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Jin L, Ding Q, Zhang L, Bai M. The first complete mitochondrial genome of the genus Homoderus and insights into phylogeny of Lucanidae (Coleoptera: Lucanidae). Mitochondrial DNA B Resour 2024; 9:981-985. [PMID: 39105176 PMCID: PMC11299458 DOI: 10.1080/23802359.2024.2385610] [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: 03/18/2024] [Accepted: 07/24/2024] [Indexed: 08/07/2024] Open
Abstract
Homoderus mellyi belongs to the Lucanidae family of Coleoptera. The first complete mitogenome of Homoderus is reported in this paper. The genome is 16,807 bp in length and contains the typical 37 genes with 22 transfer RNA genes, 13 protein coding genes, and 2 ribosomal RNA genes. The gene order is conserved across the lineage. The average base composition of the mitogenome is 36.6% for A, 20.8% for C, 11.6% for G, and 31.1% for T. The percentage of GC is 32.3%. The genome organization, nucleotide composition, and codon usage are similar to other beetles. Phylogenetic analysis shows that Lucanidae is monophyletic, and all subfamilies are monophyletic, respectively. The phylogenetic position of H. mellyi is consistent with other research.
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Affiliation(s)
- Lijie Jin
- Key Laboratory of Animal Biodiversity Conservation and Integrated Pest Management (Chinese Academy of Sciences), Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Qiang Ding
- Key Laboratory of Animal Biodiversity Conservation and Integrated Pest Management (Chinese Academy of Sciences), Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Lijie Zhang
- Science and Technical Research Center of China Customs, Beijing, China
| | - Ming Bai
- Key Laboratory of Animal Biodiversity Conservation and Integrated Pest Management (Chinese Academy of Sciences), Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Northeast Asia Biodiversity Research Center, Northeast Forestry University, Harbin, China
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Jafir M, Zhou L, Chen Y, Wan X. The first mitogenomic phylogenetic framework of Dorcus sensu lato (Coleoptera: Lucanidae), with an emphasis on generic taxonomy in Eastern Asia. BMC Ecol Evol 2024; 24:66. [PMID: 38773381 PMCID: PMC11107052 DOI: 10.1186/s12862-024-02225-2] [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: 08/18/2023] [Accepted: 03/14/2024] [Indexed: 05/23/2024] Open
Abstract
BACKGROUND Dorcus stag beetles in broad sense are one of the most diverse group in Lucanidae and important saproxylic insects playing a crucial role in nutrient recycling and forest biomonitoring. However, the dazzling morphological differentiations have caused numerous systematic confusion within the big genus, especially the puzzlingly generic taxonomy. So far, there is lack of molecular phylogenetic study to address the chaotic situation. In this study, we undertook mitochondrial genome sequencing of 42 representative species including 18 newly-sequenced ones from Eastern Asia and reconstructed the phylogenetic framework of stag beetles in Dorcus sensu lato for the first time. RESULTS The mitogenome datasets of Dorcus species have indicated the variable mitogenomic lengths ranged from 15,785 to 19,813 bp. Each mitogenome contained 13 PCGs, 2 rRNAs, 22 tRNAs, and a control region, and all PCGs were under strong purifying selection (Ka/Ks < 1). Notably, we have identified the presence of a substantial intergenic spacer (IGS) between the trnAser (UCN) and NAD1 genes, with varying lengths ranging from 129 bp (in D. hansi) to 158 bp (in D. tityus). The mitogenomic phylogenetic analysis of 42 species showed that Eastern Asia Dorcus was monophyletic, and divided into eight clades with significant genetic distance. Four of them, Clade VIII, VII, VI and I are clustered by the representative species of Serrognathus Motschulsky, Kirchnerius Schenk, Falcicornis Séguy and Dorcus s.s. respectively, which supported their fully generic positions as the previous morphological study presented. The topology also showed the remaining clades were distinctly separated from the species of Dorcus sensu lato, which implied that each of them might demonstrate independent generic status. The Linnaeus nomenclatures were suggested as Eurydorcus Didier stat. res., Eurytrachellelus Didier stat. res., Hemisodorcus Thomson stat. res. and Velutinodorcus Maes stat. res. For Clade V, IV, III and II respectively. CONCLUSION This study recognized the monophyly of Dorcus stag beetles and provided a framework for the molecular phylogeny of this group for the first time. The newly generated mitogenomic data serves as a valuable resource for future investigations on lucanid beetles. The generic relationship would facilitate the systematics of Dorcus stag beetles and thus be useful for exploring their evolutionary, ecological, and conservation aspects.
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Affiliation(s)
- Muhammad Jafir
- Department of Ecology, School of Resources and Environmental Engineering, Anhui University, 230601, Hefei, Anhui, China
| | - Liyang Zhou
- Department of Ecology, School of Resources and Environmental Engineering, Anhui University, 230601, Hefei, Anhui, China
| | - Yongjing Chen
- Department of Ecology, School of Resources and Environmental Engineering, Anhui University, 230601, Hefei, Anhui, China
| | - Xia Wan
- Department of Ecology, School of Resources and Environmental Engineering, Anhui University, 230601, Hefei, Anhui, China.
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Zhang N, Pu T, Wang J, Tan W, Yuan Z, Li C, Song Y. Phylogenetic Analysis of Two New Mitochondrial Genomes of Singapora shinshana and Seriana bacilla from the Karst Region of Southwest China. Genes (Basel) 2023; 14:1318. [PMID: 37510223 PMCID: PMC10379811 DOI: 10.3390/genes14071318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 06/16/2023] [Accepted: 06/21/2023] [Indexed: 07/30/2023] Open
Abstract
Leafhoppers have been identified as a serious threat to different plants. To explore the characteristics of mitogenomes and reveal the phylogenetic positions of two species in the Typhlocybinae, complete mitogenomes of Singapora shinshana and Seriana bacilla were sequenced and annotated for the first time with lengths of 15,402 bp and 15,383 bp, respectively. The two mitogenomes contained 13 PCGs, 22 tRNA genes and 2 rRNA genes. The genome content, gene order, nucleotide composition, codon usage and amino acid composition are similar to those of other typical mitogenomes of Typhlocybinae. All 13 PCGs started with ATN codons, except for atp8 (TTA) and nad5 (TTG). All tRNAs were folded into a typical cloverleaf secondary structure, except for tRNA-Ser1 and tRNA-Val. Moreover, phylogenetic trees were constructed and analyzed based on all the PCGs from 42 mitogenomes using maximum likelihood (ML) and Bayesian inference (BI) methods. The results supported that eleven subfamilies are all monophyletic groups, S. shinshana and S. bacilla are members of Erythroneurini, but S. shinshana and the genus Empoascanara have a very close relationship with ((((Empoascanara sipra+ Empoascanara wengangensis) + Empoascanara dwalata) + Empoascanara gracilis) + S. shinshana), and S. bacilla is closely related to the genus Mitjaevia ((Mitjaevia dworakowskae + Mitjaevia shibingensis) + S. bacilla). These results provide valuable information for future study of evolutionary relationships in Typhlocybinae.
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Affiliation(s)
- Ni Zhang
- School of Karst Science, Guizhou Normal University, Guiyang 550001, China
- State Engineering Technology Institute for Karst Desertification Control, Guiyang 550001, China
| | - Tianyi Pu
- School of Karst Science, Guizhou Normal University, Guiyang 550001, China
- State Engineering Technology Institute for Karst Desertification Control, Guiyang 550001, China
| | - Jinqiu Wang
- School of Karst Science, Guizhou Normal University, Guiyang 550001, China
- State Engineering Technology Institute for Karst Desertification Control, Guiyang 550001, China
| | - Weiwen Tan
- School of Karst Science, Guizhou Normal University, Guiyang 550001, China
- State Engineering Technology Institute for Karst Desertification Control, Guiyang 550001, China
| | - Zhouwei Yuan
- School of Karst Science, Guizhou Normal University, Guiyang 550001, China
- State Engineering Technology Institute for Karst Desertification Control, Guiyang 550001, China
| | - Can Li
- Guizhou Provincial Key Laboratory for Rare Animal and Economic Insect of the Mountainous Region, Guiyang University, Guiyang 550005, China
| | - Yuehua Song
- School of Karst Science, Guizhou Normal University, Guiyang 550001, China
- State Engineering Technology Institute for Karst Desertification Control, Guiyang 550001, China
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Hong KJ, Ki W, Lee IJ, Lee H, Park J, Lee W. The complete mitochondrial genome of Aclees taiwanensis Kôno, 1933 (Coleoptera: Curculionidae). Mitochondrial DNA B Resour 2022; 7:1460-1462. [PMID: 35979394 PMCID: PMC9377266 DOI: 10.1080/23802359.2022.2107440] [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: 11/17/2022] Open
Abstract
We sequenced the complete mitochondrial genome of Aclees taiwanensis collected in Korea. The circular mitogenome of A. taiwanensis is 17,435 bp, longer than that of Aclees cribratus, and includes 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNAs, and a control region/D-loop. The AT ratio is 75.4%. Maximum-likelihood and Bayesian inference phylogenetic trees showed that A. taiwanensis was clustered with A. cribratus with full-support values for both trees.
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Affiliation(s)
- Ki-Jeong Hong
- Department of Plant Medicine, Sunchon National University, Suncheon, Korea
| | - Woong Ki
- Department of Plant Medicine, Sunchon National University, Suncheon, Korea
| | - In-Jun Lee
- Department of Plant Medicine, Sunchon National University, Suncheon, Korea
| | - Hyobin Lee
- Department of Plant Medicine, Gyeongsang National University, Jinju, Republic of Korea
| | - Jongsun Park
- Infoboss Inc, Seoul, Republic of Korea
- Infoboss Research Center, Seoul, Republic of Korea
| | - Wonhoon Lee
- Department of Plant Medicine, Gyeongsang National University, Jinju, Republic of Korea
- Institute of Agriculture and Life Science, Gyeongsang National University, Jinju, Republic of Korea
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Xu M, Zhou S, Wan X. Phylogenetic Implication of Large Intergenic Spacers: Insights from a Mitogenomic Comparison of Prosopocoilus Stag Beetles (Coleoptera: Lucanidae). Animals (Basel) 2022; 12:ani12131595. [PMID: 35804495 PMCID: PMC9264858 DOI: 10.3390/ani12131595] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Revised: 06/12/2022] [Accepted: 06/18/2022] [Indexed: 11/16/2022] Open
Abstract
Simple Summary Insect mitochondrial genomes (mitogenomes) show high diversity in some lineages. In the mitogenome of some Coleoptera species, a large intergenic spacer (IGS) has been identified. However, very little is known about mitogenomes of lucanid beetles. In this work, to provide further insight into the phylogenic relationships among species in lucanid beetles (genus Prosopocoilus), two Prosopocoilus species (Prosopocoilus castaneus and Prosopocoilus laterotarsus) were newly sequenced and comparatively analyzed. Significantly, the two newly sequenced Prosopocoilus species contained a large IGS located between trnI and trnQ. Our phylogenomic analyses showed that P. castaneus and P. laterotarsus were clustered in a clade with typical Prosopocoilus species (Prosopocoilus confucius, Prosopocoilus blanchardi, and Prosopocoilusastacoides). These results provide valuable data for the future study of the phylogenetic relationships in this genus. Abstract To explore the characteristics of mitogenomes and discuss the phylogenetic relationships within the genus Prosopocoilus, the mitogenomes of two species (P. castaneus and P. laterotarsus) were newly sequenced and comparatively analyzed. The arrangement of the mitogenome in these two lucanid beetles was the same as that in the inferred ancestral insect, and the nucleotide composition was highly biased towards A + T as in other lucanids. The evolutionary rates of 13 protein-coding genes (PCGs) suggested that their evolution was based on purifying selection. Notably, we found evidence of the presence of a large IGS between trnI and trnQ genes, whose length varied from 375 bp (in P. castaneus) to 158 bp (in P. laterotarsus). Within the large IGS region, a short sequence (TAAAA) was found to be unique among these two species, providing insights into phylogenomic reconstruction. Phylogenetic analyses were performed using the maximum likelihood (IQ-TREE) and Bayesian (PhyloBayes) methods based on 13 protein-coding genes (PCGs) in nucleotides and amino acids (AA) from published mitogenomes (n = 29). The genus Prosopocoilus was found to constitute a distinct clade with high nodal support. Overall, our findings suggested that analysis of the characteristics of the large IGS (presence or absence, size, and location) in mitogenomes of the genus Prosopocoilus may be informative for the phylogenetic and taxonomic analyses and for evaluation of the genus Prosopocoilus, despite the dense sampling materials needed.
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Affiliation(s)
- Mengqiong Xu
- Department of Ecology, School of Resources and Environmental Engineering, Anhui University, Hefei 230601, China; (M.X.); (S.Z.)
- Anhui Province Key Laboratory of Wetland Ecosystem Protection and Restoration, Hefei 230601, China
| | - Shiju Zhou
- Department of Ecology, School of Resources and Environmental Engineering, Anhui University, Hefei 230601, China; (M.X.); (S.Z.)
- Anhui Province Key Laboratory of Wetland Ecosystem Protection and Restoration, Hefei 230601, China
| | - Xia Wan
- Department of Ecology, School of Resources and Environmental Engineering, Anhui University, Hefei 230601, China; (M.X.); (S.Z.)
- Anhui Province Key Laboratory of Wetland Ecosystem Protection and Restoration, Hefei 230601, China
- Correspondence: ; Tel.: +86-136-3709-1923
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Park J, Lee J, Park J. The investigation of intraspecific characteristics and comparative analyses of the complete mitochondrial genome of Stegobium paniceum (Linnaeus, 1758) (Coleoptera: Ptinidae) assembled from public NGS raw reads of the black truffle, Tuber melanosporum. Sci Prog 2022; 105:368504211072355. [PMID: 35040745 PMCID: PMC10358573 DOI: 10.1177/00368504211072355] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Due to the rapid development of NGS technologies, a huge amount of NGS raw reads have been accumulated in public repositories, such as the Short Read Archive of NCBI. We successfully rescued the complete mitochondrial genome of Stegobium paniceum, a drug store beetle, from public NGS raw reads of truffle generated from the whole genome project. The circular mitogenome of S. paniceum is 15,474 bp long including 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNAs, and a single large non-coding region of 803 bp. Intraspecific transfer RNAs structure and sequence variations were investigated and simple sequence repeats identified from three S. paniceum mitochondrial genomes were compared showing their diversities as fundamental data to utilize them in various aspects including developing efficient molecular markers in the family, Ptinidae. Phylogenetic analysis of 23 Bostrichoidea mitochondrial genomes presented better species identification based on phylogenetic analyses and the optimal options for constructing phylogenetic trees based on Bostrichoidea mitochondrial genomes. Our results present not only utilization of public NGS raw read sequences but also intraspecific features of S. paniceum mitochondrial genomes and comparative analysis of Bostrichoidea mitochondrial genomes in various aspects.
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Affiliation(s)
- Jongsun Park
- InfoBoss Inc., Seoul, Republic of Korea
- InfoBoss Research Center, Seoul, Republic of Korea
| | - Jungmo Lee
- InfoBoss Inc., Seoul, Republic of Korea
- InfoBoss Research Center, Seoul, Republic of Korea
| | - Jonghyun Park
- InfoBoss Inc., Seoul, Republic of Korea
- InfoBoss Research Center, Seoul, Republic of Korea
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A New Mitochondrial Genome of Sogatella furcifera (Horváth) (Hemiptera: Delphacidae) and Mitogenome-Wide Investigation on Polymorphisms. INSECTS 2021; 12:insects12121066. [PMID: 34940154 PMCID: PMC8706918 DOI: 10.3390/insects12121066] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/28/2021] [Revised: 11/16/2021] [Accepted: 11/25/2021] [Indexed: 01/23/2023]
Abstract
Simple Summary We completed one mitogenome of white-backed planthopper (WBPH), Sogatella furcifera (Horváth), with finding heteroplasmy phenomenon confirmed by PCR reaction and Sanger sequencing method. This heteroplasmy was not observed in WBPHs (n = 24) collected from the fields, suggesting that it may be uncommon in fields. We also analyzed single nucleotide polymorphisms, insertion and deletions, and simple sequence repeats among three currently available WBPH mitogenomes of Korea and China, suggesting that identified intraspecific variations could be potential candidates for developing markers to distinguish geographical populations of WBPH including Korean and Chinese. Phylogenetic analysis of 32 mitogenomes of Delphacidae including the three WBPH mitogenomes suggested that Delphacinae seems to be monophyletic and Sogatella species including WBPH are clearly formed as one clade. Abstract White-backed planthopper (WBPH), Sogatella furcifera (Horváth), is one of the major sap-sucking rice pests in East Asia. We have determined a new complete mitochondrial genome of WBPH collected in the Korean peninsula using NGS technology. Its length and GC percentages are 16,613 bp and 23.8%, respectively. We observed one polymorphic site, a non-synonymous change, in the COX3 gene with confirmation heteroplasmy phenomenon within individuals of WBPH by PCR amplification and Sanger sequencing, the first report in this species. In addition, this heteroplasmy was not observed in wild WBPH populations, suggesting that it may be uncommon in fields. We analyzed single nucleotide polymorphisms, insertion, and deletions, and simple sequence repeats among the three WBPH mitogenomes from Korea and China and found diverse intraspecific variations, which could be potential candidates for developing markers to distinguish geographical populations. Phylogenetic analysis of 32 mitogenomes of Delphacidae including the three WBPH mitogenomes suggested that Delphacinae seems to be monophyletic and Sogatella species including WBPH are clearly formed as one clade. In the future, it is expected that complete mitogenomes of individuals of geographically dispersed WBPH populations will be used for further population genetic studies to understand the migration pathway of WBPH.
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Kim M, Xi H, Park S, Yun Y, Park J. Genome-wide comparative analyses of GATA transcription factors among seven Populus genomes. Sci Rep 2021; 11:16578. [PMID: 34400697 PMCID: PMC8367991 DOI: 10.1038/s41598-021-95940-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 08/02/2021] [Indexed: 02/07/2023] Open
Abstract
GATA transcription factors (TFs) are widespread eukaryotic regulators whose DNA-binding domain is a class IV zinc finger motif (CX2CX17-20CX2C) followed by a basic region. We identified 262 GATA genes (389 GATA TFs) from seven Populus genomes using the pipeline of GATA-TFDB. Alternative splicing forms of Populus GATA genes exhibit dynamics of GATA gene structures including partial or full loss of GATA domain and additional domains. Subfamily III of Populus GATA genes display lack CCT and/or TIFY domains. 21 Populus GATA gene clusters (PCs) were defined in the phylogenetic tree of GATA domains, suggesting the possibility of subfunctionalization and neofunctionalization. Expression analysis of Populus GATA genes identified the five PCs displaying tissue-specific expression, providing the clues of their biological functions. Amino acid patterns of Populus GATA motifs display well conserved manner of Populus GATA genes. The five Populus GATA genes were predicted as membrane-bound GATA TFs. Biased chromosomal distributions of GATA genes of three Populus species. Our comparative analysis approaches of the Populus GATA genes will be a cornerstone to understand various plant TF characteristics including evolutionary insights.
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Affiliation(s)
- Mangi Kim
- InfoBoss Inc., 301 room, Haeun Bldg., 670, Seolleung-ro, Gangnam-gu, Seoul, 07766, Korea
- InfoBoss Research Center, 301 room, Haeun Bldg., 670, Seolleung-ro, Gangnam-gu, Seoul, 07766, Korea
| | - Hong Xi
- InfoBoss Inc., 301 room, Haeun Bldg., 670, Seolleung-ro, Gangnam-gu, Seoul, 07766, Korea
- InfoBoss Research Center, 301 room, Haeun Bldg., 670, Seolleung-ro, Gangnam-gu, Seoul, 07766, Korea
| | - Suhyeon Park
- InfoBoss Inc., 301 room, Haeun Bldg., 670, Seolleung-ro, Gangnam-gu, Seoul, 07766, Korea
- InfoBoss Research Center, 301 room, Haeun Bldg., 670, Seolleung-ro, Gangnam-gu, Seoul, 07766, Korea
| | - Yunho Yun
- InfoBoss Inc., 301 room, Haeun Bldg., 670, Seolleung-ro, Gangnam-gu, Seoul, 07766, Korea
- InfoBoss Research Center, 301 room, Haeun Bldg., 670, Seolleung-ro, Gangnam-gu, Seoul, 07766, Korea
| | - Jongsun Park
- InfoBoss Inc., 301 room, Haeun Bldg., 670, Seolleung-ro, Gangnam-gu, Seoul, 07766, Korea.
- InfoBoss Research Center, 301 room, Haeun Bldg., 670, Seolleung-ro, Gangnam-gu, Seoul, 07766, Korea.
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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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The Comparative Analyses of Six Complete Chloroplast Genomes of Morphologically Diverse Chenopodium album L. (Amaranthaceae) Collected in Korea. Int J Genomics 2021; 2021:6643444. [PMID: 33996994 PMCID: PMC8096589 DOI: 10.1155/2021/6643444] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 04/09/2021] [Indexed: 01/16/2023] Open
Abstract
Chenopodium album sensu stricto belonging to C. album aggregate is an annual cosmopolitan weed displaying the diversity of morphologies. We completed the six chloroplast genomes of C. album s. str. collected in Korea to understand the relationship between the diversity of chloroplast genomes and their morphological variations. All six C. album chloroplast genomes have a typical quadripartite structure with length ranging from 151,906 bp to 152,199 bp, similar to the previously sequenced C. album chloroplast genome (NC_034950). In total, 56 single nucleotide polymorphisms (SNPs) and 26 insertion and deletion (INDEL) regions (308 bp in total) were identified from the six chloroplast genomes, presenting a low level of intraspecific variations in comparison to the other angiosperm species. 376 normal simple sequence repeats were identified in all seven C. album chloroplast genomes. The phylogenetic analysis based on all available complete Amaranthaceae chloroplast genomes presents phylogenetic positions of six C. album samples as well as correlation with one of C. album morphological features. Our results provide the way to investigate intraspecific features of C. album chloroplast genomes and also the insights of understanding various intraspecific characteristics including morphological features.
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Park J, Lee J, Lee W. The complete mitochondrial genome of Aphis gossypii Glover, 1877 (Hemiptera: Aphididae) isolated from Leonurus japonicus in Korea. MITOCHONDRIAL DNA PART B-RESOURCES 2021; 6:62-65. [PMID: 33521268 PMCID: PMC7819132 DOI: 10.1080/23802359.2020.1844096] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
We have determined the mitochondrial genome of A. gossypii isolated from Leonurus japonicus in Korea. The circular mitogenome of A. gossypii is 16,044 bp, including 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNAs, and a single control region of 797 bp. AT ratio is 83.8%. 88 SNPs and 4 INDELs (175 bp) were identified against mitogenome of A. gossypii isolated from cotton species. Especially, largest INDEL (170 bp) was in the control region. Phylogenetic trees show that four A. gossypii mitogenomes were clustered in one clade.
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Affiliation(s)
- Jongsun Park
- InfoBoss Inc., Seoul, Republic of Korea.,InfoBoss Research Center, Seoul, Republic of Korea
| | - Jungmo Lee
- InfoBoss Inc., Seoul, Republic of Korea.,InfoBoss Research Center, Seoul, Republic of Korea
| | - Wonhoon Lee
- Department of Plant Medicine and Institute of Agriculture & Life Science, Gyeongsang National University, Jinju, 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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