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Yang C, Shikhsarmast FM, Fu C, Shen CY. The complete mitochondrial genome of Indo-Pacific soft coral Sinularia acuta Manuputty and van Ofwegen, 2007 (Octocorallia: Alcyonacea). Mitochondrial DNA B Resour 2023; 8:371-374. [PMID: 36926645 PMCID: PMC10013519 DOI: 10.1080/23802359.2023.2184658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2023] Open
Abstract
The complete mitochondrial genome (mitogenome) of the soft coral Sinularia acuta Manuputty and van Ofwegen, 2007 was sequenced and annotated using Illumina next-generation sequencing (NGS). The mitogenome of S. acuta was 18,730 bp in length and consisted of 14 protein-coding genes (PCGs), two ribosomal RNA genes (rRNA), and only one transfer RNA gene (tRNA-Met). The base composition was 30.18% A, 16.46% C, 19.35% G, and 34.00% T, with a total A + T content of 64.19%. The phylogenetic analysis demonstrated a close evolutionary relationship among Sinularia acuta, Sinularia penghuensis, and Sinularia maxima.
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Affiliation(s)
- Chaojie Yang
- Key Laboratory of Utilization and Conservation for Tropical Marine Bioresources, Hainan Tropical Ocean University, Sanya, China
| | - Farnaz Mahmoudi Shikhsarmast
- Key Laboratory of Utilization and Conservation for Tropical Marine Bioresources, Hainan Tropical Ocean University, Sanya, China
| | - Chunzheng Fu
- Institute of Sericulture, Chengde Medical University, Chengde, Hebei, China
| | - Chun-Yang Shen
- Department of Biology, Chengde Medical University, Chengde, Hebei, China
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Muthye V, Mackereth CD, Stewart JB, Lavrov DV. Large dataset of octocoral mitochondrial genomes provides new insights into mt-mutS evolution and function. DNA Repair (Amst) 2022; 110:103273. [DOI: 10.1016/j.dnarep.2022.103273] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 01/07/2022] [Accepted: 01/11/2022] [Indexed: 01/09/2023]
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Romanova EV, Bukin YS, Mikhailov KV, Logacheva MD, Aleoshin VV, Sherbakov DY. The Mitochondrial Genome of a Freshwater Pelagic Amphipod Macrohectopus branickii Is among the Longest in Metazoa. Genes (Basel) 2021; 12:2030. [PMID: 34946978 DOI: 10.3390/genes12122030] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 11/30/2021] [Accepted: 12/06/2021] [Indexed: 12/29/2022] Open
Abstract
There are more than 350 species of amphipods (Crustacea) in Lake Baikal, which have emerged predominantly through the course of endemic radiation. This group represents a remarkable model for studying various aspects of evolution, one of which is the evolution of mitochondrial (mt) genome architectures. We sequenced and assembled the mt genome of a pelagic Baikalian amphipod species Macrohectopus branickii. The mt genome is revealed to have an extraordinary length (42,256 bp), deviating significantly from the genomes of other amphipod species and the majority of animals. The mt genome of M. branickii has a unique gene order within amphipods, duplications of the four tRNA genes and Cox2, and a long non-coding region, that makes up about two thirds of the genome’s size. The extension of the mt genome was most likely caused by multiple duplications and inversions of regions harboring ribosomal RNA genes. In this study, we analyzed the patterns of mt genome length changes in amphipods and other animal phyla. Through a statistical analysis, we demonstrated that the variability in the mt genome length may be a characteristic of certain phyla and is primarily conferred by expansions of non-coding regions.
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Shen CY, Wang PZ, Xue W, Liu ZH, Zhao JY, Tong XB, Liu C, Wu XF, Mao X, Tian S, Fu C. The complete mitochondrial genome of soft coral Sinularia penghuensis Ofwegen and Benayahu, 2012 (Octocorallia: Alcyonacea): the analysis of mitogenome organization and phylogeny. Mitochondrial DNA B Resour 2021; 6:1348-1350. [PMID: 33889745 PMCID: PMC8043561 DOI: 10.1080/23802359.2021.1906174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The complete mitochondrial genome of Sinularia penghuensis was sequenced and analyzed using next-generation sequencing. The present mitochondrial genome was 18730 bp in length, containing 14 protein-coding genes (PCGs) (cox1-cox3.nad1-nad6, nad4L, atp6, atp8, cytb, and MutS), two ribosomal RNA genes (rRNAs) (12S and 16S), and one transfer RNA gene (Met-tRNA). The phylogenetic analysis of family Alcyoniidae revealed that S. penghuensis and Sinularia maxima cluster together. Five species in Sinularia reveals high identity in mitogenome sequences that the lowest variable sites (SNPs) were found between S. penghuensis and S. maxima.
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Affiliation(s)
- Chun-Yang Shen
- Department of Biology, Chengde Medical University, Hebei Province, Chengde, PR China
| | - Pei-Zheng Wang
- College of Ecology and Environment, Hainan Tropical Ocean University, Sanya, PR China
| | - Wei Xue
- Department of Chemical Engineering, Chengde Petroleum College, Chengde, PR China
| | - Zhao-Hui Liu
- Department of Biology, Chengde Medical University, Hebei Province, Chengde, PR China
| | - Jing-Yi Zhao
- Department of Functional Center, Chengde Medical University, Hebei Province, Chengde, PR China
| | - Xiao-Bo Tong
- Hemorheology Center, Chengde Medical University, Hebei Province, Chengde, PR China
| | - Chunwei Liu
- College of Ecology and Environment, Hainan Tropical Ocean University, Sanya, PR China
| | - Xiao-Fang Wu
- College of Ecology and Environment, Hainan Tropical Ocean University, Sanya, PR China
| | - Xiaonan Mao
- Department of Biology, Chengde Medical University, Hebei Province, Chengde, PR China
| | - Sihan Tian
- Department of Biology, Chengde Medical University, Hebei Province, Chengde, PR China
| | - Chunzheng Fu
- Institute of Sericulture, Chengde Medical University, Hebei Province, Chengde, PR China
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Seligmann H. Syntenies Between Cohosted Mitochondrial, Chloroplast, and Phycodnavirus Genomes: Functional Mimicry and/or Common Ancestry? DNA Cell Biol 2019; 38:1257-1268. [DOI: 10.1089/dna.2019.4858] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Hervé Seligmann
- The National Natural History Collections, The Hebrew University of Jerusalem, Jerusalem, Israel
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Shen CY, Dan YT, Asem A, Wang PZ, Xue W, Tong XB, Li W. The complete mitochondrial genome of soft coral Sarcophyton trocheliophorum (Cnidaria: Anthozoa) using next-generation sequencing. Mitochondrial DNA B Resour 2019; 4:3734-3735. [PMID: 33366165 PMCID: PMC7707615 DOI: 10.1080/23802359.2019.1679677] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Accepted: 09/25/2019] [Indexed: 11/30/2022] Open
Abstract
The complete mitochondrial genome of Sarcophyton trocheliophorum was completed using next-generation sequencing (NGS) method. The mitochondrial genome is a circular molecule of 18,508 bp in length, containing 14 protein-coding genes, two ribosomal RNA genes and one transfer RNA gene (Met-tRNA). The base composition is 30.45% A, 16.03% C, 19.13% G, and 34.40% T, with an A + T content of 64.85%. A phylogenetic analysis of Alcyoniidae showed that genus Sarcophyton had the closest relationship with Sinularia.
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Affiliation(s)
- Chun-Yang Shen
- Department of Biology, Chengde Medical University, Chengde, Hebei Province, China
| | - Ya-Ting Dan
- College of Fisheries and Life Science, Hainan Tropical Ocean University, Sanya, China
| | - Alireza Asem
- College of Fisheries and Life Science, Hainan Tropical Ocean University, Sanya, China
| | - Pei-Zheng Wang
- College of Fisheries and Life Science, Hainan Tropical Ocean University, Sanya, China
| | - Wei Xue
- Department of Chemical Engineering, Chengde Petroleum College, Chengde, China
| | - Xiao-Bo Tong
- Department of Physiology, Chengde Medical University, Chengde, Hebei Province, China
| | - Weidong Li
- College of Fisheries and Life Science, Hainan Tropical Ocean University, Sanya, China
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Bouda E, Stapon A, Garcia-Diaz M. Mechanisms of mammalian mitochondrial transcription. Protein Sci 2019; 28:1594-1605. [PMID: 31309618 DOI: 10.1002/pro.3688] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 07/10/2019] [Accepted: 07/11/2019] [Indexed: 01/06/2023]
Abstract
Numerous age-related human diseases have been associated with deficiencies in cellular energy production. Moreover, genetic alterations resulting in mitochondrial dysfunction are the cause of inheritable disorders commonly known as mitochondrial diseases. Many of these deficiencies have been directly or indirectly linked to deficits in mitochondrial gene expression. Transcription is an essential step in gene expression and elucidating the molecular mechanisms involved in this process is critical for understanding defects in energy production. For the past five decades, substantial efforts have been invested in the field of mitochondrial transcription. These efforts have led to the discovery of the main protein factors responsible for transcription as well as to a basic mechanistic understanding of the transcription process. They have also revealed various mechanisms of transcriptional regulation as well as the links that exist between the transcription process and downstream processes of RNA maturation. Here, we review the knowledge gathered in early mitochondrial transcription studies and focus on recent findings that shape our current understanding of mitochondrial transcription, posttranscriptional processing, as well as transcriptional regulation in mammalian systems.
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Affiliation(s)
- Emilie Bouda
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, New York
| | - Anthony Stapon
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, New York
| | - Miguel Garcia-Diaz
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, New York
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Seligmann H. Giant viruses: spore‐like missing links betweenRickettsiaand mitochondria? Ann N Y Acad Sci 2019; 1447:69-79. [DOI: 10.1111/nyas.14022] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2018] [Revised: 01/10/2019] [Accepted: 01/16/2019] [Indexed: 12/27/2022]
Affiliation(s)
- Hervé Seligmann
- The National Natural History Collectionsthe Hebrew University of Jerusalem Jerusalem Israel
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Seligmann H. Giant viruses as protein-coated amoeban mitochondria? Virus Res 2018; 253:77-86. [DOI: 10.1016/j.virusres.2018.06.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Revised: 06/13/2018] [Accepted: 06/14/2018] [Indexed: 01/18/2023]
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Seligmann H. Reviewing evidence for systematic transcriptional deletions, nucleotide exchanges, and expanded codons, and peptide clusters in human mitochondria. Biosystems 2017; 160:10-24. [PMID: 28807694 DOI: 10.1016/j.biosystems.2017.08.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Revised: 07/26/2017] [Accepted: 08/04/2017] [Indexed: 12/12/2022]
Abstract
Polymerization sometimes transforms sequences by (a) systematic deletions of mono-, dinucleotides after trinucleotides, or (b) 23 systematic nucleotide exchanges (9 symmetric, X<>Y, e.g. G<>T, 14 asymmetric, X > Y > Z > X, e.g. A > G > T > A), producing del- and swinger RNAs. Some peptides correspond to del- and swinger RNA translations, also according to tetracodons, codons expanded by a silent nucleotide. Here new analyzes assume different proteolytic patterns, partially alleviating false negative peptide detection biases, expanding noncanonical mitoproteome profiles. Mito-genomic, -transcriptomic and -proteomic evidence for noncanonical transcriptions and translations are reviewed and clusters of del- and swinger peptides (also along tetracodons) are described. Noncanonical peptide clusters indicate regulated expression of cryptically encoded mitochondrial protein coding genes. These candidate noncanonical proteins don't resemble known proteins.
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