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Super-Mitobarcoding in Plant Species Identification? It Can Work! The Case of Leafy Liverworts Belonging to the Genus Calypogeia. Int J Mol Sci 2022; 23:ijms232415570. [PMID: 36555212 PMCID: PMC9779425 DOI: 10.3390/ijms232415570] [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] [Received: 11/01/2022] [Revised: 12/04/2022] [Accepted: 12/05/2022] [Indexed: 12/14/2022] Open
Abstract
Molecular identification of species is especially important where traditional taxonomic methods fail. The genus Calypogeia belongs to one of the tricky taxons. The simple morphology of these species and a tendency towards environmental plasticity make them complicated in identification. The finding of the universal single-locus DNA barcode in plants seems to be 'the Holy Grail'; therefore, researchers are increasingly looking for multiloci DNA barcodes or super-barcoding. Since the mitochondrial genome has low sequence variation in plants, species delimitation is usually based on the chloroplast genome. Unexpectedly, our research shows that super-mitobarcoding can also work! However, our outcomes showed that a single method of molecular species delimitation should be avoided. Moreover, it is recommended to interpret the results of molecular species delimitation alongside other types of evidence, such as ecology, population genetics or comparative morphology. Here, we also presented genetic data supporting the view that C. suecica is not a homogeneous species.
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A Comparative Analyses of the Complete Mitochondrial Genomes of Fungal Endosymbionts in Sogatella furcifera, White-Backed Planthoppers. Int J Genomics 2021; 2021:6652508. [PMID: 34212028 PMCID: PMC8208876 DOI: 10.1155/2021/6652508] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 04/03/2021] [Accepted: 05/08/2021] [Indexed: 12/20/2022] Open
Abstract
Sogatella furcifera Horvath, commonly known as the white-backed planthoppers (WBPH), is an important pest in East Asian rice fields. Fungal endosymbiosis is widespread among planthoppers in the infraorder Fulgoromorpha and suborder Auchenorrhyncha. We successfully obtained complete mitogenome of five WBPH fungal endosymbionts, belonging to the Ophiocordycipitaceae family, from next-generation sequencing (NGS) reads obtained from S. furcifera samples. These five mitogenomes range in length from 55,390 bp to 55,406 bp, which is shorter than the mitogenome of the fungal endosymbiont found in Ricania speculum, black planthoppers. Twenty-eight protein-coding genes (PCGs), 12 tRNAs, and 2 rRNAs were found in the mitogenomes. Two single-nucleotide polymorphisms, two insertions, and three deletions were identified among the five mitogenomes, which were fewer in number than those of four species of Ophiocordycipitaceae, Ophiocordyceps sinensis, Hirsutella thompsonii, Hirsutella rhossiliensis, and Tolypocladium inflatum. Noticeably short lengths (up to 18 bp) of simple sequence repeats were identified in the five WBPH fungal endosymbiont mitogenomes. Phylogenetic analysis based on conserved PCGs across 25 Ophiocordycipitaceae mitogenomes revealed that the five mitogenomes were clustered with that of R. speculum, forming an independent clade. In addition to providing the full mitogenome sequences, obtaining complete mitogenomes of WBPH endosymbionts can provide insights into their phylogenetic positions without needing to isolate the mtDNA from the host. This advantage is of value to future studies involving fungal endosymbiont mitogenomes.
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Choi SS, Bakalin VA, Kwon W, Park J. The complete mitochondrial genome of Douinia plicata (Lindb.) Konstant. et. Vilnet (Scapaniaceae, Jungermanniales). Mitochondrial DNA B Resour 2021; 6:789-791. [PMID: 33763579 PMCID: PMC7954511 DOI: 10.1080/23802359.2021.1882901] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 01/24/2021] [Indexed: 12/20/2022] Open
Abstract
Douinia plicata (Lindb.) Konstant. & Vilnet is the endemic species in Northeast Asia. Here, we reported complete mitochondrial genome of D. plicata. It is 144,206 bp long and includes 72 genes (42 protein-coding genes, three rRNAs, and 27 tRNAs). The overall GC content is 45.1%. Intergeneic variations against S. amplicata, which is slightly higher than intraspecific variations of S. ampliata and W. denudata. Phylogenetic trees show D. plicatum is clustered with three Scapania mitochondrial genomes with high supportive values, which is congruent with previous studies.
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Affiliation(s)
- Seung Se Choi
- Team of National Ecosystem Survey, National Institute of Ecology, Seocheon, Republic of Korea
| | - Vadim A. Bakalin
- Laboratory of Cryptogamic Biota, Botanical Garden-Institute FEB RAS, Vladivostok, Russia
| | - Woochan Kwon
- InfoBoss Inc., Seoul, Republic of Korea
- InfoBoss Research Center, Seoul, Republic of Korea
| | - Jongsun Park
- InfoBoss Inc., Seoul, Republic of Korea
- InfoBoss Research Center, Seoul, Republic of Korea
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Choi SS, Min J, Kwon W, Park J. The complete mitochondrial genome of Scapania ampliata Steph., 1897 (Scapaniaceae, Jungermanniales). Mitochondrial DNA B Resour 2021; 6:686-688. [PMID: 33718609 PMCID: PMC7928006 DOI: 10.1080/23802359.2021.1882892] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Accepted: 01/24/2021] [Indexed: 10/31/2022] Open
Abstract
Scapania ampliata Steph. is the endemic species in East Asia. To investigate intraspecific variations on mitochondrial genomes of S. ampliata, we completed mitochondrial genome of S. ampliata isolated in Korea. It is 143,664 bp long and contains 73 genes (41 protein-coding genes, three rRNAs, 28 tRNAs, and one pseudogene). 823 single nucleotide polymorphisms (SNPs; 0.057%) and 2,242 insertions and deletions were identified between two S. ampliata mitochondrial genomes, which is large number of intraspecific variations in comparison to the other cases of Bryophyte mitochondrial genomes. Phylogenetic trees show that S. ampliata is clustered with those of two Scapania species with high supportive values.
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Affiliation(s)
- Seung Se Choi
- Team of National Ecosystem survey, National Institute of Ecology, Seocheon, Republic of Korea
| | - Juhyeon Min
- InfoBoss Inc., Seoul, Republic of Korea
- InfoBoss Research Center, Seoul, Republic of Korea
| | - Woochan Kwon
- InfoBoss Inc., Seoul, Republic of Korea
- InfoBoss Research Center, Seoul, Republic of Korea
| | - Jongsun Park
- InfoBoss Inc., Seoul, Republic of Korea
- InfoBoss Research Center, Seoul, Republic of Korea
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Park J, Xi H, Kim Y, Nam S, Heo KI. The complete mitochondrial genome of new species candidate of Rosa rugosa (Rosaceae). Mitochondrial DNA B Resour 2020; 5:3435-3437. [PMID: 33458196 PMCID: PMC7782103 DOI: 10.1080/23802359.2020.1821820] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 09/04/2020] [Indexed: 01/13/2023] Open
Abstract
Completed mitochondrial genome of a new species candidate of Rosa rugosa, named as Rosa angusta, is 303,484 bp long. The overall GC content of this mitochondrial genome is 45.2%. It contains 52 genes covering 31 protein-coding genes, 17 tRNAs, and 3 rRNAs. In comparison to R. rugosa mitochondrial genome assembled from the public NGS raw reads, 124 SNPs and 769 INDELs were identified. Phylogenetic trees suggest that more Rosa mitochondrial genomes will be needed to understand phylogenetic relationship of the two Rosa species.
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Affiliation(s)
- Jongsun Park
- InfoBoss Inc., Seoul, Republic of Korea
- InfoBoss Research Center, Seoul, Republic of Korea
| | - Hong Xi
- InfoBoss Inc., Seoul, Republic of Korea
- InfoBoss Research Center, Seoul, Republic of Korea
| | - Yongsung Kim
- InfoBoss Inc., Seoul, Republic of Korea
- InfoBoss Research Center, Seoul, Republic of Korea
| | - Suhwan Nam
- Baekdudaegan National Arboretum, Gyeongsangbuk-do, Korea
| | - Kyeong-In Heo
- InfoBoss Inc., Seoul, Republic of Korea
- InfoBoss Research Center, Seoul, Republic of Korea
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Choi SS, Min J, Kwon W, Park J. The complete mitochondrial genome of Wiesnerella denudata (Mitt.) Steph. (Wiesnerellaceae, Marchantiophyta): large number of intraspecific variations on mitochondrial genomes of W. denudata. Mitochondrial DNA B Resour 2020; 5:3351-3353. [PMID: 33458166 PMCID: PMC7782032 DOI: 10.1080/23802359.2020.1821814] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 09/04/2020] [Indexed: 10/25/2022] Open
Abstract
Wiesnerella denudata (Mitt.) Steph. is a thallose liverwort distributed in Asian subtropical to tropical regions. It is the only one species in genus Wiesnerella and family Wiesnerellaceae. To investigate intraspecific variations on mitochondrial genomes of W. denudata, we completed mitochondrial genome of W. denudata. Its length is 185,640 bp, longer than that of the previously sequenced mitochondrial genome by 71 bp and contains 73 genes (41 protein-coding genes, 3 rRNAs, 28 tRNAs, and 1 pseudogene). A total of 149 single nucleotide polymorphisms (SNPs) and 3,033 insertions and deletions are identified, much higher than those of Marchantia polymorpha subsp. ruderalis and Riccia fluitans. Phylogenetic trees show that W. denudata is clustered with Monosolenium tenerum belonging to Monosoleniaceae.
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Affiliation(s)
- Seung Se Choi
- Team of National Ecosystem Survey, National Institute of Ecology, Seocheon, Republic of Korea
| | - Juhyeon Min
- InfoBoss Inc., Seoul, Republic of Korea
- InfoBoss Research Center, Seoul, Republic of Korea
| | - Woochan Kwon
- InfoBoss Inc., Seoul, Republic of Korea
- InfoBoss Research Center, Seoul, Republic of Korea
| | - Jongsun Park
- InfoBoss Inc., Seoul, Republic of Korea
- InfoBoss Research Center, Seoul, Republic of Korea
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Choi SS, Kwon W, Park J. The complete chloroplast genome of Wiesnerella denudata (Mitt.) Steph. (Wiesnerellaceae, Marchantiophyta). MITOCHONDRIAL DNA PART B-RESOURCES 2020; 5:3124-3126. [PMID: 33458082 PMCID: PMC7782009 DOI: 10.1080/23802359.2020.1800431] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
We completed chloroplast genome of Wiesnerella denudata (Mitt.) Steph, only one species of the monotypic Wiesnerella genus and family Wiesnerellaceae Inoue. It is 122,500 bp and has four subregions: 82,143 bp of large single copy (LSC) and 20,009 bp of small single copy (SSC) regions are separated by 10,174 bp of inverted repeat (IR) regions including 132 genes (88 protein-coding genes, eight rRNAs, and 36 tRNAs). The overall GC content is 28.8% and those in the LSC, SSC, and IR regions are 26.4, 24.6, and 42.8%, respectively. Phylogenetic trees show incongruencies of phylogenetic relationship of W. denudata, requiring additional research.
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Affiliation(s)
- Seung Se Choi
- Team of National Ecosystem Survey, National Institute of Ecology, Seocheon, Republic of Korea
| | - Woochan Kwon
- InfoBoss Inc., Seoul, Republic of Korea.,InfoBoss Research Center, Seoul, Republic of Korea
| | - Jongsun Park
- InfoBoss Inc., Seoul, Republic of Korea.,InfoBoss Research Center, Seoul, Republic of Korea
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