribosome, and is reported to be implicated in cell proliferation, viability and apoptosis of HeLa cells. This study was conducted to investigate the role of ICT1 in human breast cancer. Oncomine database was used to investigate ICT1 expression in human breast cancer tissues compared to normal tissues. The results showed that ICT1 was highly overexpressed in various human breast cancer subtypes. Then short hairpin RNA (shRNA)-mediated knockdown of ICT1 was performed in human breast cancer ZR-75-30 and T-47D cells. A series of functional analysis, including MTT, colony formation and flow cytometry assays were conducted after ICT1 knockdown. Our results demonstrated that knockdown of ICT1 significantly suppressed cell viability and proliferation through cell cycle arrest at the G2/M phase and induced apoptosis in breast cancer cells. Furthermore, knockdown of ICT1 altered signaling pathways associated with cell growth and apoptosis, including phospho‑BAD (Ser112), phospho-PRAS40 (Thr246) and induction of phospho‑AMPKα (Thr172). Additionally, it was further confirmed by western blot analysis that ICT1 knockdown altered the expression of apoptosis- or cell cycle‑related proteins such as Bcl-2, caspase-3, CDK1, CDK2 and cyclin B. In conclusion, targeting ICT1 in breast cancer cells may provide a new strategy for breast cancer gene therapy.
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Affiliation(s)
- Chen Wang
- Department of Oncology, First Clinical Medical College, Wenzhou Medical University, Wenzhou, Zhejiang 325000, P.R. China
| | - Chenlu Liang
- Department of Breast Surgery, Zhejiang Cancer Hospital, Hangzhou, Zhejiang 310022, P.R. China
| | - Weiliang Feng
- Department of Breast Surgery, Zhejiang Cancer Hospital, Hangzhou, Zhejiang 310022, P.R. China
| | - Xianghou Xia
- Department of Breast Surgery, Zhejiang Cancer Hospital, Hangzhou, Zhejiang 310022, P.R. China
| | - Feng Chen
- Department of Breast Surgery, Zhejiang Cancer Hospital, Hangzhou, Zhejiang 310022, P.R. China
| | - Enqi Qiao
- Department of Breast Surgery, Zhejiang Cancer Hospital, Hangzhou, Zhejiang 310022, P.R. China
| | - Xiping Zhang
- Department of Breast Surgery, Zhejiang Cancer Hospital, Hangzhou, Zhejiang 310022, P.R. China
| | - Daobao Chen
- Department of Breast Surgery, Zhejiang Cancer Hospital, Hangzhou, Zhejiang 310022, P.R. China
| | - Zhiqiang Ling
- Department of Breast Surgery, Zhejiang Cancer Hospital, Hangzhou, Zhejiang 310022, P.R. China
| | - Hongjian Yang
- Department of Oncology, First Clinical Medical College, Wenzhou Medical University, Wenzhou, Zhejiang 325000, P.R. China
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Yuan S, Xia Y, Zheng Y, Zeng X. Next-generation sequencing of mixed genomic DNA allows efficient assembly of rearranged mitochondrial genomes in Amolops chunganensis and Quasipaa boulengeri. PeerJ 2016; 4:e2786. [PMID: 27994980 PMCID: PMC5162401 DOI: 10.7717/peerj.2786] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Accepted: 11/11/2016] [Indexed: 01/01/2023] Open
Abstract
Recent improvements in next-generation sequencing (NGS) technologies can facilitate the obtainment of mitochondrial genomes. However, it is not clear whether NGS could be effectively used to reconstruct the mitogenome with high gene rearrangement. These high rearrangements would cause amplification failure, and/or assembly and alignment errors. Here, we choose two frogs with rearranged gene order, Amolops chunganensis and Quasipaa boulengeri, to test whether gene rearrangements affect the mitogenome assembly and alignment by using NGS. The mitogenomes with gene rearrangements are sequenced through Illumina MiSeq genomic sequencing and assembled effectively by Trinity v2.1.0 and SOAPdenovo2. Gene order and contents in the mitogenome of A. chunganensis and Q. boulengeri are typical neobatrachian pattern except for rearrangements at the position of "WANCY" tRNA genes cluster. Further, the mitogenome of Q. boulengeri is characterized with a tandem duplication of trnM. Moreover, we utilize 13 protein-coding genes of A. chunganensis, Q. boulengeri and other neobatrachians to reconstruct the phylogenetic tree for evaluating mitochondrial sequence authenticity of A. chunganensis and Q. boulengeri. In this work, we provide nearly complete mitochondrial genomes of A. chunganensis and Q. boulengeri.
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Affiliation(s)
- Siqi Yuan
- Department of Herpetology, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Sichuan, China; University of Chinese Academy of Sciences, Beijing, China
| | - Yun Xia
- Department of Herpetology, Chengdu Institute of Biology, Chinese Academy of Sciences , Chengdu , Sichuan , China
| | - Yuchi Zheng
- Department of Herpetology, Chengdu Institute of Biology, Chinese Academy of Sciences , Chengdu , Sichuan , China
| | - Xiaomao Zeng
- Department of Herpetology, Chengdu Institute of Biology, Chinese Academy of Sciences , Chengdu , Sichuan , China
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Wei S, Wang X, Bi C, Xu Y, Wu D, Ye N. Assembly and analysis of the complete Salix purpurea L. (Salicaceae) mitochondrial genome sequence. SPRINGERPLUS 2016; 5:1894. [PMID: 27843751 PMCID: PMC5084139 DOI: 10.1186/s40064-016-3521-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Accepted: 10/11/2016] [Indexed: 11/10/2022]
Abstract
Plant mitochondrial (mt) genomes possess several complex features, including a variable size, a dynamic genome structure, and complicated patterns of gene loss and gain throughout evolutionary history. Studies of plant mt genomes can, therefore, provide unique insights into organelle evolution. We assembled the complete Salix purpurea L. mt genome by screening genomic sequence reads generated by a Roche-454 pyrosequencing platform. The pseudo-molecule obtained has a typical circular structure 598,970 bp long, with an overall GC content of 55.06%. The S. purpurea mt genome contains 52 genes: 31 protein-coding, 18 tRNAs, and three rRNAs. Eighteen tandem repeats and 404 microsatellites are distributed unevenly throughout the S. purpurea mt genome. A phylogenetic tree of 23 representative terrestrial plants strongly supports S. purpurea inclusion in the Malpighiales clade. Our analysis contributes toward understanding the organization and evolution of organelle genomes in Salicaceae species.
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Affiliation(s)
- Suyun Wei
- College of Forestry, Nanjing Forestry University, Nanjing, 210037 Jiangsu China ; The Southern Modern Forestry Collaborative Innovation Center, Nanjing Forestry University, Nanjing, 210037 Jiangsu China ; College of Information Science and Technology, Nanjing Forestry University, Nanjing, 210037 Jiangsu China
| | - Xuelin Wang
- College of Information Science and Technology, Nanjing Forestry University, Nanjing, 210037 Jiangsu China
| | - Changwei Bi
- College of Information Science and Technology, Nanjing Forestry University, Nanjing, 210037 Jiangsu China
| | - Yiqing Xu
- College of Information Science and Technology, Nanjing Forestry University, Nanjing, 210037 Jiangsu China ; School of Computer Science and Engineering, Southeast University, Nanjing, 211189 Jiangsu China
| | - Dongyang Wu
- College of Forestry, Nanjing Forestry University, Nanjing, 210037 Jiangsu China ; The Southern Modern Forestry Collaborative Innovation Center, Nanjing Forestry University, Nanjing, 210037 Jiangsu China ; College of Information Science and Technology, Nanjing Forestry University, Nanjing, 210037 Jiangsu China
| | - Ning Ye
- The Southern Modern Forestry Collaborative Innovation Center, Nanjing Forestry University, Nanjing, 210037 Jiangsu China ; College of Information Science and Technology, Nanjing Forestry University, Nanjing, 210037 Jiangsu China
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Guan B, Guo H, Zhou Z. Illumina next-generation sequencing reveals the mitochondrial genome of Ducetia japonica (Orthoptera: Tettigoniidae). MITOCHONDRIAL DNA PART B-RESOURCES 2016; 1:361-362. [PMID: 33473484 PMCID: PMC7799970 DOI: 10.1080/23802359.2016.1168717] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Using Illumina next-generation sequencing (NGS), the complete mitochondrial genome (mitogenome) of Ducetia japonica was sequenced in the present study. The mitogenome of D. japonica (Genbank accession no. KU885974) is 16,276 bp in size, had the typical invertebrate mitochondrial gene arrangement and containing 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNA), 2 ribosomal RNA genes (rRNA) and a control region. Except for the control region (868 bp), one novel larger intergenic (616 bp) was found between nad2 and trnW. Phylogenetic results unambiguously support the monophyly of Phaneropterinae, although the gene order of two Sinochlora species different with other Tettigoniidae species. Using Illumina NGS platforms for mitogenome sequencing will provide rather essential and important DNA molecular data for the further phylogenetic analysis across major ensiferan lineages.
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Affiliation(s)
- Bei Guan
- College of Life Sciences, Hebei University, Baoding, China
| | - Huifang Guo
- College of Life Sciences, Hebei University, Baoding, China
| | - Zhijun Zhou
- College of Life Sciences, Hebei University, Baoding, China
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Moreira DA, Furtado C, Parente TE. The use of transcriptomic next-generation sequencing data to assemble mitochondrial genomes of Ancistrus spp. (Loricariidae). Gene 2015; 573:171-5. [DOI: 10.1016/j.gene.2015.08.059] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Revised: 08/20/2015] [Accepted: 08/28/2015] [Indexed: 11/27/2022]
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Abstract
Mitochondrial dysfunction underlies many human disorders, including those that affect the visual system. The retinal ganglion cells, whose axons form the optic nerve, are often damaged by mitochondrial-related diseases which result in blindness. Both mitochondrial DNA (mtDNA) and nuclear gene mutations impacting many different mitochondrial processes can result in optic nerve disease. Of particular importance are mutations that impair mitochondrial network dynamics (fusion and fission), oxidative phosphorylation (OXPHOS), and formation of iron-sulfur complexes. Current genetic knowledge can inform genetic counseling and suggest strategies for novel gene-based therapies. Identifying new optic neuropathy-causing genes and defining the role of current and novel genes in disease will be important steps toward the development of effective and potentially neuroprotective therapies.
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Affiliation(s)
- Janey L Wiggs
- Department of Ophthalmology, Harvard Medical School and Massachusetts Eye and Ear, Boston, Massachusetts 02114;
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Moreira DA, Magalhães MGP, de Andrade PCC, Furtado C, Val AL, Parente TE. An RNA-based approach to sequence the mitogenome of Hypoptopoma incognitum (Siluriformes: Loricariidae). Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:3784-6. [PMID: 26370305 DOI: 10.3109/19401736.2015.1079903] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Hypoptopoma incognitum is a fish of the fifth most species-rich family of vertebrates and abundant in rivers from the Brazilian Amazon. Only two species of Loricariidae fish have their complete mitogenomes sequence deposited in the Genbank. An innovative RNA-based approach was used to assemble the complete mitogenome of H. incognitum with an average coverage depth of 5292×. The typical vertebrate mitochondrial features were found; 22 tRNA genes, two rRNA genes, 13 protein-coding genes, and a non-coding control region. Moreover, the use of this approach allowed the measurement of mtRNA expression levels, the punctuation pattern of editing, and the detection of heteroplasmies.
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Affiliation(s)
- Daniel Andrade Moreira
- a Laboratório de Toxicologia Ambiental , Fundação Oswaldo Cruz (FIOCRUZ) , Rio de Janeiro , Brasil
| | - Maithê G P Magalhães
- a Laboratório de Toxicologia Ambiental , Fundação Oswaldo Cruz (FIOCRUZ) , Rio de Janeiro , Brasil
| | - Paula C C de Andrade
- a Laboratório de Toxicologia Ambiental , Fundação Oswaldo Cruz (FIOCRUZ) , Rio de Janeiro , Brasil
| | - Carolina Furtado
- b Divisão de Genética , Instituto Nacional do Cancer (INCA) , Rio de Janeiro , Brasil , and
| | - Adalberto L Val
- c Laboratório de Ecofisiologia e Evolução Molecular , Instituto Nacional de Pesquisas da Amazônia (INPA) , Manaus , Brasil
| | - Thiago Estevam Parente
- a Laboratório de Toxicologia Ambiental , Fundação Oswaldo Cruz (FIOCRUZ) , Rio de Janeiro , Brasil
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Wang Z, Zhu R, Zhang S, Bian Y, Lu D, Li C. Differentiating between monozygotic twins through next-generation mitochondrial genome sequencing. Anal Biochem 2015; 490:1-6. [PMID: 26327617 DOI: 10.1016/j.ab.2015.08.024] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2015] [Revised: 08/02/2015] [Accepted: 08/19/2015] [Indexed: 01/04/2023]
Abstract
Monozygotic (MZ) twins, considered to be genetically identical, cannot be distinguished from one another by standard forensic DNA testing. A recent study employed whole genome sequencing to identify extremely rare mutations and reported that mutation analysis could be used to differentiate between MZ twins. Compared with nuclear DNA, mitochondrial DNA (mtDNA) has higher mutation rates; therefore, minor differences theoretically exist in MZ twins' mitochondrial genome (mtGenome). However, conventional Sanger-type sequencing (STS) is neither amenable to, nor feasible for, the detection of low-level sequence variants. The recent introduction of massively parallel sequencing (MPS) has the capability to sequence many targeted regions of multiple samples simultaneously with desirable depth of coverage. Thus, the aim of this study was to assess whether full mtGenome sequencing analysis can be used to differentiate between MZ twins. Ten sets of MZ twins provided blood samples that underwent extraction, quantification, mtDNA enrichment, library preparation, and ultra-deep sequencing. Point heteroplasmies were observed in eight sets of MZ twins, and a single nucleotide variant (nt15301) was detected in five sets of MZ twins. Thus, this study demonstrates that ultra-deep mtGenome sequencing could be used to differentiate between MZ twins.
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Affiliation(s)
- Zheng Wang
- Shanghai Key Laboratory of Forensic Medicine, Institute of Forensic Science, Ministry of Justice, P. R. China, Shanghai 200063, China; State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Science, Fudan University, Shanghai 200433, China
| | - Ruxin Zhu
- Shanghai Key Laboratory of Forensic Medicine, Institute of Forensic Science, Ministry of Justice, P. R. China, Shanghai 200063, China
| | - Suhua Zhang
- Shanghai Key Laboratory of Forensic Medicine, Institute of Forensic Science, Ministry of Justice, P. R. China, Shanghai 200063, China; State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Science, Fudan University, Shanghai 200433, China
| | - Yinnan Bian
- Shanghai Key Laboratory of Forensic Medicine, Institute of Forensic Science, Ministry of Justice, P. R. China, Shanghai 200063, China
| | - Daru Lu
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Science, Fudan University, Shanghai 200433, China
| | - Chengtao Li
- Shanghai Key Laboratory of Forensic Medicine, Institute of Forensic Science, Ministry of Justice, P. R. China, Shanghai 200063, China.
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13
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Wilding M. Potential long-term risks associated with maternal aging (the role of the mitochondria). Fertil Steril 2015; 103:1397-401. [PMID: 25936236 DOI: 10.1016/j.fertnstert.2015.03.034] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Revised: 03/18/2015] [Accepted: 03/27/2015] [Indexed: 12/25/2022]
Abstract
The mean age at which women create families in Western society is increasing. This is in spite of the fact that reproduction in later life is subject to various difficulties, such as the lower probability of conception in relation to maternal age, the increase in spontaneous pregnancy loss, and higher obstetric risk. In this review of recent data, we suggest that a fourth effect, the decrease in lifespan of children in relation to the age of conception of the mother, can be added to the list. We discuss this effect in relation to the transmission of the mitochondria exclusively through the female germ line and the effect of age on this organelle. Data from our own studies and the animal literature as a whole suggest that this effect could be due to the transmission of damaged mitochondrial DNA, and further indicate that the effect is more widespread than previously considered.
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