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Cadorna CAE, Pahayo DG, Rey JD. The first mitochondrial genome of Calophyllum soulattri Burm.f. Sci Rep 2024; 14:5112. [PMID: 38429360 PMCID: PMC10907642 DOI: 10.1038/s41598-024-55016-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 02/19/2024] [Indexed: 03/03/2024] Open
Abstract
Calophyllum soulattri Burm.f. is traditionally used to treat skin infections and reduce rheumatic pain, yet genetic and genomic studies are still limited. Here, we present the first complete mitochondrial genome of C. soulattri. It is 378,262 bp long with 43.97% GC content, containing 55 genes (30 protein-coding, 5 rRNA, and 20 tRNA). Repeat analysis of the mitochondrial genome revealed 194 SSRs, mostly mononucleotides, and 266 pairs of dispersed repeats ( ≥ 30 bp) that were predominantly palindromic. There were 23 homologous fragments found between the mitochondrial and plastome genomes. We also predicted 345 C-to-U RNA editing sites from 30 protein-coding genes (PCGs) of the C. soulatrii mitochondrial genome. These RNA editing events created the start codon of nad1 and the stop codon of ccmFc. Most PCGs of the C. soulattri mitochondrial genome underwent negative selection, but atp4 and ccmB experienced positive selection. Phylogenetic analyses showed C. soulattri is a sister taxon of Garcinia mangostana. This study has shed light on C. soulattri's evolution and Malpighiales' phylogeny. As the first complete mitochondrial genome in Calophyllaceae, it can be used as a reference genome for other medicinal plant species within the family for future genetic studies.
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Affiliation(s)
- Charles Anthon E Cadorna
- Plant Molecular Phylogenetics Laboratory, Institute of Biology, College of Science, University of the Philippines, Diliman, 1101, Quezon City, Philippines
| | - Dexter G Pahayo
- Plant Molecular Phylogenetics Laboratory, Institute of Biology, College of Science, University of the Philippines, Diliman, 1101, Quezon City, Philippines
| | - Jessica D Rey
- Plant Molecular Phylogenetics Laboratory, Institute of Biology, College of Science, University of the Philippines, Diliman, 1101, Quezon City, Philippines.
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Cho SE, Kang H, Lee DH, Seo ST, Kim N, Lee S, Kim M, Shin K. The complete mitochondrial genome of a wood-decaying fungus Vanderbylia fraxinea (Polyporaceae, Polyporales). Mitochondrial DNA B Resour 2023; 8:1187-1191. [PMID: 37937099 PMCID: PMC10627039 DOI: 10.1080/23802359.2023.2275832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 10/21/2023] [Indexed: 11/09/2023] Open
Abstract
Vanderbylia fraxinea (Bull.) D.A. Reid, 1973 is an important wood-inhabiting fungus that plays a significant role in nutrient recycling in most forest ecosystems. In this study, the complete mitochondrial genome of V. fraxinea was characterized through de novo assembly using Illumina sequencing data and genome annotation. The mitochondrial genome is a circular molecule of 115,473 bp with a GC content of 28.66%. It comprises a total of 62 genes. Among these, 36 are protein-coding genes including 21 free-standing open reading frames (ORFs), 24 transfer RNA genes, and two ribosomal RNA genes. Core gene set commonly found in fungal mitochondrial genomes is also present in this genome, such as the apocytochrome b (cob), three subunits of the cytochrome c oxidase (cox1, cox2, and cox3), seven subunits of the NADH dehydrogenase (nad1, nad2, nad3, nad4, nad4L, nad5, and nad6), and three subunits of the ATP synthase (atp6, atp8, and atp9), as well as ribosomal RNA subunits (rns and rnl) and a set of transfer RNA genes. Phylogenetic analysis of the protein-coding sequences from the mitochondrial genome revealed a close relationship between V. fraxinea and the Ganoderma species within the Polyporaceae family.
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Affiliation(s)
- Sung-Eun Cho
- Institute of Agriculture and Life Science, Gyeongsang National University, Jinju, South Korea
| | - Heonil Kang
- Division of Forest Diseases and Insect Pests, National Institute of Forest Science, Seoul, South Korea
| | - Dong-Hyeon Lee
- Department of Environment and Forest Resources, Chungnam National University, Daejeon, Republic of Korea
| | - Sang-Tae Seo
- Division of Forest Diseases and Insect Pests, National Institute of Forest Science, Seoul, South Korea
| | - Namkyu Kim
- Forest Healing Department, Catholic Kwandong University, Gangneung, South Korea
| | - Sanggon Lee
- Department of Forest Environmental Resources, Gyeongsang National University, Jinju, South Korea
| | - Misong Kim
- Department of Forest Environmental Resources, Gyeongsang National University, Jinju, South Korea
| | - Keumchul Shin
- Institute of Agriculture and Life Science, Gyeongsang National University, Jinju, South Korea
- Department of Forest Environmental Resources, Gyeongsang National University, Jinju, South Korea
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Chen G, Kang R, Wang Z, Jiang Y, Zhou H, Abuduaini A, Suo F, Huang L. The complete mitochondrial genome of Cuminum cyminum (Apiales: Apiaceae) and phylogenetic analysis. Mitochondrial DNA B Resour 2023; 8:760-765. [PMID: 37521907 PMCID: PMC10375935 DOI: 10.1080/23802359.2023.2238357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 07/13/2023] [Indexed: 08/01/2023] Open
Abstract
Cumin (Cuminum cyminum L). belongs to the family Apiaceae and the order Apiales, which is a widely grown spice and medicinal plant in Xinjiang province, China. In the current study, whole genome sequencing of C. cyminum was performed using the Illumina HiSeq 4000 platform, and the complete mitogenome sequence was assembled and annotated. We found that the single circular mitogenome of C. cyminum was 246,721 bp in length, and has about 45.5% GC content. It comprised 73 genes in the coding region (35 protein-coding genes, 18 tRNA genes, 3 rRNA genes, and 15 open-reading frames) and a non-coding region. Phylogenetic analysis indicated that C. cyminum is closely related to Daucus carota and the subtribes Daucinae. The mitogenome of C. cyminum revealed its phylogenetic relationships with other species in the Apiaceae family, which would further help in understanding its evolution.
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Affiliation(s)
- Ge Chen
- College of Life Science and Technology, Guangxi University, Nanning, Guangxi, China
| | - Ruiping Kang
- College of Life Science and Technology, Xinjiang University, Urumchi, Xinjiang, China
| | - Zihao Wang
- College of Life Science and Technology, Guangxi University, Nanning, Guangxi, China
| | - Yu Jiang
- College of Life Science and Technology, Guangxi University, Nanning, Guangxi, China
| | - Huiying Zhou
- College of Life Science and Technology, Xinjiang University, Urumchi, Xinjiang, China
| | - Aifeire Abuduaini
- College of Life Science and Technology, Xinjiang University, Urumchi, Xinjiang, China
| | - Feiya Suo
- College of Life Science and Technology, Xinjiang University, Urumchi, Xinjiang, China
| | - Luodong Huang
- College of Life Science and Technology, Guangxi University, Nanning, Guangxi, China
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Lee DJ, Choi JW, Kang JN, Lee SM, Park GH, Kim CK. Chromosome-Scale Genome Assembly and Triterpenoid Saponin Biosynthesis in Korean Bellflower (Platycodon grandiflorum). Int J Mol Sci 2023; 24:ijms24076534. [PMID: 37047506 PMCID: PMC10095269 DOI: 10.3390/ijms24076534] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 03/24/2023] [Accepted: 03/29/2023] [Indexed: 04/03/2023] Open
Abstract
Platycodon grandiflorum belongs to the Campanulaceae family and is an important medicinal and food plant in East Asia. However, on the whole, the genome evolution of P. grandiflorum and the molecular basis of its major biochemical pathways are poorly understood. We reported a chromosome-scale genome assembly of P. grandiflorum based on a hybrid method using Oxford Nanopore Technologies, Illumina sequences, and high-throughput chromosome conformation capture (Hi-C) analysis. The assembled genome was finalized as 574 Mb, containing 41,355 protein-coding genes, and the genome completeness was assessed as 97.6% using a Benchmarking Universal Single-Copy Orthologs analysis. The P. grandiflorum genome comprises nine pseudo-chromosomes with 56.9% repeat sequences, and the transcriptome analysis revealed an expansion of the 14 beta-amylin genes related to triterpenoid saponin biosynthesis. Our findings provide an understanding of P. grandiflorum genome evolution and enable genomic-assisted breeding for the mass production of important components such as triterpenoid saponins.
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Cho SE, Oh JY, Lee DH. The complete mitochondrial genome of Cladosporium anthropophilum (cladosporiaceae, dothideomycetes). Mitochondrial DNA B Resour 2023; 8:164-166. [PMID: 36713294 PMCID: PMC9879183 DOI: 10.1080/23802359.2023.2167474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
The genus Cladosporium (Cladosporiaceae, Capnodiales) is a large genus of Ascomycota. Although the genus is mostly reported as saprobes from a wide range of substrates with a worldwide distribution, members of this genus comprise infectious agents in animals and plants. Of those, Cladosporium anthropophilum is a common saprophytic fungus and has been found to be a human opportunistic pathogen and plant pathogen. The complete mitochondrial genome of C. anthropophilum is characterized through the de novo assembly of Illumina sequencing data. The mitochondrial genome is a circular molecule of 35,937 bp with 30.23% GC content and has a total of 47 genes including 16 protein-coding genes, 29 transfer RNA genes, and two ribosomal RNA genes. Based on protein-coding sequences of the mitochondrial genome sequence, a phylogenetic tree was constructed to demonstrate the phylogenetic relationship of C. anthropophilum and its related genera.
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Affiliation(s)
- Sung-Eun Cho
- Forest Biodiversity Division, Korea National Arboretum, Pocheon, South Korea
| | - Ji Yeon Oh
- Division of Forest Insect Pests and Diseases, National Institute of Forest Science, Seoul, South Korea
| | - Dong-Hyeon Lee
- Division of Forest Insect Pests and Diseases, National Institute of Forest Science, Seoul, South Korea,CONTACT Dong-Hyeon Lee Division of Forest Insect Pests and Diseases, National Institute of Forest Science, Seoul, 02455, South Korea
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Lee HY, Jo JW, Kwak YN, Lee H, Ryu H, Sung J, So YS, Kim CS, Chung JW. The complete mitochondrial genome of the poisonous mushroom Trichoderma cornu-damae (Hypocreaceae). Mitochondrial DNA B Resour 2022; 7:1899-1901. [PMID: 36353061 PMCID: PMC9639550 DOI: 10.1080/23802359.2022.2135393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Trichoderma cornu-damae is a poisonous mushroom that contains trichothecene mycotoxins. The complete mitochondrial genome of this mushroom was determined using next-generation sequencing. This mitogenome is a circular molecule 94,608 bp in length with a GC content of 27.94% and contains 15 protein-coding genes, two rRNA genes (rnl and rns), and 25 tRNA genes. Phylogenetic analysis placed T. cornu-damae in the family Hypocreaceae group, which includes the genus Trichoderma. The mitogenome of T. cornu-damae will contribute to our understanding of the phylogeny, taxonomy, and population genetics of this mushroom.
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Affiliation(s)
- Hwa-Yong Lee
- Department of Forest Science, Chungbuk National University, Cheongju, Republic of Korea
| | - Jong Won Jo
- Forest Biodiversity Research Division, Korea National Arboretum, Pocheon, Republic of Korea
| | - Young-Nam Kwak
- Forest Biodiversity Research Division, Korea National Arboretum, Pocheon, Republic of Korea
| | - Hyun Lee
- Forest Biodiversity Research Division, Korea National Arboretum, Pocheon, Republic of Korea
| | - Hojin Ryu
- Department of Biology, Chungbuk National University, Cheongju, Republic of Korea
| | - Jwakyung Sung
- Department of Crop Science, Chungbuk National University, Cheongju, Republic of Korea
| | - Yoon-Sup So
- Department of Crop Science, Chungbuk National University, Cheongju, Republic of Korea
| | - Chang-Sun Kim
- Forest Biodiversity Research Division, Korea National Arboretum, Pocheon, Republic of Korea
| | - Jong-Wook Chung
- Department of Industrial Plant Science and Technology, Chungbuk National University, Cheongju, Republic of Korea
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Cho SE, Kwag YN, Han SK, Lee DH, Kim CS. Complete mitochondrial genome sequence of Pulveroboletus ravenelii (Boletales, Basidiomycota). Mitochondrial DNA B Resour 2022; 7:1581-1582. [PMID: 36082043 PMCID: PMC9448388 DOI: 10.1080/23802359.2022.2110006] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Pulveroboletus ravenelii, an ectomycorrhizal fungus, has long been used in traditional Chinese medicine and mushroom dyes; however, its mitogenome and phylogenetic relationship with other taxa remain unexplored. Here, we sequenced the mitochondrial genome of P. ravenelii using next-generation sequencing and found that its mitogenome, a circular DNA molecule of 43,528 bp, comprised 15 protein-coding genes, 15 transfer RNA genes, and two ribosomal RNA genes. The mitogenome had a base composition of A (37.52%), C (11.14%), G (12.21%), and T (39.13%) and a GC content of 23.35%. A phylogenetic tree was constructed to determine the phylogenetic relationship of this species with other taxa based on the mitochondrial genome sequence. This study revealed the phylogenetic positions of P. ravenelii and its related genera for the first time.
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Affiliation(s)
- Sung-Eun Cho
- Forest Biodiversity Division, Korea National Arboretum, Pocheon, South Korea
| | - Young-Nam Kwag
- Forest Biodiversity Division, Korea National Arboretum, Pocheon, South Korea
| | - Sang-Kuk Han
- Forest Biodiversity Division, Korea National Arboretum, Pocheon, South Korea
| | - Dong-Hyeon Lee
- Division of Forest Insect Pests and Diseases, National Institute of Forest Science, Seoul, South Korea
| | - Chang Sun Kim
- Forest Biodiversity Division, Korea National Arboretum, Pocheon, South Korea
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Cho KS, Lee HO, Lee SC, Park HJ, Seo JH, Cho JH, Park YE, Choi JG, Yang TJ. Mitochondrial genome recombination in somatic hybrids of Solanum commersonii and S. tuberosum. Sci Rep 2022; 12:8659. [PMID: 35606486 PMCID: PMC9127095 DOI: 10.1038/s41598-022-12661-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 05/12/2022] [Indexed: 11/19/2022] Open
Abstract
Interspecific somatic hybridization has been performed in potato breeding experiments to increase plant resistance against biotic and abiotic stress conditions. We analyzed the mitochondrial and plastid genomes and 45S nuclear ribosomal DNA (45S rDNA) for the cultivated potato (S. tuberosum, St), wild potato (S. commersonii, Sc), and their somatic hybrid (StSc). Complex genome components and structure, such as the hybrid form of 45S rDNA in StSc, unique plastome in Sc, and recombinant mitogenome were identified. However, the mitogenome exhibited dynamic multipartite structures in both species as well as in the somatic hybrid. In St, the mitogenome is 756,058 bp and is composed of five subgenomes ranging from 297,014 to 49,171 bp. In Sc, it is 552,103 bp long and is composed of two sub-genomes of 338,427 and 213,676 bp length. StSc has 447,645 bp long mitogenome with two subgenomes of length 398,439 and 49,206 bp. The mitogenome structure exhibited dynamic recombination mediated by tandem repeats; however, it contained highly conserved genes in the three species. Among the 35 protein-coding genes of the StSc mitogenome, 21 were identical for all the three species, and 12 and 2 were unique in Sc and St, respectively. The recombinant mitogenome might be derived from homologous recombination between both species during somatic hybrid development.
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Affiliation(s)
- Kwang-Soo Cho
- Department of Southern Area Crop Science, National Institute of Crop Science, Rural Development Administration, Miryang, 50424, Republic of Korea.
| | - Hyun-Oh Lee
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea.,Phyzen Genomics Institute, Baekgoong Plaza 1, Bundang-gu, Seongnam, 13558, Republic of Korea
| | - Sang-Choon Lee
- Phyzen Genomics Institute, Baekgoong Plaza 1, Bundang-gu, Seongnam, 13558, Republic of Korea
| | - Hyun-Jin Park
- Highland Agriculture Research Institute, National Institute of Crop Science, Rural Development Administration, Pyeongchang, 25342, Republic of Korea
| | - Jin-Hee Seo
- Highland Agriculture Research Institute, National Institute of Crop Science, Rural Development Administration, Pyeongchang, 25342, Republic of Korea
| | - Ji-Hong Cho
- Highland Agriculture Research Institute, National Institute of Crop Science, Rural Development Administration, Pyeongchang, 25342, Republic of Korea
| | - Young-Eun Park
- Highland Agriculture Research Institute, National Institute of Crop Science, Rural Development Administration, Pyeongchang, 25342, Republic of Korea
| | - Jang-Gyu Choi
- Highland Agriculture Research Institute, National Institute of Crop Science, Rural Development Administration, Pyeongchang, 25342, Republic of Korea
| | - Tae-Jin Yang
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea.
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Complete Mitochondrial Genome Sequence of
Colletotrichum siamense
Isolated in South Korea. Microbiol Resour Announc 2022; 11:e0105521. [PMID: 35471060 PMCID: PMC9119044 DOI: 10.1128/mra.01055-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
The complete mitochondrial genome of Colletotrichum siamense is characterized. The circular genome has a size of 52,710 bp, with a GC content of 34.45%, and contains 15 protein-coding genes, 23 tRNA genes, and 2 rRNA genes.
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Kim W, Ryu S, Song JH, Sim S. Complete chloroplast genome of Sphagnum subsecundum Nees from Korea. Mitochondrial DNA B Resour 2021; 6:3416-3417. [PMID: 34869865 PMCID: PMC8635543 DOI: 10.1080/23802359.2021.1999186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
Affiliation(s)
- Wonhee Kim
- Plant Resources Division, National Institute of Biological Resources, Incheon, Republic of Korea
| | - Seah Ryu
- Plant Resources Division, National Institute of Biological Resources, Incheon, Republic of Korea
| | - Ji-Hee Song
- Plant Resources Division, National Institute of Biological Resources, Incheon, Republic of Korea
| | - Sunhee Sim
- Plant Resources Division, National Institute of Biological Resources, Incheon, Republic of Korea
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Cho SE, Jo JW, Kwag YN, Lee H, Chung JW, Oh SH, Kim CS. Complete mitochondrial genome sequence of Gymnopilus junonius. Mitochondrial DNA B Resour 2021; 6:1020-1021. [PMID: 33796724 PMCID: PMC7995907 DOI: 10.1080/23802359.2021.1895692] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Gymnopilus junonius, a well-known poisonous mushroom, is distributed worldwide. It contains a hallucinogenic alkaloid psilocybin and several other bioactive compounds. The mitochondrial genome, a circular DNA molecule of 161,145 bp, comprises 15 protein-coding genes, 24 transfer RNA genes, and 2 ribosomal RNA genes. The guanine-cytosine content was 31.56%. Based on the mitochondrial genome sequence, a phylogenetic tree was constructed to demonstrate the phylogenetic relationship. In this study, the phylogenetic positions of G. junonius and its related genera were determined.
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Affiliation(s)
- Sung Eun Cho
- Forest Biodiversity Division, Korea National Arboretum, Pocheon, South Korea
| | - Jong Won Jo
- Forest Biodiversity Division, Korea National Arboretum, Pocheon, South Korea
| | - Young-Nam Kwag
- Forest Biodiversity Division, Korea National Arboretum, Pocheon, South Korea
| | - Hyun Lee
- Forest Biodiversity Division, Korea National Arboretum, Pocheon, South Korea
| | - Jong-Wook Chung
- Department of Industrial Plant Science and Technology, Chungbuk National University, South Korea
| | - Seung Hwan Oh
- Forest Biodiversity Division, Korea National Arboretum, Pocheon, South Korea
| | - Chang Sun Kim
- Forest Biodiversity Division, Korea National Arboretum, Pocheon, South Korea
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Kim JU, Kim JH. Complete mitochondrial genome of the snow petrel, Pagodroma nivea. MITOCHONDRIAL DNA PART B-RESOURCES 2020; 5:3337-3338. [PMID: 33458159 PMCID: PMC7783026 DOI: 10.1080/23802359.2020.1820389] [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: 11/17/2022]
Abstract
The snow petrel, Pagodroma nivea is a small sea bird endemic to Antarctica and the Southern Ocean. Herein, we assembled a complete mitochondrial genome of the snow petrel as a first revealed genetic resource in Pagodroma family. The mitogenome is 17,279 bp in length and consists of 13 protein-coding genes (PCGs), 22 tRNA genes, and two rRNA genes. Base composition is 31.3% A, 25.3% T, 30.1% C, and 13.2% G with CG content of 43.4%. These results will provide a useful basis for further genetic and phylogenetic studies of this species.
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Affiliation(s)
- Jong-U Kim
- Korea Polar Research Institute, Incheon, South Korea
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Kim JU, Kim JH. Complete mitochondrial genome and phylogenetic analysis of the Weddell seal, Leptonychotes weddellii. MITOCHONDRIAL DNA PART B-RESOURCES 2020; 5:3339-3340. [PMID: 33458160 PMCID: PMC7783060 DOI: 10.1080/23802359.2020.1820390] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The Weddell seal, Leptonychotes weddellii, which belongs to the family Phocidae, is an abundant pinniped that inhabits the Antarctica. Here, we present the complete mitochondrial genome and phylogeny of L. weddellii. The total length of the mitogenome is 16,762 bp, consisting of 13 protein-coding genes (PCGs), 22 tRNA genes, and 2 rRNA genes. The base composition of the mitogenome is 34.26% (A), 25.51% (T), 27.09% (C), and 13.11% (G), and 40.22% for overall GC contents. The description of this mitogenome can provide information about variations at the intra-species level and aid phylogenetic studies in family Phocidae.
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Affiliation(s)
- Jong-U Kim
- Korea Polar Research Institute, Incheon, South Korea
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Jung JW, Lee H, Choi HG, Kim JH. Complete mitogenome of the Cape petrel Daption capense from Barton Peninsula, King George Island, Antarctica. MITOCHONDRIAL DNA PART B 2019. [DOI: 10.1080/23802359.2019.1607585] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Jin-Woo Jung
- Korea Polar Research Institute, Incheon, Yeonsu-gu, South Korea
| | - Hyoungseok Lee
- Korea Polar Research Institute, Incheon, Yeonsu-gu, South Korea
| | - Han-Gu Choi
- Korea Polar Research Institute, Incheon, Yeonsu-gu, South Korea
| | - Jeong-Hoon Kim
- Korea Polar Research Institute, Incheon, Yeonsu-gu, South Korea
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Wang S, Song Q, Li S, Hu Z, Dong G, Song C, Huang H, Liu Y. Assembly of a Complete Mitogenome of Chrysanthemum nankingense Using Oxford Nanopore Long Reads and the Diversity and Evolution of Asteraceae Mitogenomes. Genes (Basel) 2018; 9:E547. [PMID: 30424578 PMCID: PMC6267336 DOI: 10.3390/genes9110547] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2018] [Revised: 11/03/2018] [Accepted: 11/07/2018] [Indexed: 12/22/2022] Open
Abstract
Diversity in structure and organization is one of the main features of angiosperm mitochondrial genomes (mitogenomes). The ultra-long reads of Oxford Nanopore Technology (ONT) provide an opportunity to obtain a complete mitogenome and investigate the structural variation in unprecedented detail. In this study, we compared mitogenome assembly methods using Illumina and/or ONT sequencing data and obtained the complete mitogenome (208 kb) of Chrysanthemum nankingense based on the hybrid assembly method. The mitogenome encoded 19 transfer RNA genes, three ribosomal RNA genes, and 34 protein-coding genes with 21 group II introns disrupting eight intron-contained genes. A total of seven medium repeats were related to homologous recombination at different frequencies as supported by the long ONT reads. Subsequently, we investigated the variations in gene content and constitution of 28 near-complete mitogenomes from Asteraceae. A total of six protein-coding genes were missing in all Asteraceae mitogenomes, while four other genes were not detected in some lineages. The core fragments (~88 kb) of the Asteraceae mitogenomes had a higher GC content (~46.7%) than the variable and specific fragments. The phylogenetic topology based on the core fragments of the Asteraceae mitogenomes was highly consistent with the topologies obtained from the corresponding plastid datasets. Our results highlighted the advantages of the complete assembly of the C. nankingense mitogenome and the investigation of its structural variation based on ONT sequencing data. Moreover, the method based on local collinear blocks of the mitogenomes could achieve the alignment of highly rearrangeable and variable plant mitogenomes as well as construct a robust phylogenetic topology.
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Affiliation(s)
- Shuaibin Wang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, the Chinese Academy of Sciences, Guangzhou 510650, China.
- Guangdong Provincial Key Laboratory of Applied Botany, Guangzhou 510650, China.
- University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Qingwei Song
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, the Chinese Academy of Sciences, Guangzhou 510650, China.
- Guangdong Provincial Key Laboratory of Applied Botany, Guangzhou 510650, China.
- University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Shanshan Li
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, the Chinese Academy of Sciences, Guangzhou 510650, China.
- Guangdong Provincial Key Laboratory of Applied Botany, Guangzhou 510650, China.
- University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Zhigang Hu
- College of Pharmacy, Hubei University of Chinese Medicine, Wuhan 430065, China.
| | | | - Chi Song
- Wuhan Benagen Tech Solutions Company Limited, Wuhan 430070, China.
| | - Hongwen Huang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, the Chinese Academy of Sciences, Guangzhou 510650, China.
| | - Yifei Liu
- College of Pharmacy, Hubei University of Chinese Medicine, Wuhan 430065, China.
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