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Xu H, Zhu Z, Tian Z, Wei C, Fan Q, Wang Y, Shen S, Deng G, Ding M. The Mitogenomic Characterization and Phylogenetic Analysis of the Plant Pathogen Phyllosticta yuccae. Genes (Basel) 2024; 15:111. [PMID: 38255000 PMCID: PMC10815617 DOI: 10.3390/genes15010111] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 01/11/2024] [Accepted: 01/16/2024] [Indexed: 01/24/2024] Open
Abstract
Phyllosticta yuccae is an important plant pathogen causing leaf spot disease in Yucca gigantea Lem. It is imperative to note that the amount of information available about the mitogenome of this subject is severely limited. This must be addressed immediately, as it is crucial to our understanding and progress in this field. To better understand the mitogenomic characteristics of P. yuccae, we conducted its sequencing by MGISEQ. Afterwards, the mitogenome was assembled and annotated. The mitogenomic characteristics and phylogenetic placement of the P. yuccae strain KUMCC 6213 were analyzed. The study revealed that the mitogenome of P. yuccae is a circular DNA molecule, consisting of 178,540 base pairs. It contains a total of 64 genes, including 14 protein-coding genes (PCGs), 26 transfer RNA genes (tRNA), 2 ribosomal RNA genes (rRNA), and 22 open reading frame genes (ORF), accounting for 80.98% of the total size. Repetitive sequences accounted for 15.42% of the mitogenome. The analysis of codon usage indicated that the codon UUA was the most commonly utilized, whereas the amino acid Leu was the most frequently employed. A comparative analysis of mitogenomes between P. yuccae and Macrophomina phaseolina (Tassi) Goid. showed notable variations in the position and size of gene clusters, with cox1, nad4, and nad4L genes exhibiting relatively low conservation. Phylogenetic analysis based on the 14 PCGs revealed that P. yuccae has the closest genetic relationship with M. phaseolina (Botryosphaeriaceae, Botryosphaeriales). This study first reports the mitogenome of P. yuccae and validates its phylogenetic placement. The findings enhance the knowledge of mitogenomes in Botryosphaeriales, offering novel perspectives on the genetics and evolution of the plant pathogen P. yuccae. This is crucial for the accurate prevention and management of leaf spot disease in Y. gigantea.
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Affiliation(s)
- Hui Xu
- School of Agriculture, Yunnan University, Kunming 650091, China; (H.X.)
- Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Ziyi Zhu
- School of Agriculture, Yunnan University, Kunming 650091, China; (H.X.)
- Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Zeyuan Tian
- Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Cuiyuan Wei
- School of Agriculture, Yunnan University, Kunming 650091, China; (H.X.)
- Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Qi Fan
- Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Yuanbing Wang
- Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Shikang Shen
- School of Ecology and Environmental Science, Yunnan University, Kunming 650091, China
| | - Gang Deng
- School of Agriculture, Yunnan University, Kunming 650091, China; (H.X.)
| | - Mingliang Ding
- Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- Food Crops Research Institute, Yunnan Academy of Agriculture Sciences, Kunming 650200, China
- Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing 100083, China
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Liu X, Zhang D, Yu Z, Zeng B. Assembly and analysis of the complete mitochondrial genome of the Chinese wild dwarf almond ( Prunus tenella). Front Genet 2024; 14:1329060. [PMID: 38283144 PMCID: PMC10811783 DOI: 10.3389/fgene.2023.1329060] [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] [Received: 10/27/2023] [Accepted: 12/18/2023] [Indexed: 01/30/2024] Open
Abstract
Background: The wild dwarf almond (Prunus tenella) is one of the national key grade II-protected wild plants in China. It is a relic deciduous forest species from the middle Eocene of the ancient Mediterranean Sea and is also known as a "living fossil of plants." It is distributed in Southeast Europe, West Asia, Central Asia, Siberia, and Xinjiang (Tacheng) and other areas of China. The plant grows on arid slopes, steppes, depressions, and valleys at an altitude of 1,200 m. The seeds of wild dwarf almonds are frost resistant and contain oil and bitter lentil glycosides, which possess medicinal value. Additionally, the seeds of wild dwarf almonds can be used as the original material for breeding new varieties of almonds and obtain ornamental flowers and trees. Results: The complete mitochondrial genome of P. tenella was sequenced and assembled using two sequencing platforms, namely, Illumina Novaseq6000 and Oxford Nanopore PromethION. The assembled genome was 452,158-bp long with a typical loop structure. The total number of A, T, C, and G bases in the genome was 122,066 (26.99%), 124,114 (27.45%), 103,285 (22.84%), and 102,693 (22.71%), respectively, with a GC content of 45.55%. A total of 63 unique genes, including 36 protein-coding genes, 24 tRNA genes, and 3 rRNA genes, were identified in the genome. Furthermore, codon usage, sequence duplication, RNA editing, and mitochondrial and chloroplast DNA fragment transfer events in the genome were analyzed. A phylogenetic tree was also constructed using 30 protein-coding genes that are common to the mitochondrial genomes of 24 species, which indicated that the genome of wild lentils is highly conserved with those of apples and pears belonging to Rosaceae. Conclusion: Assembly and annotation of the P. tenella mitochondrial genome provided comprehensive information about the mitochondrial genome of wild dwarf almonds, This study provides information on the mitochondrial genome of Prunus species and serves as a reference for further evolutionary studies on wild dwarf almonds.
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Affiliation(s)
| | | | | | - Bin Zeng
- College of Horticulture, Xinjiang Agricultural University, Urumqi, China
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Gao RR, Lei QL, Jin X, Zafar I, Yang XK, Su CY, Hao JS, Nie RE. Characterization of Four Complete Mitogenomes of Monolepta Species and Their Related Phylogenetic Implications. Insects 2024; 15:50. [PMID: 38249056 PMCID: PMC10816406 DOI: 10.3390/insects15010050] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 01/05/2024] [Accepted: 01/08/2024] [Indexed: 01/23/2024]
Abstract
Monolepta is one of the diverse genera in the subfamily Galerucinae, including 708 species and 6 sub-species worldwide. To explore the information on the mitogenome characteristics and phylogeny of the section "Monoleptites", especially the genus Monolepta, we obtained the newly completed mitochondrial genomes (mitogenomes) of four Monolepta species using high-throughput sequencing technology. The lengths of these four new mitochondrial genomes are 16,672 bp, 16,965 bp, 16,012 bp, and 15,866 bp in size, respectively. All four mitochondrial genomes include 22 transfer RNA genes (tRNAs), 13 protein-coding genes (PCGs), 2 ribosomal RNA genes (rRNAs), and one control region, which is consistent with other Coleoptera. The results of the nonsynonymous with synonymous substitution rates showed that ND6 had the highest evolution rate, while COI displayed the lowest evolution rate. The substitution saturation of three datasets (13 PCGs_codon1, 13 PCGs_codon2, 13 PCGs_codon3) showed that there was no saturation across all datasets. Phylogenetic analyses based on three datasets (ND1, 15 genes of mitogenomes, and 13 PCGs_AA) were carried out using maximum likelihood (ML) and Bayesian inference (BI) methods. The results showed that mitogenomes had a greater capacity to resolve the main clades than the ND1 gene at the suprageneric and species levels. The section "Monoleptites" was proven to be a monophyletic group, while Monolepta was a non-monophyletic group. Based on ND1 data, the newly sequenced species whose antennal segment 2 was shorter than 3 were split into several clades, while, based on the mitogenomic dataset, the four newly sequenced species had close relationships with Paleosepharia. The species whose antennal segment 2 was as long as 3 were split into two clades, which indicated that the characteristic of "antennal segment 2 as long as 3" of the true "Monolepta" evolved multiple times in several subgroups. Therefore, to explore the relationships among the true Monolepta, the most important thing is to perform a thorough revision of Monolepta and related genera in the future.
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Affiliation(s)
- Rong-Rong Gao
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu 241000, China; (R.-R.G.); (X.J.); (I.Z.); (C.-Y.S.)
| | - Qi-Long Lei
- Department of Entomology, China Agricultural University, Beijing 100193, China;
| | - Xu Jin
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu 241000, China; (R.-R.G.); (X.J.); (I.Z.); (C.-Y.S.)
| | - Iqbal Zafar
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu 241000, China; (R.-R.G.); (X.J.); (I.Z.); (C.-Y.S.)
| | - Xing-Ke Yang
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangzhou 510260, China
| | - Cheng-Yong Su
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu 241000, China; (R.-R.G.); (X.J.); (I.Z.); (C.-Y.S.)
| | - Jia-Sheng Hao
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu 241000, China; (R.-R.G.); (X.J.); (I.Z.); (C.-Y.S.)
| | - Rui-E Nie
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu 241000, China; (R.-R.G.); (X.J.); (I.Z.); (C.-Y.S.)
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Dai X, Chen Q, Wang W, Wang X. The first complete mitochondrial genome of the agricultural pest Micromelalopha sieversi (Staudinger, 1892) (Lepidoptera: Notodontidae). Mitochondrial DNA B Resour 2024; 9:50-54. [PMID: 38197053 PMCID: PMC10776056 DOI: 10.1080/23802359.2023.2301005] [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] [Received: 02/28/2023] [Accepted: 12/27/2023] [Indexed: 01/11/2024] Open
Abstract
Micromelalopha sieversi (Staudinger, 1892) is a significant pest of Poplar trees in China. In this study, we used high-throughput sequencing to sequence the whole mitochondrial genome of M. sieversi. The length of the genome was 15,373 base pairs. The nucleotide composition was 39.8%, 11.5%, 8.0%, and 40.7% for A, C, G, and T, respectively. We used the maximum-likelihood method to construct a molecular phylogenetic tree based on complete mitogenome sequences of 19 Noctuoidea species as ingroups and five Geometroidea species as outgroups. The results indicate that the genus Micromelalopha is closely related to the genus Clostera in family Notodontidae.
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Affiliation(s)
- Xuan Dai
- College of Plant Protection, Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Changsha, China
| | - Qi Chen
- College of Plant Protection, Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Changsha, China
| | - Wei Wang
- Research Center for Wild Animal and Plant Resource Protection and Utilization, Qiongtai Normal University, Haikou, China
| | - Xing Wang
- Research Center for Wild Animal and Plant Resource Protection and Utilization, Qiongtai Normal University, Haikou, China
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55
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Zeng YP, Huang JY, Tu L, Zhao K. Complete mitochondrial genome sequence of Butyriboletus hainanensis (Boletales, Basidiomycota). Mitochondrial DNA B Resour 2024; 9:46-49. [PMID: 38197052 PMCID: PMC10776047 DOI: 10.1080/23802359.2023.2300473] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 12/22/2023] [Indexed: 01/11/2024] Open
Abstract
Butyriboletus hainanensis, a macrofungus belonging to the Boletaceae family, is named after its collection location on Hainan Island, China. However, little is known about its mitochondrial genome and its phylogenetic relationship with other boletes. In this study, we utilized next-generation sequencing technology to sequence the mitochondrial genome of Bu. hainanensis. Our findings revealed that the mitochondrial genome of this species is presumably a circular DNA molecule spanning 36,592 bp. It consists of 15 protein-coding genes, 27 transfer RNA genes, and two ribosomal RNA genes. The base composition of the mitochondrial genome is as follows: A (36.64%), C (12.22%), G (11.73%), and T (39.41%), with a GC content of 23.95%. Additionally, a phylogenetic tree was constructed based on 22 mitochondrial genomes, which provided valuable insights into the phylogenetic relationships of Bu. hainanensis with other boletes for the first time.
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Affiliation(s)
- Ya-ping Zeng
- College of Life Science, Jiangxi Science and Technology Normal University, Nanchang, China
| | - Jie-yu Huang
- College of Life Science, Jiangxi Science and Technology Normal University, Nanchang, China
| | - Lei Tu
- Jiulingshan National Nature Reserve Administration of Jiangxi Province, Jing’an, China
| | - Kuan Zhao
- College of Life Science, Jiangxi Science and Technology Normal University, Nanchang, China
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56
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Skalon EK, Starunova ZI, Petrov SA, Smirnov RV, Zaitseva OV, Starunov VV. The Mitochondrial Genomes of Siboglinum plumosum and Oligobrachia dogieli (Annelida: Siboglinidae) and Their Phylogenetic Analysis. Genes (Basel) 2024; 15:77. [PMID: 38254966 PMCID: PMC10815697 DOI: 10.3390/genes15010077] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 12/25/2023] [Accepted: 01/03/2024] [Indexed: 01/24/2024] Open
Abstract
Frenulates are a group of sedentary Annelida within the family Siboglinidae that inhabit the ocean floor and present a unique challenge for comprehensive molecular and phylogenetic investigations. In this study, we focused on the frenulates, specifically assembling the mitochondrial genomes of Siboglinum plumosum and Oligobrachia dogieli. The phylogenetic reconstruction placed S. plumosum as a sister taxon to S. ekmani, and O. dogieli as a sister taxon to S. fiordicum, supporting the non-monophyletic nature of the genus Siboglinum. Overall, this study supports the phylogeny of the family Siboglinidae while highlighting the need for additional molecular data within frenulates.
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Affiliation(s)
| | | | | | | | | | - Viktor V. Starunov
- Zoological Institute, Russian Academy of Sciences, 199034 Saint-Petersburg, Russia; (E.K.S.); (Z.I.S.); (S.A.P.); (R.V.S.); (O.V.Z.)
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57
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Fu X, Ballantyne L. An Overview of Aquatica Fu et al., a Phylogeny of Aquatic Fireflies Using Mitochondrial Genomes, a Description of Two New Species, and a New Record of Aquatic Fireflies in China (Coleoptera: Lampyridae: Luciolinae). Insects 2024; 15:31. [PMID: 38249037 PMCID: PMC10817006 DOI: 10.3390/insects15010031] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 12/23/2023] [Accepted: 12/27/2023] [Indexed: 01/23/2024]
Abstract
There are now seven species in the genus Aquatica Fu & Ballantyne, with all but one known from the characteristics of males, females, and larvae. Molecular information is combined with morphological taxonomy for the delimitation of both genus and species. The monophyly of the genus Aquatica is strongly supported in six trees, and its position as sister to the genus Nipponoluciola Ballantyne Kawashima Jusoh et Suzuki is stable across maximum likelihood and Bayesian inference results. Two new species of Aquatica Fu & Ballantyne, A. qingshen sp. nov. and A. xianning sp. nov., described from the features of males, females, and larvae, are closely related within a single clade within the genus Aquatica. Females have distinctively shaped median oviduct plates. A Chinese population identified as A. lateralis was found to be morphologically similar to the Japanese population, but genetic distances suggest that it is a distinctive species. No larvae are associated with this species. Definitions of the aquatic status of Luciolinae fireflies are expanded.
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Affiliation(s)
- Xinhua Fu
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China;
- Hubei Insect Resources Utilization and Sustainable Pest Management Key Laboratory, Wuhan 430070, China
- Firefly Conservation Research Centre, Wuhan 430070, China
| | - Lesley Ballantyne
- School of Agricultural, Environmental and Veterinary Sciences, Charles Sturt University, P.O. Box 588, Wagga Wagga 2678, Australia
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58
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Mu XH, Liang XX, Zheng YT, Zhao K. Complete mitochondrial genome sequence of Aureoboletus raphanaceus (Boletales, Basidiomycota). Mitochondrial DNA B Resour 2024; 9:20-23. [PMID: 38187009 PMCID: PMC10769141 DOI: 10.1080/23802359.2023.2294887] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 12/10/2023] [Indexed: 01/09/2024] Open
Abstract
Aureoboletus raphanaceus is a member of boletoid mushroom, which is named after its distinctive radish smell. The mitochondrial genome and phylogenetic relationships with other boletes need to be investigated to gain a comprehensive understanding of it. In this study, we sequenced the mitochondrial genome of A. raphanaceus using next-generation sequencing technology and found that its mitochondrial genome is a circular DNA molecule measuring 42,157 bp. It consists of 15 core protein-coding genes, 27 transfer RNA genes, and two ribosomal RNA genes. The mitochondrial genome had a base composition of A (39.89%), C (11.06%), G (11.67%), and T (37.38%), with a GC content of 22.73%. A phylogenetic tree based on 22 mitochondrial genomes was constructed, which provided the first insights into the phylogenetic relationships of this species with related boletes.
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Affiliation(s)
- Xin-Hua Mu
- College of Life Science, Jiangxi Science and Technology Normal University, Nanchang, China
| | - Xin-Xin Liang
- College of Life Science, Jiangxi Science and Technology Normal University, Nanchang, China
| | - Yu-Ting Zheng
- College of Life Science, Jiangxi Science and Technology Normal University, Nanchang, China
| | - Kuan Zhao
- College of Life Science, Jiangxi Science and Technology Normal University, Nanchang, China
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Li DX, Yang RJ, Chen HX, Kuzmina TA, Spraker TR, Li L. Characterization of the complete mitochondrial genomes of the zoonotic parasites Bolbosoma nipponicum and Corynosoma villosum (Acanthocephala: Polymorphida) and the molecular phylogeny of the order Polymorphida. Parasitology 2024; 151:45-57. [PMID: 37955106 PMCID: PMC10941042 DOI: 10.1017/s0031182023001099] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 10/26/2023] [Accepted: 11/07/2023] [Indexed: 11/14/2023]
Abstract
Acanthocephalans of the order Polymorphida mainly parasitic in birds and mammals, are of veterinary, medical and economic importance. However, the evolutionary relationships of its 3 families (Centrorhynchidae, Polymorphidae and Plagiorhynchidae) remain under debate. Additionally, some species of Polymorphida (i.e. Bolbosoma spp. and Corynosoma spp.) are recognized as zoonotic parasites, associated with human acanthocephaliasis, but the mitochondrial genomes for representatives of Bolbosoma and Corynosoma have not been reported so far. In the present study, the complete mitochondrial genomes B. nipponicum and C. villosum (Acanthocephala: Polymorphidae) are reported for the first time, which are 14 296 and 14 241 bp in length, respectively, and both contain 36 genes [including 12 PCGs, 22 tRNA genes and 2 rRNA genes] and 2 non-coding regions (NCR1 and NCR2). The gene arrangement of some tRNAs in the mitogenomes of B. nipponicum and C. villosum differs from that found in all other acanthocephalans, except Polymorphus minutus. Phylogenetic results based on concatenated amino acid (AA) sequences of the 12 protein-coding genes (PCGs) strongly supported that the family Polymorphidae is a sister to the Centrorhynchidae rather than the Plagiorhynchidae, and also confirmed the sister relationship of the genera Bolbosoma and Corynosoma in the Polymorphidae based on the mitogenomic data for the first time. Our present findings further clarified the phylogenetic relationships of the 3 families Plagiorhynchidae, Centrorhynchidae and Polymorphidae, enriched the mitogenome data of the phylum Acanthocephala (especially the order Polymorphida), and provided the resource of genetic data for diagnosing these 2 pathogenic parasites of human acanthocephaliasis.
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Affiliation(s)
- Dai-Xuan Li
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology; Hebei Collaborative Innovation Center for Eco-Environment; College of Life Sciences, Hebei Normal University, 050024 Shijiazhuang, Hebei Province, P. R. China
- Hebei Research Center of the Basic Discipline Cell Biology; Ministry of Education Key Laboratory of Molecular and Cellular Biology; 050024 Shijiazhuang, Hebei Province, P. R. China
| | - Rui-Jia Yang
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology; Hebei Collaborative Innovation Center for Eco-Environment; College of Life Sciences, Hebei Normal University, 050024 Shijiazhuang, Hebei Province, P. R. China
- Hebei Research Center of the Basic Discipline Cell Biology; Ministry of Education Key Laboratory of Molecular and Cellular Biology; 050024 Shijiazhuang, Hebei Province, P. R. China
| | - Hui-Xia Chen
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology; Hebei Collaborative Innovation Center for Eco-Environment; College of Life Sciences, Hebei Normal University, 050024 Shijiazhuang, Hebei Province, P. R. China
- Hebei Research Center of the Basic Discipline Cell Biology; Ministry of Education Key Laboratory of Molecular and Cellular Biology; 050024 Shijiazhuang, Hebei Province, P. R. China
| | - Tetiana A. Kuzmina
- I. I. Schmalhausen Institute of Zoology National Academy of Sciences of Ukraine, 15, Bogdan Khmelnytsky Street, Kyiv 01054, Ukraine
- Institute of Parasitology, Slovak Academy of Sciences, Hlinkova 3, 04001, Košice, Slovak Republic
| | - Terry R. Spraker
- Diagnostic Laboratory, Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO 80526, USA
| | - Liang Li
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology; Hebei Collaborative Innovation Center for Eco-Environment; College of Life Sciences, Hebei Normal University, 050024 Shijiazhuang, Hebei Province, P. R. China
- Hebei Research Center of the Basic Discipline Cell Biology; Ministry of Education Key Laboratory of Molecular and Cellular Biology; 050024 Shijiazhuang, Hebei Province, P. R. China
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Yang WJ, He GQ, Huang CB, Zhou SY, Jia FH, Zeng JP. Application of noninvasive sampling technique in mitochondrial genome intraspecific phylogeny of the endangered butterfly, Teinopalpus aureus (Lepidoptera: Papilionidae). J Insect Sci 2024; 24:16. [PMID: 38412293 PMCID: PMC10898791 DOI: 10.1093/jisesa/ieae008] [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] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 12/22/2023] [Accepted: 01/20/2024] [Indexed: 02/29/2024]
Abstract
The butterfly genus of Teinopalpus, endemic to Asia, embodies a distinct species of mountain-dwelling butterflies with specific habitat requirements. These species are rare in the wild and hold high conservation and research value. Similar to other protected species, the genetic analysis of the rare Teinopalpus aureus poses challenges due to the complexity of sampling. In this study, we successfully extracted DNA and amplified mitochondrial genomic DNA from various noninvasive sources such as larval feces, larval exuviae, larval head capsules, pupal exuviaes, and filamentous gland secretions, all integral parts of butterfly metamorphosis. This was conducted as part of a research initiative focused on the artificial conservation of T. aureus population in Jinggang Shan Nature Reserve. Our findings illustrated the successful extraction of DNA from multiple noninvasive sources, achieved through modified DNA extraction methodologies. Although the DNA concentration obtained from noninvasive samples was lower than that from muscle tissues of newly dead larvae during rearing, all samples met the requirements for PCR amplification and sequencing, yielding complete circular sequences. These sequences are pivotal for both interspecific and intraspecific genetic relationship analysis. Our methods can be extended to other insects, especially scarce species.
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Affiliation(s)
- Wen-Jing Yang
- Key Laboratory of National Forestry and Grass and Administration on Forest Ecosystem Protection and Restoration of Poyang Lake Watershed, College of Forestry, Jiangxi Agricultural University, Nanchang 330045, PR China
- Jiulianshan Forest Ecosystem Observation Station, Longnan 341701, PR China
| | - Gui-Qiang He
- Jinggangshan National Nature Reserve of Jiangxi, Jinggangshan 343600, PR China
| | - Chao-Bin Huang
- Nanning Institute of Termite Control, Nanning 530000, PR China
| | - Shan-Yi Zhou
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Ministry of Education, College of Life Science, Guangxi Normal University, Guilin 541006, PR China
| | - Feng-Hai Jia
- Jiangxi University of Chinese Medicine, Nanchang 330004, PR China
| | - Ju-Ping Zeng
- Key Laboratory of National Forestry and Grass and Administration on Forest Ecosystem Protection and Restoration of Poyang Lake Watershed, College of Forestry, Jiangxi Agricultural University, Nanchang 330045, PR China
- Jiulianshan Forest Ecosystem Observation Station, Longnan 341701, PR China
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Meng X, Wang D, Pang Q, Wang H, Zhou H. Multiple independent origins of duplicated mitochondrial control regions indicate an apomorphy in the Thysanoptera (Insecta). Arch Insect Biochem Physiol 2024; 115:e22087. [PMID: 38288498 DOI: 10.1002/arch.22087] [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] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 12/20/2023] [Accepted: 01/11/2024] [Indexed: 02/01/2024]
Abstract
The mitochondrial genome (mitogenome) of thrips is characterized by the presence of control region (CR) duplication. However, the evolution pattern of duplicated CRs in thrips is still unclear. In this study, the multiple independent origins of duplicated CR indicated that the CR duplication was not an ancestral state for Thysanoptera. The macroevolutionary pattern suggested that the earliest CR duplication event occurred in the middle Cretaceous (94.85 Ma) coincided with rearrangement events forming the ancestors of Aeolothripidae, but much later than that forming the ancestors of the suborder Terebrantia. The mitogenome with duplicated CRs showed a higher rate of gene rearrangement. The sequence similarity of the CR copies and divergence time were negatively correlated, indicating age-related deterioration of mitochondrial function. No significant differences were found in the mitochondrial DNA, the P123 and P4FD between the single and multiple-CR charactered mitogenomes, which suggested that the duplicated CRs may not affect the replication process in thrip mitogenome. The mitogenomes with duplicated CRs (mean: 0.0088 subs/s/my) show a significantly increased evolutionary rate than that with a single one (mean: 0.0058 subs/s/my). However, it seems that this higher evolutionary rate did not have adaptive mechanisms in Terebrantia. We speculated that the duplicated CRs may cause a more intense production of energy by mitochondria, and an accelerated mutation and substitution rate is expected in such mitogenomes. Our study provided new insights into the presence of CR duplications and their evolution in the mitogenomes of thrips.
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Affiliation(s)
| | - Dong Wang
- Qingdao Technical College, Qingdao, China
| | - Qiang Pang
- Qingdao Technical College, Qingdao, China
| | - Heng Wang
- Rizhao Agricultural Technology Service Center, Rizhao, China
| | - Hongxu Zhou
- Research Center for Environment-Friendly Agricultural Pest Management, College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, China
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UCHIDA Y, UCHIDA H, SATO T, NISHIMOTO Y, TSUTSUMI K, OI T, TANIGUCHI M, INOUE K, SUZUKI Y. Cytochrome c oxidase subunit I gene in Thalassiosira nordenskioeldii strains inhabiting in cold and warm sea waters. Proc Jpn Acad Ser B Phys Biol Sci 2024; 100:140-148. [PMID: 38346753 PMCID: PMC10978971 DOI: 10.2183/pjab.100.010] [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] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2023] [Accepted: 11/28/2023] [Indexed: 02/15/2024]
Abstract
From the biota beneath the sea ice in Lake Saroma, which is adjacent to Sea of Okhotsk, a diatom culture of Saroma 16 was isolated. Strutted processes and a labiate process in Saroma 16 were characteristic of those in Thalassiosira nordenskioeldii. Similarity search analysis showed that the 826-bp rbcL-3P region sequence of this strain was 100% identical to multiple sequences registered as T. nordenskioeldii in a public database. The 4305-bp PCR-amplified mitochondrial cytochrome c oxidase subunit I (COI) gene (COI)-5P region of Saroma 16 included a 1060-bp open reading frame (ORF), which was interrupted by 934-bp and 2311-bp introns that included frame-shifted ORFs encoding reverse-transcriptase (RTase)-like proteins. Previous reports showed that a strain of the same species, CNS00052, originating from the East China Sea included no introns in the COI, whereas North Atlantic Ocean strains of the same species, such as CCMP992, CCMP993, and CCMP997, included a 2.3-kb intron in the same position as Saroma 16.
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Affiliation(s)
- Yoshie UCHIDA
- Department of Food Business, School of Health and Human Life, Nagoya Bunri University, Inazawa, Aichi, Japan
| | - Hidenobu UCHIDA
- Department of Food Business, School of Health and Human Life, Nagoya Bunri University, Inazawa, Aichi, Japan
- Research Institute for Integrated Science, Kanagawa University, Yokohama, Kanagawa, Japan
| | - Takeshi SATO
- Research Institute for Integrated Science, Kanagawa University, Yokohama, Kanagawa, Japan
- Department of Science, Faculty of Science, Kanagawa University, Yokohama, Kanagawa, Japan
| | - Yuko NISHIMOTO
- Department of Science, Faculty of Science, Kanagawa University, Yokohama, Kanagawa, Japan
| | - Koichi TSUTSUMI
- Department of Food Business, School of Health and Human Life, Nagoya Bunri University, Inazawa, Aichi, Japan
| | - Takao OI
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Aichi, Japan
| | - Mitsutaka TANIGUCHI
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Aichi, Japan
| | - Kazuhito INOUE
- Research Institute for Integrated Science, Kanagawa University, Yokohama, Kanagawa, Japan
- Department of Biochemistry and Biotechnology, Faculty of Chemistry and Biochemistry, Kanagawa University, Yokohama, Kanagawa, Japan
| | - Yoshihiro SUZUKI
- Research Institute for Integrated Science, Kanagawa University, Yokohama, Kanagawa, Japan
- Department of Science, Faculty of Science, Kanagawa University, Yokohama, Kanagawa, Japan
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Lu Z, Lin Q, Zhang H. Characterization of the Complete Mitochondrial Genome of Agelas nakamurai from the South China Sea. Int J Mol Sci 2023; 25:357. [PMID: 38203529 PMCID: PMC10779334 DOI: 10.3390/ijms25010357] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 12/21/2023] [Accepted: 12/25/2023] [Indexed: 01/12/2024] Open
Abstract
The Agelas genus sponges are widely distributed and provide shelter for organisms that inhabit reefs. However, there is a lack of research on the genetic diversity of the Agelas sponges. Additionally, only one Agelas mitochondrial genome has been documented, leaving the characteristics of the Agelas genus's mitogenome in need of further clarification. To address this research gap, we utilized Illumina HiSeq4000 sequencing and de novo assembly to ascertain the complete mitochondrial genome of Agelas sp. specimens, sourced from the South China Sea. Our analysis of the cox1 barcoding similarity and phylogenetic relationship reveals that taxonomically, the Agelas sp. corresponds to Agelas nakamurai. The mitogenome of Agelas nakamurai is 20,885 bp in length, encoding 14 protein-coding genes, 24 transfer RNA genes, and 2 ribosomal RNA genes. Through a comparison of the mitochondrial genes, we discovered that both Agelas nakamurai and Agelas schmidti have an identical gene arrangement. Furthermore, we observed a deletion in the trnD gene and duplication and remodeling of the trnL gene in the Agelas nakamurai's mitogenome. Our evolutionary analysis also identified lineage-specific positive selection sites in the nad3 and nad5 genes of the Agelas sponges' mitogenome. These findings shed light on the gene rearrangement events and positive selection sites in the mitogenome of Agelas nakamurai, providing valuable molecular insights into the evolutionary processes of this genus.
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Affiliation(s)
- Zijian Lu
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology (LMB), Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510000, China;
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 510000, China
- University of Chinese Academy of Sciences, Beijing 100000, China
| | - Qiang Lin
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology (LMB), Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510000, China;
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 510000, China
- University of Chinese Academy of Sciences, Beijing 100000, China
| | - Huixian Zhang
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology (LMB), Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510000, China;
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 510000, China
- University of Chinese Academy of Sciences, Beijing 100000, China
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Xu X, Hou C, Shen Y. The complete mitochondrial genome of the Kandelia obovata Sheue, H.Y.Liu & J.W.H.Yong (Rhizophoraceae). Mitochondrial DNA B Resour 2023; 8:1440-1444. [PMID: 38173916 PMCID: PMC10763820 DOI: 10.1080/23802359.2023.2294889] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 12/09/2023] [Indexed: 01/05/2024] Open
Abstract
Kandelia obovata Sheue, H.Y.Liu & J.W.H.Yong is one of the most cold-resistant true mangrove species, and it is widely distributed from the South China Sea to southern Japan. In the current study, the complete mitochondrial genome sequence of K. obovata was assembled using Illumina reads. It is the first mitochondrial genome of the Kandelia genus within the family Rhizophoraceae to be sequenced. The mitochondrial genome size is 312,146 bp with a total of 49 predicted genes, including 29 protein-coding genes, 17 transfer RNA genes, and 3 ribosomal RNA genes. The overall GC content of the genome is 41.87%. A phylogenetic tree constructed using nine complete mitochondrial genomes revealed that K. obovata is more closely related to Bruguiera species. This study enriches the plastid genome of Kandelia, furnishing valuable genetic insights for the investigation of evolutionary and population genetics in Kandelia and other mangrove species.
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Affiliation(s)
- Xiuming Xu
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, Fujian Key Laboratory of Coastal Pollution Prevention and Control, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Chengcheng Hou
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, Fujian Key Laboratory of Coastal Pollution Prevention and Control, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Yingjia Shen
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, Fujian Key Laboratory of Coastal Pollution Prevention and Control, College of the Environment and Ecology, Xiamen University, Xiamen, China
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65
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Gao B, Du S, Zhu F, Xu D, Meng Q, Jia C, Sun R. The complete mitochondrial genome of the spotted knifejaw Oplegnathus punctatus. Mitochondrial DNA B Resour 2023; 8:1435-1439. [PMID: 38173917 PMCID: PMC10763843 DOI: 10.1080/23802359.2023.2292737] [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] [Received: 08/08/2023] [Accepted: 12/04/2023] [Indexed: 01/05/2024] Open
Abstract
In this study, the mitochondrial genome was sequenced in a new commercial species, spotted knifejaw (O. punctatus), using next-generation sequencing and PCR-based methods. The overall length of the female O. punctatus mitochondrial genome was 16,508 bp. It contained 13 PCGs, 2 r-RNA genes, 22 t-RNA genes, and a displacement loop locus (a control region). The total nucleotide composition was 28.75% A, 25.69% T, 29.70% C, and 15.86% G, with a total A + T content of 54.44%. The results demonstrated that the mitochondrial genome of O. punctatus has a high sequence identity with that of another species of Perciformes. This finding provides a deeper understanding of mitogenomic diversity and evolution in marine fish.
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Affiliation(s)
- Bo Gao
- Marine Fisheries Research Institute of Jiangsu Province, Nantong, China
- Jiangsu Key Laboratory for Genetics and Breeding of Marine Fishes, Nantong, China
| | - Shuran Du
- Marine Fisheries Research Institute of Jiangsu Province, Nantong, China
- Jiangsu Key Laboratory for Genetics and Breeding of Marine Fishes, Nantong, China
| | - Fei Zhu
- Marine Fisheries Research Institute of Jiangsu Province, Nantong, China
- Jiangsu Key Laboratory for Genetics and Breeding of Marine Fishes, Nantong, China
| | - Dafeng Xu
- Marine Fisheries Research Institute of Jiangsu Province, Nantong, China
- Jiangsu Key Laboratory for Genetics and Breeding of Marine Fishes, Nantong, China
| | - Qian Meng
- Marine Fisheries Research Institute of Jiangsu Province, Nantong, China
- Jiangsu Key Laboratory for Genetics and Breeding of Marine Fishes, Nantong, China
| | - Chaofeng Jia
- Marine Fisheries Research Institute of Jiangsu Province, Nantong, China
- Jiangsu Key Laboratory for Genetics and Breeding of Marine Fishes, Nantong, China
| | - Ruijian Sun
- Marine Fisheries Research Institute of Jiangsu Province, Nantong, China
- Jiangsu Key Laboratory for Genetics and Breeding of Marine Fishes, Nantong, China
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Park J, Cheon SJ, Choi JH, Park SM, Sung HC, Lee DH. Complete mitochondrial genome of the razor-backed musk turtle ( Sternotherus carinatus, testudines: emydidae) in Korea. Mitochondrial DNA B Resour 2023; 8:1396-1400. [PMID: 38189026 PMCID: PMC10768728 DOI: 10.1080/23802359.2023.2292744] [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] [Received: 08/29/2023] [Accepted: 12/04/2023] [Indexed: 01/09/2024] Open
Abstract
Sternotherus carinatus has been considered as a potential invasive species in Korea. However, the mitochondrial genome information of S. carinatus which can be used to control its effect on ecosystem is lacking. In this study, the complete mitochondrial genome of S. carinatus in Korea was sequenced and characterized. The mitochondrial genome consists of 37 genes (13 protein-coding genes, 22 transfer RNA genes, and 2 ribosomal RNA genes) and a noncoding region. Phylogenetic analysis based on the mitochondrial genome sequences showed that S. carinatus from Korea is separated from other turtles which are the invasive species in Korea. Sequence divergence calculations indicated near-zero divergence between S. carinatus populations in Korea, the USA, and China, suggesting limited genetic differentiation. In the context of the broader issue of invasive species disrupting ecosystems, this research contributes to the identification of mitochondrial genomes for various freshwater turtle species, emphasizing the need for extended data collection to discern genetic mixing trends between native and non-native species. This study is a significant step toward managing S. carinatus as a potential invasive species in Korea.
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Affiliation(s)
- Jaehong Park
- School of Biological Sciences and Biotechnology, Chonnam National University, Gwangju, Korea
| | - Seung-Ju Cheon
- School of Biological Sciences and Biotechnology, Chonnam National University, Gwangju, Korea
| | - Jae-Hyuk Choi
- School of Biological Sciences and Biotechnology, Chonnam National University, Gwangju, Korea
| | - Seung-Min Park
- School of Biological Sciences and Biotechnology, Chonnam National University, Gwangju, Korea
| | - Ha-Cheol Sung
- Research Center of Ecomimetics, Chonnam National University, Gwangju, Korea
- Department of Biological Sciences, College of Natural Sciences, Chonnam National University, Gwangju, Korea
| | - Dong-Hyun Lee
- Research Center of Ecomimetics, Chonnam National University, Gwangju, Korea
- Department of Biological Sciences, College of Natural Sciences, Chonnam National University, Gwangju, Korea
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Yang F, Long L. Complete mitochondrial genome and phylogenetic analysis of the marine microalga Symbiochlorum hainanensis (Ulvophyceae, Chlorophyta). Mitochondrial DNA B Resour 2023; 8:1377-1380. [PMID: 38130734 PMCID: PMC10732211 DOI: 10.1080/23802359.2023.2290353] [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] [Received: 03/15/2023] [Accepted: 11/28/2023] [Indexed: 12/23/2023] Open
Abstract
Symbiochlorum hainanensis Gong et al. (2018). is a unicellular green alga belonging to Ulvophyceae, Chlorophyta, and considered as an important species in coral-algae symbiont areas. In this study, we revealed firstly the mitochondrial genome sequence of the S. hainanensis. This mitochondrial genome was a circular DNA molecule of 59,508 bp, including 24 transfer RNA genes, 3 ribosomal RNA genes, and 31 protein-coding genes. The GC content of the genome was 35.4%. The phylogenetic tree suggested that S. hainandiae was a sister to the OUU clade within the class Ulvophyceae. The mitochondrial genome structure and gene content of S. hainanensis supported that S. hainanensis was a new unidentified green alga in Ulvophyceae.
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Affiliation(s)
- Fangfang Yang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Lijuan Long
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
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Zheng X, Huang X, Yang J, Yang H, Zhang X. The complete mitochondrial genome of Nycteribia formosana (Diptera, Nycteribiidae). Mitochondrial DNA B Resour 2023; 8:1406-1410. [PMID: 38130733 PMCID: PMC10732201 DOI: 10.1080/23802359.2023.2290127] [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] [Received: 05/19/2023] [Accepted: 11/27/2023] [Indexed: 12/23/2023] Open
Abstract
The family Hippoboscidae is an ectoparasite that primarily inhabits bats and relies on the host's blood for sustenance. This research provides the first complete mitochondrial genome of Nycteribia formosana, which shares similar characteristics with other dipteran insects. The circularized mitochondrial genome, spanning 15,107 bp, encompasses 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNA), two ribosomal RNA genes, and a control region. The nucleotide composition of A, C, G, and T is 40.4%, 10.9%, 6.7%, and 42.0%, respectively. The findings from the phylogenetic analysis suggest that the species under investigation forms a cluster with other species belonging to the family Nycteribiidae. Consequently, this study provides valuable insights for the identification of N. formosana.
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Affiliation(s)
- Xiaoyan Zheng
- Institute of Pathogens and Vectors, Yunnan Provincial Key Laboratory for Zoonosis Control and Prevention, Dali University, Dali, China
| | - Xiaobin Huang
- Institute of Pathogens and Vectors, Yunnan Provincial Key Laboratory for Zoonosis Control and Prevention, Dali University, Dali, China
| | - Jinting Yang
- Institute of Pathogens and Vectors, Yunnan Provincial Key Laboratory for Zoonosis Control and Prevention, Dali University, Dali, China
| | - Huijuan Yang
- Institute of Pathogens and Vectors, Yunnan Provincial Key Laboratory for Zoonosis Control and Prevention, Dali University, Dali, China
| | - Xianzheng Zhang
- Institute of Pathogens and Vectors, Yunnan Provincial Key Laboratory for Zoonosis Control and Prevention, Dali University, Dali, China
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Turanov SV, Barabanshchikov EI. Characterization of the Cambaroides wladiwostokiensis Birstein & Vinogradov, 1934 (Decapoda: Astacidea) Mitochondrial Genome Using Genome Skimming and the Phylogenetic Implications within the Astacidea Infraorder. Front Biosci (Schol Ed) 2023; 15:15. [PMID: 38163955 DOI: 10.31083/j.fbs1504015] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 11/15/2023] [Accepted: 11/24/2023] [Indexed: 01/03/2024]
Abstract
BACKGROUND The mitochondrial genome is a powerful tool for exploring and confirming species identity and understanding evolutionary trajectories. The genus Cambaroides, which consists of freshwater crayfish, is recognized for its evolutionary and morphological complexities. However, comprehensive genetic and mitogenomic data on species within this genus, such as C. wladiwostokiensis, remain scarce, thereby necessitating an in-depth mitogenomic exploration to decipher its evolutionary position and validate its species identity. METHODS The mitochondrial genome of C. wladiwostokiensis was obtained through shallow Illumina paired-end sequencing of total DNA, followed by hybrid assembly using both de novo and reference-based techniques. Comparative analysis was performed using available Cambaroides mitochondrial genomes obtained from National Center for Biotechnology Information (NCBI). Additionally, phylogenetic analyses of 23 representatives from three families within the Astacidea infraorder were employed using the PhyloSuite platform for sequence management and phylogenetic preparation, to elucidate phylogenetic relationships via Bayesian Inference (BI), based on concatenated mitochondrial fragments. RESULTS The resulting genome, which spans 16,391 base pairs was investigated, revealing 13 protein-coding genes, rRNAs (12S and 16S), 19 tRNAs, and a putative control region. Comparative analysis together with five other Cambaroides mitogenomes retrieved from GenBank unveiled regions that remained unread due to challenges associated with the genome skimming technique. Protein-coding genes varied in size and typically exhibited common start (ATG) and stop (TAA) codons. However, exceptions were noted in ND5 (start codon: GTG) and ND1 (stop codon: TAG). Landscape analysis was used to explore sequence variation across the five available mitochondrial genomes of Cambaroides. CONCLUSIONS Collectively, these findings reveal variable sites and contribute to a deeper understanding of the genetic diversity in this genus alongside the further development of species-specific primers for noninvasive monitoring techniques. The partitioned phylogenetic analysis of Astacidea revealed a paraphyletic origin of Asian cambarids, which confirms the data in recent studies based on both multilocus analyses and integrative approaches.
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Affiliation(s)
- Sergei V Turanov
- Laboratory of Deep Sea Research, A.V. Zhirmunsky National Scientific Center of Marine Biology, Far Eastern Branch, Russian Academy of Sciences (NSCMB FEB RAS), 690041 Vladivostok, Russia
- Chair of Water Biological Resources and Aquaculture, Far Eastern State Technical Fisheries University, 690087 Vladivostok, Russia
| | - Evgeny I Barabanshchikov
- Laboratory of Biological Resources Continental Reservoirs and Fishes Estuarine Systems, Pacific branch of Russian Federal Research Institute of Fisheries and Oceanography (TINRO), 690950 Vladivostok, Russia
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Panitsina VA, Bodrov SY, Boulygina ES, Slobodova NV, Kosintsev PA, Abramson NI. In Search of the Elusive North: Evolutionary History of the Arctic Fox ( Vulpes lagopus) in the Palearctic from the Late Pleistocene to the Recent Inferred from Mitogenomic Data. Biology (Basel) 2023; 12:1517. [PMID: 38132343 PMCID: PMC10740874 DOI: 10.3390/biology12121517] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 12/07/2023] [Accepted: 12/09/2023] [Indexed: 12/23/2023]
Abstract
Despite the high level of interest, the population history of arctic foxes during the Late Pleistocene and Holocene remains poorly understood. Here we aimed to fill gaps in the demographic and colonization history of the arctic fox by analyzing new ancient DNA data from fossil specimens aged from 50 to 1 thousand years from the Northern and Polar Urals, historic DNA from museum specimens from the Novaya Zemlya Archipelago and the Taymyr Peninsula and supplementing these data by previously published sequences of recent and extinct arctic foxes from other regions. This dataset was used for reconstruction of a time-calibrated phylogeny and a temporal haplotype network covering four time intervals: Late Pleistocene (ranging from 30 to 13 thousand years bp), Holocene (ranging from 4 to 1 thousand years bp), historical (approximately 150 years), and modern. Our results revealed that Late Pleistocene specimens showed no genetic similarity to either modern or historical specimens, thus supporting the earlier hypothesis on local extinction rather than habitat tracking.
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Affiliation(s)
- Valentina A. Panitsina
- Zoological Institute, Russian Academy of Sciences, 199034 Saint-Petersburg, Russia; (V.A.P.); (S.Y.B.)
| | - Semyon Yu. Bodrov
- Zoological Institute, Russian Academy of Sciences, 199034 Saint-Petersburg, Russia; (V.A.P.); (S.Y.B.)
| | | | | | - Pavel A. Kosintsev
- Institute of Plant and Animal Ecology, Ural Branch, Russian Academy of Sciences, 620144 Yekaterinburg, Russia
| | - Natalia I. Abramson
- Zoological Institute, Russian Academy of Sciences, 199034 Saint-Petersburg, Russia; (V.A.P.); (S.Y.B.)
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Singh M, Saini VP, Mohindra V, Ojha ML, Lal KK, Singh RK. Complete mitochondrial genome of golden variant of freshwater fish Labeo rajasthanicus (Cypriniformes: Cyprinidae): endemic to India. Mitochondrial DNA B Resour 2023; 8:1364-1367. [PMID: 38196791 PMCID: PMC10776062 DOI: 10.1080/23802359.2023.2290128] [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] [Received: 07/10/2023] [Accepted: 11/27/2023] [Indexed: 01/11/2024] Open
Abstract
The complete mitochondrial genome of the freshwater fish species Labeo rajasthanicus was obtained, using Illumina NovaSeq 6000 with 2 × 150 bp paired-end sequencing. The mitogenome of L. rajasthanicus is 16,738 bp in length (GenBank accession no.: OQ834146), comprised of 13 protein-coding genes, 22 tRNA genes, two rRNA genes, and a control region, i.e. D-loop. The arrangement of genes was found to be identical to other Cypriniformes fish mitogenome, available in the NCBI database. The taxonomic status of L. rajasthanicus as a valid species was debated by some researchers and it was considered a synonym of L. boggut. However, phylogenetic analysis in the present study supports the species validity of L. rajasthanicus, as it showed a distinct node well separated from L. boggut and supported by a high bootstrap value. Furtherly, the pairwise genetic divergence among studied species showed the divergence between L. rajasthanicus and L. boggut as 1.6% whereas the minimum divergence was found to be 0.13% with L. dussumieri followed by L. fimbriatus (0.58%) and L. gonius (0.63%). The complete mitogenome of L. rajasthanicus will also be useful as a baseline reference genome for the reconstruction and annotation of the mitogenome of other Labeo species.
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Affiliation(s)
- Mamta Singh
- College of Fisheries, Bihar Animal Sciences University, Kishanganj, India
| | - Ved Prakash Saini
- College of Fisheries, Bihar Animal Sciences University, Kishanganj, India
| | | | - Manohar Lal Ojha
- College of Fisheries, Maharana Pratap University of Agriculture & Technology, Udaipur, India
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Wang Y, Shang P, Dai Y, Xu D, Dong Y, Huang Z. The complete mitochondrial genome of a new species of the genus Schizothorax from Sichuan, China (Cypriniformes: Cyprinidae). Mitochondrial DNA B Resour 2023; 8:1356-1359. [PMID: 38196799 PMCID: PMC10776055 DOI: 10.1080/23802359.2023.2288437] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Accepted: 11/21/2023] [Indexed: 01/11/2024] Open
Abstract
Schizothorax gulinensis sp. nov. is a new species of the genus Schizothorax from Sichuan, China (Cypriniformes: Cyprinidae). In this study, we have first reported the complete mitochondrial genome of S. gulinensis with Illumina sequencing. There were 16,587 nucleotide pairs in the mitochondrial genome (mitogenome) of S. gulinensis, including 13 protein-coding genes (PCGs), two ribosomal RNAs (rRNAs), and 22 transfer RNAs (tRNAs), as well as one non-coding control region (CR). The proportion of nucleotides in mitochondrial genome was 29.67% (A), 25.45% (T), 17.84% (G), 27.05% (C), and A + T content was 55.12%. All PCGs have the same start codon of the standard ATG, excepting for that of NADH dehydrogenase subunit 1 (nad1) which was the ATC, NADH dehydrogenase subunit 5 (nad5) which was the ATT and cytochrome c oxidase 1 (cox1) which was the ATC. Phylogenetic analysis results supported that S. gulinensis was closely related to Schizothorax grahami. The complete mitochondrial sequence of S. gulinensis will contribute to mitochondrial genome database and provide useful resources for population genetics and evolution analyses.
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Affiliation(s)
- Ying Wang
- Key Laboratory of Application of Ecology and Environmental Protection in Plateau Wetland of Sichuan, Xichang University, Xichang, PR China
| | - Pan Shang
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, Shanghai Ocean University, Shanghai, PR China
| | - Yuanxing Dai
- Gulin County Bureau of Agriculture and Rural Affairs, Luzhou, PR China
| | - Dayong Xu
- Key Laboratory of Application of Ecology and Environmental Protection in Plateau Wetland of Sichuan, Xichang University, Xichang, PR China
| | - Yanzhen Dong
- Key Laboratory of Application of Ecology and Environmental Protection in Plateau Wetland of Sichuan, Xichang University, Xichang, PR China
| | - Zhiqiu Huang
- Key Laboratory of Application of Ecology and Environmental Protection in Plateau Wetland of Sichuan, Xichang University, Xichang, PR China
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Liu Q, Wu Z, Tian C, Yang Y, Liu L, Feng Y, Li Z. Complete mitochondrial genome of the endangered Prunus pedunculata (Prunoideae, Rosaceae) in China: characterization and phylogenetic analysis. Front Plant Sci 2023; 14:1266797. [PMID: 38155854 PMCID: PMC10753190 DOI: 10.3389/fpls.2023.1266797] [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] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 11/20/2023] [Indexed: 12/30/2023]
Abstract
Introduction Prunus pedunculata (Prunoideae: Rosaceae), a relic shrub with strong resistance and multiple application values, is endangered in China. Extensive research had been devoted to gene expression, molecular markers, plastid genome analysis, and genetic background investigations of P. pedunculata. However, the mitochondrial genome of this species has not been systematically described, owing to the complexity of the plant mitogenome. Methods In the present research, the complete mitochondrial genome of P. pedunculata was assembled, annotated, and characterized. The genomic features, gene content and repetitive sequences were analyzed. The genomic variation and phylogenetic analysis have been extensively enumerated. Results and discussion The P. pedunculata mitogenome is a circular molecule with a total length of 405,855 bp and a GC content of 45.63%, which are the smallest size and highest GC content among the known Prunus mitochondrial genomes. The mitogenome of P. pedunculata encodes 62 genes, including 34 unique protein-coding genes (PCGs, excluding three possible pseudogenes), three ribosomal RNA genes, and 19 transfer RNA genes. The mitogenome is rich in repetitive sequences, counting 112 simple sequence repeats, 15 tandem repeats, and 50 interspersed repetitive sequences, with a total repeat length of 11,793 bp, accounting for 2.91% of the complete genome. Leucine (Leu) was a predominant amino acid in PCGs, with a frequency of 10.67%, whereas cysteine (Cys) and tryptophan (Trp) were the least adopted. The most frequently used codon was UUU (Phe), with a relative synonymous codon usage (RSCU) value of 1.12. Selective pressure was calculated based on 20 shared PCGs in the mitogenomes of the 32 species, most of which were subjected to purifying selection (Ka/Ks < 1), whereas ccmC and ccmFn underwent positive selection. A total of 262 potential RNA editing sites in 26 PCGs were identified. Furthermore, 56 chloroplast-derived fragments were ascertained in the mitogenome, ranging from 30 to 858 bp, and were mainly located across IGS (intergenic spacer) regions or rRNA genes. These findings verify the occurrence of intracellular gene transfer events from the chloroplast to the mitochondria. Furthermore, the phylogenetic relationship of P. pedunculata was supported by the mitogenome data of 30 other taxa of the Rosaceae family. Understanding the mitochondrial genome characteristics of P. pedunculata is of great importance to promote comprehension of its genetic background and this study provides a basis for the genetic breeding of Prunus.
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Affiliation(s)
- Qian Liu
- Institute of Grassland Research, Chinese Academy of Agricultural Sciences, Hohhot, China
| | - Zinian Wu
- Institute of Grassland Research, Chinese Academy of Agricultural Sciences, Hohhot, China
- Key Laboratory of Grassland Resources and Utilization of Ministry of Agriculture, Hohhot, China
| | - Chunyu Tian
- Institute of Grassland Research, Chinese Academy of Agricultural Sciences, Hohhot, China
| | - Yanting Yang
- Institute of Grassland Research, Chinese Academy of Agricultural Sciences, Hohhot, China
| | - Lemeng Liu
- Institute of Grassland Research, Chinese Academy of Agricultural Sciences, Hohhot, China
| | - Yumei Feng
- Institute of Grassland Research, Chinese Academy of Agricultural Sciences, Hohhot, China
| | - Zhiyong Li
- Institute of Grassland Research, Chinese Academy of Agricultural Sciences, Hohhot, China
- Key Laboratory of Grassland Resources and Utilization of Ministry of Agriculture, Hohhot, China
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Park C, Kim EB, Ju SJ. The complete mitochondrial genome of deep-sea ophiuroid Ophioleila elegans (Echinodermata: Ophiuroidea) from the Shkolnik Guyot, a northwest Pacific seamount. Mitochondrial DNA B Resour 2023; 8:1334-1338. [PMID: 38189027 PMCID: PMC10768936 DOI: 10.1080/23802359.2023.2288441] [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] [Received: 06/25/2023] [Accepted: 11/21/2023] [Indexed: 01/09/2024] Open
Abstract
Ophiuroids are a diversified benthic taxon in the deep sea. Given their various dispersal strategies, they are considered an adequate group to assess genetic connectivity, especially in the seamounts that function as islands. Ophioleila elegans A.H. Clark, 1949, in the family Ophiothamnidae, was previously reported from the Caiwei Guyot, a seamount in the northwest Pacific Ocean. Here, we described the mitochondrial genome of O. elegans collected from another seamount in the northwest Pacific. The whole mitogenome is 16,376 bp in length and encodes 13 protein-coding genes, two ribosomal RNA genes, and 22 transfer RNA genes. Phylogenetic analysis based on the mitogenome sequences showed that O. elegans was clustered with Histampica sp., the only species for which mitogenome sequence has been reported within the family Ophiothamnidae. The complete mitogenome of O. elegans first reported in the present study provides useful information for population genetics and evolutionary relationship of this taxon, especially in the northwest Pacific seamounts.
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Affiliation(s)
- Chailinn Park
- Ocean Georesources Research Department, Korea Institute of Ocean Science and Technology, Busan, Republic of Korea
- Ocean Science Major, University of Science and Technology, Daejeon, Republic of Korea
| | - Eun-Bi Kim
- Ocean Georesources Research Department, Korea Institute of Ocean Science and Technology, Busan, Republic of Korea
| | - Se-Jong Ju
- Ocean Science Major, University of Science and Technology, Daejeon, Republic of Korea
- Marine Resources & Environment Research Division, Korea Institute of Ocean Science and Technology, Busan, Republic of Korea
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Park S, Park S. Intrageneric structural variation in organelle genomes from the genus Dystaenia (Apiaceae): genome rearrangement and mitochondrion-to-plastid DNA transfer. Front Plant Sci 2023; 14:1283292. [PMID: 38116150 PMCID: PMC10728875 DOI: 10.3389/fpls.2023.1283292] [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] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 11/14/2023] [Indexed: 12/21/2023]
Abstract
Introduction During plant evolution, intracellular DNA transfer (IDT) occurs not only from organelles to the nucleus but also between organelles. To further comprehend these events, both organelle genomes and transcriptomes are needed. Methods In this study, we constructed organelle genomes and transcriptomes for two Dystaenia species and described their dynamic IDTs between their nuclear and mitochondrial genomes, or plastid and mitochondrial genomes (plastome and mitogenome). Results and Discussion We identified the putative functional transfers of the mitochondrial genes 5' rpl2, rps10, rps14, rps19, and sdh3 to the nucleus in both Dystaenia species and detected two transcripts for the rpl2 and sdh3 genes. Additional transcriptomes from the Apicaceae species also provided evidence for the transfers and duplications of these mitochondrial genes, showing lineage-specific patterns. Intrageneric variations of the IDT were found between the Dystaenia organelle genomes. Recurrent plastid-to-mitochondrion DNA transfer events were only identified in the D. takeshimana mitogenome, and a pair of mitochondrial DNAs of plastid origin (MIPTs) may generate minor alternative isoforms. We only found a mitochondrion-to-plastid DNA transfer event in the D. ibukiensis plastome. This event may be linked to inverted repeat boundary shifts in its plastome. We inferred that the insertion region involved an MIPT that had already acquired a plastid sequence in its mitogenome via IDT. We propose that the MIPT acts as a homologous region pairing between the donor and recipient sequences. Our results provide insight into the evolution of organelle genomes across the family Apiaceae.
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Affiliation(s)
- Seongjun Park
- Institute of Natural Science, Yeungnam University, Gyeongsan, Republic of Korea
| | - SeonJoo Park
- Department of Life Sciences, Yeungnam University, Gyeongsan, Republic of Korea
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76
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Park J, Park SM, Choi JH, Sung HC, Lee DH. Complete mitochondrial genome of the western painted turtle ( Chrysemys picta bellii, Testudines: Emydidae) in Korea. Mitochondrial DNA B Resour 2023; 8:1316-1319. [PMID: 38196795 PMCID: PMC10776060 DOI: 10.1080/23802359.2023.2288439] [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] [Received: 08/29/2023] [Accepted: 11/21/2023] [Indexed: 01/11/2024] Open
Abstract
The complete mitochondrial genome of Chrysemys picta bellii in Korea was sequenced and characterized. The mitochondrial genome consists of 37 genes (13 protein-coding genes, 22 transfer RNA genes, and 2 ribosomal RNA genes) and a noncoding region. Phylogenetic analysis based on the mitochondrial genome sequences revealed that C. p. bellii from Korea formed a cluster with C. p. bellii from China and C. picta from the USA, while showing clear separation from other turtle species within the C. picta cluster. This study presented the first complete mitochondrial genome from C. p. bellii in Korea, offering crucial information for managing invasive species and protecting the local ecosystem.
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Affiliation(s)
- Jaehong Park
- School of Biological Sciences and Biotechnology Graduate School, Chonnam National University, Gwangju, Korea
| | - Seung-Min Park
- School of Biological Sciences and Biotechnology Graduate School, Chonnam National University, Gwangju, Korea
| | - Jae-Hyuk Choi
- School of Biological Sciences and Biotechnology Graduate School, Chonnam National University, Gwangju, Korea
| | - Ha-Cheol Sung
- Research Center of Ecomimetics, Chonnam National University, Gwangju, Korea
- Department of Biological Sciences, College of Natural Sciences, Chonnam National University, Gwangju, Korea
| | - Dong-Hyun Lee
- Research Center of Ecomimetics, Chonnam National University, Gwangju, Korea
- Department of Biological Sciences, College of Natural Sciences, Chonnam National University, Gwangju, Korea
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Lee HE, Ki JS. The complete mitochondrial genome of the mauve stinger jellyfish Pelagia noctiluca Forskål, 1775 (Cnidaria, Scyphozoa, Semaeostomeae) with phylogenetic analysis. Mitochondrial DNA B Resour 2023; 8:1239-1242. [PMID: 38188449 PMCID: PMC10769544 DOI: 10.1080/23802359.2023.2281028] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 11/02/2023] [Indexed: 01/09/2024] Open
Abstract
This study determined the complete mitochondrial genome of the jellyfish Pelagia noctiluca (Scyphozoa, Semaeostomeae) for the first time. The genome was a linear molecule of 16,390 bp in length and 59.3% AT. It comprised of 13 typical protein-coding genes (cox1-3, nd1-6, nd4L, atp6, atp8, and cytB), two ribosomal RNAs (16S and 12S rRNA), and two tRNAs (trnM and trnW). In addition, we detected two additional open reading frames (polB and ORF314) at one end of the genome. The gene-coding structures were identical to those of other scyphozoans. Based on a molecular phylogeny constructed using 13 protein-coding genes, P. noctiluca has the closest genetic relationship with the genus Chrysaora (Semaeostomeae).
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Affiliation(s)
- Ha-Eun Lee
- Department of Biotechnology, Sangmyung University, Seoul, South Korea
| | - Jang-Seu Ki
- Department of Biotechnology, Sangmyung University, Seoul, South Korea
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Sun KK, Ding Y, Chen L, Sun JT. A Comparative Analysis of Selection Pressures Suffered by Mitochondrial Genomes in Two Planthopper Species with Divergent Climate Distributions. Int J Mol Sci 2023; 24:16847. [PMID: 38069176 PMCID: PMC10706623 DOI: 10.3390/ijms242316847] [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] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 11/23/2023] [Accepted: 11/25/2023] [Indexed: 12/18/2023] Open
Abstract
Mitochondrial DNA (mtDNA) has been widely used as a valuable tool in studies related to evolution and population genetics, under the implicit assumption of neutral evolution. However, recent studies suggest that natural selection also plays a significant role in shaping mitochondrial genome evolution, although the specific driving forces remain elusive. In this study, we aimed to investigate whether and how climate influences mitochondrial genome evolution by comparing the selection pressures acting on mitochondrial genomes between two rice planthoppers, Sogatella furcifera (Horváth) and Laodelphax striatellus (Fallén), which have different climate distributions. We employed the dN/dS method, MK test and Tajima's D tests for our analysis. Our results showed that the mitochondrial genomes of the two species appear to undergo predominantly purifying selection, consistent with the nearly neutral evolution model. However, we observed varied degrees of purifying selection among the 13 protein-coding genes. Notably, ND1, ND2, ND6, COIII, and ATP8 exhibited significantly stronger purifying selection and greater divergence between the two species compared to the other genes. Additionally, we observed relatively stronger purifying selection in the mitochondrial genomes of S. furcifera compared to L. striatellus. This difference could be attributed to varying metabolic requirements arising from distinct habitats or other factors that are unclear here. Furthermore, we speculate that mito-nuclear epistatic interactions may play a role in maintaining nonsynonymous polymorphisms, particularly for COI and COII. Overall, our results shed some light on the influence of climate on mitochondrial genome evolution.
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Affiliation(s)
| | | | | | - Jing-Tao Sun
- Department of Entomology, Nanjing Agricultural University, Nanjing 210095, China; (K.-K.S.); (Y.D.)
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79
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Xia W, Jiang H, Fan W, Li X, Liu Y, Xu L, Gou X. Complete mitochondrial genome of Mastigias papua (Scyphozoa: Rhizostomeae: Mastigiidae) based on next-generation sequencing and phylogenetic analysis. Mitochondrial DNA B Resour 2023; 8:1294-1297. [PMID: 38188436 PMCID: PMC10769521 DOI: 10.1080/23802359.2023.2281033] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 11/02/2023] [Indexed: 01/09/2024] Open
Abstract
We assembled the complete mitochondrial genome (mitogenome) of Mastigias papua (Scyphozoa: Rhizostomeae: Mastigiidae) by the data generated from the next-generation sequencing platform. The complete mitogenome of M. papua was 16,560 bp in length, containing 14 protein-coding genes, two transfer RNA genes, and two ribosomal RNA genes. The base compositions were A 30.65%, C 15.16%, G 16.34%, and T 37.86%, with a gene arrangement similar to the mitogenomes derived from other representatives of Scyphozoa. Based on the 13 common protein-coding genes of 16 species within Scyphozoa, we constructed the phylogenetic tree and found that M. papua has a close relationship with Cassiopea andromeda and Cassiopea xamachana. All these species belong to an order of jellyfish Rhizostomeae, which have similar morphological characteristics. This is agreement with the conclusion we got by the phylogenetic relationship analysis using molecular data. This research has practical implications for advancing understanding of the phylogenetic relationships, taxonomic classifications, and phylogeography within Scyphozoa.
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Affiliation(s)
- Wangxiao Xia
- Institute of Basic Translational Medicine, Shaanxi Key Laboratory of Brain Disorders, Xi'an Medical University, Xi'an, China
- Department of Anesthesiology, School of Stomatology, State Key Laboratory of Military Stomatology & National Clinical Research Center for Oral Diseases & Shaanxi Engineering Research Center for Dental Materials and Advanced Manufacture, Air Force Military Medical University, Xi'an, China
| | - Hui Jiang
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, Zhoushan, China
| | - Wenbo Fan
- Department of Anesthesiology, School of Stomatology, State Key Laboratory of Military Stomatology & National Clinical Research Center for Oral Diseases & Shaanxi Engineering Research Center for Dental Materials and Advanced Manufacture, Air Force Military Medical University, Xi'an, China
| | - Xiaomin Li
- Department of Anesthesiology, School of Stomatology, State Key Laboratory of Military Stomatology & National Clinical Research Center for Oral Diseases & Shaanxi Engineering Research Center for Dental Materials and Advanced Manufacture, Air Force Military Medical University, Xi'an, China
| | - Yaowen Liu
- College of Veterinary Medicine, Yunnan Agricultural University, Kunming, China
| | - Lixian Xu
- Department of Anesthesiology, School of Stomatology, State Key Laboratory of Military Stomatology & National Clinical Research Center for Oral Diseases & Shaanxi Engineering Research Center for Dental Materials and Advanced Manufacture, Air Force Military Medical University, Xi'an, China
| | - Xingchun Gou
- Institute of Basic Translational Medicine, Shaanxi Key Laboratory of Brain Disorders, Xi'an Medical University, Xi'an, China
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Zadra N, Tatti A, Silverj A, Piccinno R, Devilliers J, Lewis C, Arnoldi D, Montarsi F, Escuer P, Fusco G, De Sanctis V, Feuda R, Sánchez-Gracia A, Rizzoli A, Rota-Stabelli O. Shallow Whole-Genome Sequencing of Aedes japonicus and Aedes koreicus from Italy and an Updated Picture of Their Evolution Based on Mitogenomics and Barcoding. Insects 2023; 14:904. [PMID: 38132578 PMCID: PMC10743467 DOI: 10.3390/insects14120904] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 11/20/2023] [Accepted: 11/21/2023] [Indexed: 12/23/2023]
Abstract
Aedes japonicus and Aedes koreicus are two invasive mosquitoes native to East Asia that are quickly establishing in temperate regions of Europe. Both species are vectors of arboviruses, but we currently lack a clear understanding of their evolution. Here, we present new short-read, shallow genome sequencing of A. japonicus and A. koreicus individuals from northern Italy, which we used for downstream phylogenetic and barcode analyses. We explored associated microbial DNA and found high occurrences of Delftia bacteria in both samples, but neither Asaia nor Wolbachia. We then assembled complete mitogenomes and used these data to infer divergence times estimating the split of A. japonicus from A. koreicus in the Oligocene, which was more recent than that previously reported using mitochondrial markers. We recover a younger age for most other nodes within Aedini and other Culicidae. COI barcoding and phylogenetic analyses indicate that A. japonicus yaeyamensis, A. japonicus amamiensis, and the two A. koreicus sampled from Europe should be considered as separate species within a monophyletic species complex. Our studies further clarify the evolution of A. japonicus and A. koreicus, and indicate the need to obtain whole-genome data from putative species in order to disentangle their complex patterns of evolution.
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Affiliation(s)
- Nicola Zadra
- Center Agriculture Food Environment (C3A), University of Trento, 38010 San Michele all’Adige, Italy; (N.Z.); (A.T.); (A.S.); (R.P.)
- CIBIO Department, University of Trento, 38123 Trento, Italy;
- Research and Innovation Centre, Fondazione Edmund Mach, 38010 San Michele all’Adige, Italy; (D.A.); (A.R.)
| | - Alessia Tatti
- Center Agriculture Food Environment (C3A), University of Trento, 38010 San Michele all’Adige, Italy; (N.Z.); (A.T.); (A.S.); (R.P.)
- Research and Innovation Centre, Fondazione Edmund Mach, 38010 San Michele all’Adige, Italy; (D.A.); (A.R.)
- Department of Biology, University of Padova, 35121 Padova, Italy;
- University School for Advanced Studies IUSS Pavia, 27100 Pavia, Italy
| | - Andrea Silverj
- Center Agriculture Food Environment (C3A), University of Trento, 38010 San Michele all’Adige, Italy; (N.Z.); (A.T.); (A.S.); (R.P.)
- CIBIO Department, University of Trento, 38123 Trento, Italy;
- Research and Innovation Centre, Fondazione Edmund Mach, 38010 San Michele all’Adige, Italy; (D.A.); (A.R.)
| | - Riccardo Piccinno
- Center Agriculture Food Environment (C3A), University of Trento, 38010 San Michele all’Adige, Italy; (N.Z.); (A.T.); (A.S.); (R.P.)
- Research and Innovation Centre, Fondazione Edmund Mach, 38010 San Michele all’Adige, Italy; (D.A.); (A.R.)
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, 27100 Pavia, Italy
| | - Julien Devilliers
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK; (J.D.); (C.L.); (R.F.)
| | - Clifton Lewis
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK; (J.D.); (C.L.); (R.F.)
| | - Daniele Arnoldi
- Research and Innovation Centre, Fondazione Edmund Mach, 38010 San Michele all’Adige, Italy; (D.A.); (A.R.)
| | - Fabrizio Montarsi
- Istituto Zooprofilattico Sperimentale Delle Venezie, 35020 Legnaro, Italy;
| | - Paula Escuer
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, 08028 Barcelona, Spain; (P.E.); (A.S.-G.)
- Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, 08007 Barcelona, Spain
| | - Giuseppe Fusco
- Department of Biology, University of Padova, 35121 Padova, Italy;
| | | | - Roberto Feuda
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK; (J.D.); (C.L.); (R.F.)
| | - Alejandro Sánchez-Gracia
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, 08028 Barcelona, Spain; (P.E.); (A.S.-G.)
- Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, 08007 Barcelona, Spain
| | - Annapaola Rizzoli
- Research and Innovation Centre, Fondazione Edmund Mach, 38010 San Michele all’Adige, Italy; (D.A.); (A.R.)
| | - Omar Rota-Stabelli
- Center Agriculture Food Environment (C3A), University of Trento, 38010 San Michele all’Adige, Italy; (N.Z.); (A.T.); (A.S.); (R.P.)
- CIBIO Department, University of Trento, 38123 Trento, Italy;
- Research and Innovation Centre, Fondazione Edmund Mach, 38010 San Michele all’Adige, Italy; (D.A.); (A.R.)
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Zhang Q, Li F, Li G, Dong Y, Wang J, Chen D, Shen Z. The complete mitochondrial genome of a new geographical population of freshwater fish Macropodus hongkongensis (Freyhof & Herder, 2002). Mitochondrial DNA B Resour 2023; 8:1298-1300. [PMID: 38188427 PMCID: PMC10769546 DOI: 10.1080/23802359.2023.2278819] [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] [Received: 07/19/2023] [Accepted: 10/29/2023] [Indexed: 01/09/2024] Open
Abstract
Macropodus hongkongensis (Freyhof & Herder, 2002), is sparsely distributed in Hong Kong and Guangdong provinces. Recently, a new geographical population of M. hongkongensis was discovered in the Wanquan River in the Hainan province. Therefore, this study focused on sequencing the complete mitochondrial genome of the new geographical population of Macropodus hongkongensis from the Wanquan River. The circular mtDNA molecule was 16,492 bp in size, and the overall base compositions were A (30.30%), C (24.90%), T (29.80%), and G (15.00%), with a slight bias toward A + T. The complete mitogenome encoded 13 protein-coding genes (PCGs), 22 tRNA genes, 2 rRNA genes, and a control region. Phylogenetic analysis indicated that M. hongkongensis of the Hainan Wanquan River was most closely related to the M. hongkongensis of the Gongdong population. These results provide useful genetic information for species identification and phylogenetic studies of Macropodus species.
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Affiliation(s)
- Qingfeng Zhang
- Research Institute of Freshwater Fisheries, Hainan Academy of Ocean and Fisheries Sciences, Haikou, China
- Research Center for Freshwater Bioresource and Eco-environment Protection in Hainan Province, Haikou, China
| | - Fangyuan Li
- Research Institute of Freshwater Fisheries, Hainan Academy of Ocean and Fisheries Sciences, Haikou, China
- Research Center for Freshwater Bioresource and Eco-environment Protection in Hainan Province, Haikou, China
| | - Gaojun Li
- Research Institute of Freshwater Fisheries, Hainan Academy of Ocean and Fisheries Sciences, Haikou, China
- Research Center for Freshwater Bioresource and Eco-environment Protection in Hainan Province, Haikou, China
| | - Yang Dong
- Research Institute of Freshwater Fisheries, Hainan Academy of Ocean and Fisheries Sciences, Haikou, China
- Research Center for Freshwater Bioresource and Eco-environment Protection in Hainan Province, Haikou, China
| | - Ji Wang
- Research Institute of Freshwater Fisheries, Hainan Academy of Ocean and Fisheries Sciences, Haikou, China
| | - Dikai Chen
- Research Institute of Freshwater Fisheries, Hainan Academy of Ocean and Fisheries Sciences, Haikou, China
| | - Zhixin Shen
- Research Institute of Freshwater Fisheries, Hainan Academy of Ocean and Fisheries Sciences, Haikou, China
- Research Center for Freshwater Bioresource and Eco-environment Protection in Hainan Province, Haikou, China
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Zhang R, Zhu T, Yu F. The New Mitochondrial Genome of Hemiculterella wui (Cypriniformes, Xenocyprididae): Sequence, Structure, and Phylogenetic Analyses. Genes (Basel) 2023; 14:2110. [PMID: 38136932 PMCID: PMC10742607 DOI: 10.3390/genes14122110] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 11/19/2023] [Accepted: 11/20/2023] [Indexed: 12/24/2023] Open
Abstract
Hemiculterella wui is an endemic small freshwater fish, distributed in the Pearl River system and Qiantang River, China. In this study, we identified and annotated the complete mitochondrial genome sequence of H. wui. The mitochondrial genome was 16,619 bp in length and contained 13 protein coding genes (PCGs), two rRNA genes, 22 tRNA genes, and one control region. The nucleotide composition of the mitochondrial genome was 29.9% A, 25.3% T, 27.4% C, and 17.5% G, respectively. Most PCGs used the ATG start codon, except COI and ATPase 8 started with the GTG start codon. Five PCGs used the TAA termination codon and ATPase 8 ended with the TAG stop codon, and the remaining seven genes used two incomplete stop codons (T and TA). Most of the tRNA genes showed classical cloverleaf secondary structures, except that tRNASer(AGY) lacked the dihydrouracil loop. The average Ka/Ks value of the ATPase 8 gene was the highest, while the average Ka/Ks value of the COI gene was the lowest. Phylogenetic analyses showed that H. wui has a very close relationship with Pseudohemiculter dispar and H. sauvagei. This study will provide a valuable basis for further studies of taxonomy and phylogenetic analyses in H. wui and Xenocyprididae.
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83
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Liu M, Luo Y, Jallow BJJ, Meng F. Characterization of Complete Mitochondrial Genome and Phylogenetic Analysis of a Nocturnal Wasps- Provespa barthelemyi (Hymenoptera: Vespidae). Curr Issues Mol Biol 2023; 45:9368-9377. [PMID: 38132433 PMCID: PMC10742571 DOI: 10.3390/cimb45120587] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 11/13/2023] [Accepted: 11/17/2023] [Indexed: 12/23/2023] Open
Abstract
Genus Provespa contains nocturnal wasps mainly found in the southeastern region of Asia. There are no complete genome resources available of this genus, which hinders the study of its phylogenetic evolution and the origin of nocturnal behavior in the Vespidae family. Through high-throughput sequencing, we obtained the mitochondrial genome of Provespa barthelemyi (Hymenoptera: Vespidae), which is 17,721 base pairs in length and contains 13 protein-coding genes (PCGs), 22 tRNAs, and two rRNAs. We identified four gene rearrangement events of P. barthelemyi that frequently occur in the Vespidae family. We used Maximum Likelihood (ML) methodologies to construct a phylogenetic tree based on the sequenced mitochondrial genome and the available data of reported species belonging to Vespinae. Our findings confirmed the monophyly of Vespinae. Our study reports the first complete mitochondrial genome of Provespa and compares its characteristics with other mitochondrial genomes in the family Vespidae. This research should shed light on the phylogenetic relationships and ecological characteristics of the Vespidae family.
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Affiliation(s)
| | | | | | - Fanming Meng
- College of Basic Medical Science, Central South University, Changsha 410017, China; (M.L.); (Y.L.); (B.J.J.J.)
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84
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Chen Y, Guo Y, Wei Z, Zhao X. The complete mitochondrial genome of Neolissochilus soroides (Duncker, 1904) (Cypriniformes: Cyprinidae). Mitochondrial DNA B Resour 2023; 8:1258-1262. [PMID: 38188434 PMCID: PMC10769550 DOI: 10.1080/23802359.2023.2281032] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 11/02/2023] [Indexed: 01/09/2024] Open
Abstract
In this paper, we first report the complete mitochondrial genome of Neolissochilus soroides. The main purpose of this study was to determine the mitochondrial genome and phylogenetic status of N. soroides. The length mitogenome was 16584 bp, containing 2 ribosomal RNA genes, 13 protein-coding genes, 22 transfer RNA genes, and 3 non-coding control regions. The genome showed a slight A + T bias (A + T = 56.47%). 12 genes (ND1, COX2, ATP6, ND4L, ND5, ND6, ND2, ATP8, ND3, ND4, Cytb, COX3) start with ATG codon, besides one gene (COX1) start with GTG codon. Six genes (ND1, COX1, ATP6, ND4L, ND5, ND6) end with a TAA codon, 3 genes (ND2, ATP8, ND3) end with a TAG codon, and four genes (COX2, ND4, Cytb, COX3) end with the TA or T codon. The phylogenetic analysis showed that N. soroides was closely related to N. hendersoni. The mitogenome could have important implications for phylogeny, population genetics, and conservation of the N. soroides.
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Affiliation(s)
- Ye Chen
- Key Laboratory of Sustainable Utilization of Technology Research for Fisheries Resources of Zhejiang Province, Zhejiang Marine Fisheries Research Institute, Zhoushan, China
- Marine and Fishery Institute, Zhejiang Ocean University, Zhoushan, Chinaof
| | - Yongyao Guo
- College of Fisheries, Zhejiang Ocean University, Zhoushan, Zhejiang Province, China
| | - Zhenzhu Wei
- College of Fisheries, Zhejiang Ocean University, Zhoushan, Zhejiang Province, China
| | - Xiaoli Zhao
- Endoscopic Center, Shengzhou Hospital of Traditional Chinese Medicine, Shengzhou, Zhejiang Province, China
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85
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Muhammad N, Li DX, Ru SS, Suleman, Saood D, Alvi MA, Li L. Characterization of the complete mitochondrial genome of Acanthogyrus ( Acanthosentis) bilaspurensis Chowhan, Gupta & Khera, 1987 (Eoacanthocephala: Quadrigyridae), the smallest mitochondrial genome in Acanthocephala, and its phylogenetic implications. J Helminthol 2023; 97:e87. [PMID: 37969070 DOI: 10.1017/s0022149x23000561] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2023]
Abstract
The phylum Acanthocephala is an important group of parasites with more than 1,300 species parasitizing intestine of all major vertebrate groups. However, our present knowledge of the mitochondrial genomes of Acanthocephala remains very limited. In the present study, we sequenced and annotated the complete mitochondrial genome of Acanthogyrus (Acanthosentis) bilaspurensis (Gyracanthocephala: Quadrigyridae) for the first time based on the specimens recovered from the intestine of common carp Cyprinus carpio Linnaeus (Cyprinidae) in Pakistan. The mitochondrial genome of A. bilaspurensis is 13,360 bp in size and contains 36 genes, representing the smallest mitogenome of acanthocephalans reported so far. The mitogenome of A. bilaspurensis also has the lowest level of overall A+T contents (59.3%) in the mitogenomes of Eoacanthocephala, and the non-coding region 3 (NCR3) lies between trnS2 and trnI, which is different from all of the other acanthocephalan species. Phylogenetic analyses based on concatenating the amino acid sequences of 12 protein-coding genes using maximum likelihood (ML) and Bayesian inference (BI) methods revealed that the family Pseudoacanthocephalidae is a sister to the Arhythmacanthidae rather than the Cavisomatidae, and the families Rhadinorhynchidae and Cavisomatidae showed sister relationships.
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Affiliation(s)
- Nehaz Muhammad
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology; Hebei Collaborative Innovation Center for Eco-Environment; College of Life Sciences, Hebei Normal University, 050024Shijiazhuang, Hebei Province, P. R. China
- Hebei Research Center of the Basic Discipline Cell Biology; Ministry of Education Key Laboratory of Molecular and Cellular Biology; 050024Shijiazhuang, Hebei Province, P. R. China
- Biology Postdoctoral Research Mobile Station, Hebei Normal University, 050024Shijiazhuang, Hebei Province, P. R. China
| | - D-X Li
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology; Hebei Collaborative Innovation Center for Eco-Environment; College of Life Sciences, Hebei Normal University, 050024Shijiazhuang, Hebei Province, P. R. China
| | - S-S Ru
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology; Hebei Collaborative Innovation Center for Eco-Environment; College of Life Sciences, Hebei Normal University, 050024Shijiazhuang, Hebei Province, P. R. China
| | - Suleman
- Department of Zoology, University of Swabi, Anbar, Swabi, 23561, Khyber Pakhtunkhwa, Pakistan
| | - D Saood
- Department of Zoology, Abdul Wali Khan University MardanKhyber Pakhtunkhwa, Pakistan
| | - M A Alvi
- Department of Clinical Medicine and Surgery, University of Agriculture, Faisalabad, Pakistan
| | - L Li
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology; Hebei Collaborative Innovation Center for Eco-Environment; College of Life Sciences, Hebei Normal University, 050024Shijiazhuang, Hebei Province, P. R. China
- Hebei Research Center of the Basic Discipline Cell Biology; Ministry of Education Key Laboratory of Molecular and Cellular Biology; 050024Shijiazhuang, Hebei Province, P. R. China
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86
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Zou D, Yuan J, Ding J, Li J, Zhang H. The complete mitochondrial genome of Semiothisa cinerearia Bremer & Grey 1853 (Lepidoptera: Geometridae: Ennominae) and its phylogenetic analysis. Mitochondrial DNA B Resour 2023; 8:1248-1252. [PMID: 38188431 PMCID: PMC10769541 DOI: 10.1080/23802359.2023.2278820] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 10/29/2023] [Indexed: 01/09/2024] Open
Abstract
Semiothisa cinerearia Bremer & Grey, 1853 belongs to the lepidopteran family Geometridae, subfamily Ennominae. We sequenced the complete mitochondrial genome of S. cinerearia by PCR and Sanger sequencing method. The mitochondrial genome of S. cinerearia is 15,523 bp in length and contains a typical set of 37 genes with 'MIQ' type gene arrangement and a 394 bp AT-rich regions. Except for cox1 using CGA as initiation codon, all protein-coding genes (PCGs) start with ATN codons and except for nad2 and nad4l using TAG as termination codon, all PCGs terminated with TAA codon. A phylogenetic tree including 39 genus of subfamily Ennominae was first reconstructed based on the mitochondrial genome sequences with nucleotide substitution model GTR + G + I, which showed that the genera Amraica, Jankowskia, and Ectropis are not monophyletic and S. cinerearia and Macaria notata are classified together.
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Affiliation(s)
- Deng Zou
- College of Life Sciences, Huaibei Normal University, Huaibei, China
| | - Jun Yuan
- College of Life Sciences, Huaibei Normal University, Huaibei, China
| | - Jie Ding
- College of Life Sciences, Huaibei Normal University, Huaibei, China
| | - Jun Li
- College of Life Sciences, Huaibei Normal University, Huaibei, China
| | - Haijun Zhang
- College of Life Sciences, Huaibei Normal University, Huaibei, China
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87
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Tian S, Jiang Y, Lai Y, Wang S, Liu X, Wang Y. New Mitogenomes of the Green Lacewing Tribe Ankylopterygini (Neuroptera: Chrysopidae: Chrysopinae) and Phylogenetic Implications of Chrysopidae. Insects 2023; 14:878. [PMID: 37999077 PMCID: PMC10672194 DOI: 10.3390/insects14110878] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 11/09/2023] [Accepted: 11/10/2023] [Indexed: 11/25/2023]
Abstract
Chrysopidae (green lacewings) are a cosmopolitan and species-rich family of Neuroptera, with remarkable significance of biological control against various agricultural and forestry pests. However, the phylogenetic position of Chrysopidae in Neuroptera and the internal relationships within the family remain equivocal among previous studies based on different types of data and sampling. Here we sequenced the mitochondrial genomes (mitogenomes) of two species of the genus Ankylopteryx in the chrysopine tribe Ankylopterygini for the first time. The characteristics of these mitogenomes were analyzed in comparison with other green lacewing mitogenomes published to date. In the phylogeny herein reconstructed based on mitogenomes, Chrysopinae were recovered as the sister group to Apochrysinae + Nothochrysinae. Within the subfamily of Chrysopinae, Nothancylini were recovered as the sister group to (Leucochrysini + Belonopterygini) + (Ankylopterygini + Chrysopini). The divergence time estimation suggested an Early Cretaceous initial divergence within the extant Chrysopidae. Within Chrysopinae, the four tribes except Nothancylini diverged around mid-Cretaceous.
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Affiliation(s)
- Shuo Tian
- College of Plant Protection, Hebei Agricultural University, Baoding 071001, China; (S.T.); (Y.J.); (S.W.)
| | - Yunlan Jiang
- College of Plant Protection, Hebei Agricultural University, Baoding 071001, China; (S.T.); (Y.J.); (S.W.)
| | - Yan Lai
- Department of Entomology, China Agricultural University, Beijing 100193, China;
| | - Shutong Wang
- College of Plant Protection, Hebei Agricultural University, Baoding 071001, China; (S.T.); (Y.J.); (S.W.)
| | - Xingyue Liu
- Department of Entomology, China Agricultural University, Beijing 100193, China;
| | - Yuyu Wang
- College of Plant Protection, Hebei Agricultural University, Baoding 071001, China; (S.T.); (Y.J.); (S.W.)
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88
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Wang C, Ye P, Pillans R, Chen X, Wang J, Feutry P. Evolution of the Critically Endangered Green Sawfish Pristis zijsron (Rhinopristiformes, Pristidae), Inferred from the Whole Mitochondrial Genome. Genes (Basel) 2023; 14:2052. [PMID: 38002995 PMCID: PMC10671267 DOI: 10.3390/genes14112052] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 10/28/2023] [Accepted: 11/02/2023] [Indexed: 11/26/2023] Open
Abstract
The green sawfish Pristis zijsron (Bleeker, 1851), a species of sawfish in the family Pristidae (Rhinopristiformes), mainly inhabits the Indo-West Pacific region. In this study, the complete mitochondrial genome of the critically endangered green sawfish is first described. The length of the genome is 16,804 bp, with a nucleotide composition of 32.0% A, 24.8% C, 13.1% G, and 30.0% T. It contains 37 genes in the typical gene order of fish. Two start (GTG and ATG) and two stop (TAG and TAA/T-) codons are found in the thirteen protein-coding genes. The 22 tRNA genes range from 67 bp (tRNA-Ser) to 75 bp (tRNA-Leu). The ratio of nonsynonymous substitution (Ka) and synonymous substitution (Ks) indicates that the family Pristidae are suffering a purifying selection. The reconstruction of Bayesian inference and the maximum likelihood phylogenetic tree show the same topological structure, and the family Pristidae is a monophyletic group with strong posterior probability. Pristis zijsron and P. pectinata form a sister group in the terminal clade. And the divergence time of Rhinopristiformes show that P. zijsron and P. pectinata diverged as two separate species in about Paleogene 31.53 Mya. Complete mitochondrial genomes of all five sawfishes have been published and phylogenetic relationships have been analyzed. The results of our study will provide base molecular information for subsequent research (e.g., distribution, conservation, phylogenetics, etc.) on this endangered group.
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Affiliation(s)
- Chen Wang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361000, China;
- College of Marine Sciences, South China Agricultural University, Guangzhou 510642, China; (P.Y.); (X.C.)
| | - Peiyuan Ye
- College of Marine Sciences, South China Agricultural University, Guangzhou 510642, China; (P.Y.); (X.C.)
| | - Richard Pillans
- CSIRO Environment, Boggo Road, Dutton Park, QLD 4102, Australia;
| | - Xiao Chen
- College of Marine Sciences, South China Agricultural University, Guangzhou 510642, China; (P.Y.); (X.C.)
| | - Junjie Wang
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, School of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Pierre Feutry
- CSIRO Environment, Castray Esplanade, Hobart, TAS 7000, Australia
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89
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Platz KR, Rudisel EJ, Paluch KV, Laurin TR, Dittenhafer-Reed KE. Assessing the Role of Post-Translational Modifications of Mitochondrial RNA Polymerase. Int J Mol Sci 2023; 24:16050. [PMID: 38003238 PMCID: PMC10671485 DOI: 10.3390/ijms242216050] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 11/02/2023] [Accepted: 11/02/2023] [Indexed: 11/26/2023] Open
Abstract
The mitochondrial proteome is subject to abundant post-translational modifications, including lysine acetylation and phosphorylation of serine, threonine, and tyrosine. The biological function of the majority of these protein modifications is unknown. Proteins required for the transcription and translation of mitochondrial DNA (mtDNA) are subject to modification. This suggests that reversible post-translational modifications may serve as a regulatory mechanism for mitochondrial gene transcription, akin to mechanisms controlling nuclear gene expression. We set out to determine whether acetylation or phosphorylation controls the function of mitochondrial RNA polymerase (POLRMT). Mass spectrometry was used to identify post-translational modifications on POLRMT. We analyzed three POLRMT modification sites (lysine 402, threonine 315, threonine 993) found in distinct structural regions. Amino acid point mutants that mimic the modified and unmodified forms of POLRMT were employed to measure the effect of acetylation or phosphorylation on the promoter binding ability of POLRMT in vitro. We found a slight decrease in binding affinity for the phosphomimic at threonine 315. We did not identify large changes in viability, mtDNA content, or mitochondrial transcript level upon overexpression of POLRMT modification mimics in HeLa cells. Our results suggest minimal biological impact of the POLRMT post-translational modifications studied in our system.
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90
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Nguyen PT, Lee S, Jeong J, Kim J, Han DW, Kim IC, Lee JH, Park J, Kim JH. Complete mitochondrial genome of Trematomus newnesi (Perciformes, Nototheniidae). Mitochondrial DNA B Resour 2023; 8:1196-1199. [PMID: 38196755 PMCID: PMC10776061 DOI: 10.1080/23802359.2023.2194456] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Accepted: 03/19/2023] [Indexed: 01/11/2024] Open
Abstract
The complete mitochondrial genome of Trematomus newnesi was sequenced using an Illumina platform. The 18,602 bp mitogenome contains 13 protein-coding genes, two rRNAs, and 23 tRNAs (tRNAMet is duplicated). The eight stop codons are TAA, TAG, CTT, GTA, AAT, ACT, AGG, and TTA. Two start codons ATG and GTG are present. The GC content is 44.4% and AT content is 55.6%. A phylogenetic tree was generated using 13 species from three families. The results showed that T. newnesi is closely related to Pagothenia borchgrevinki in Nototheniidae. This study provides fundamental data for further genetic evolutionary studies on T. newnesi.
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Affiliation(s)
- Phuong Thi Nguyen
- Division of Life Sciences, Korea Polar Research Institute, Incheon, Korea
- Polar Science, University of Science and Technology, Daejeon, Korea
| | - Seungyeon Lee
- Division of Life Sciences, Korea Polar Research Institute, Incheon, Korea
- Polar Science, University of Science and Technology, Daejeon, Korea
| | - Jihye Jeong
- Division of Life Sciences, Korea Polar Research Institute, Incheon, Korea
| | - Jihun Kim
- Division of Life Sciences, Korea Polar Research Institute, Incheon, Korea
- Polar Science, University of Science and Technology, Daejeon, Korea
| | - Dong-Won Han
- Division of Life Sciences, Korea Polar Research Institute, Incheon, Korea
| | - Il-Chan Kim
- Division of Life Sciences, Korea Polar Research Institute, Incheon, Korea
| | - Jun Hyuck Lee
- Polar Science, University of Science and Technology, Daejeon, Korea
- Research Unit of Cryogenic Novel Material, Korea Polar Research Institute, Inchon, Korea
| | - Jisoo Park
- Polar Science, University of Science and Technology, Daejeon, Korea
- Division of Ocean Sciences, Korea Polar Research Institute, Inchon, Korea
| | - Jin-Hyoung Kim
- Division of Life Sciences, Korea Polar Research Institute, Incheon, Korea
- Polar Science, University of Science and Technology, Daejeon, Korea
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91
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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] [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: 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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92
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Zhou X, Lei Y, Dietrich CH, Huang M. Investigating Monophyly of Typhlocybini Based on Complete Mitochondrial Genomes with Characterization and Comparative Analysis of 19 Species (Hemiptera: Cicadellidae: Typhlocybinae). Insects 2023; 14:842. [PMID: 37999041 PMCID: PMC10671860 DOI: 10.3390/insects14110842] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 10/26/2023] [Accepted: 10/27/2023] [Indexed: 11/25/2023]
Abstract
Tribes of the leafhopper subfamily Typhlocybinae have traditionally been defined based on differences in forewing and hindwing venation. Except for Typhlocybini (sensu lato), the classification of tribes is relatively stable. The monophyly of Typhlocybini needs to be examined, and the relationships among genera within Typhlocybini have not been resolved. Few mitogenome sequences representative of major lineages of Typhlocybini have been available to facilitate a comprehensive phylogenetic analysis of the tribe. In this study, the complete mitogenomes of 19 species of Typhlocybini were sequenced. The gene arrangements of the 19 new mitogenomes are consistent with ancestral insect mitogenomes. Phylogenetic analyses by both maximum-likelihood and Bayesian methods of 67 species of Typhlocybinae suggest that Zyginellini is paraphyletic with respect to Typhlocybini. The phylogenetic relationships within Typhlocybini are discussed, and the major results show that the Farynala and Linnavuoriana complexes previously recognized based on morphological characters correspond to monophyletic lineages.
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Affiliation(s)
- Xian Zhou
- Key Laboratory of Plant Protection Resources and Pest Management of Ministry of Education, Entomological Museum, College of Plant Protection, Northwest A&F University, Xianyang 712100, China; (X.Z.); (Y.L.)
| | - Yuejie Lei
- Key Laboratory of Plant Protection Resources and Pest Management of Ministry of Education, Entomological Museum, College of Plant Protection, Northwest A&F University, Xianyang 712100, China; (X.Z.); (Y.L.)
| | - Christopher H. Dietrich
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois, 1816 S. Oak St., Champaign, IL 61820, USA;
| | - Min Huang
- Key Laboratory of Plant Protection Resources and Pest Management of Ministry of Education, Entomological Museum, College of Plant Protection, Northwest A&F University, Xianyang 712100, China; (X.Z.); (Y.L.)
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93
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Zheng J, Li F, Fan M, Gu Z, Liu C, Wang A, Yang Y. Mitogenomic Phylogeny of Tonnoidea Suter, 1913 (1825) (Gastropoda: Caenogastropoda). Animals (Basel) 2023; 13:3342. [PMID: 37958096 PMCID: PMC10649890 DOI: 10.3390/ani13213342] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 10/01/2023] [Accepted: 10/25/2023] [Indexed: 11/15/2023] Open
Abstract
The Tonnoidea Suter, 1913 (1825) is a moderately diverse group of large predatory gastropods, the systematics of which remain unclear. In the present study, the complete mitochondrial genomes of nine Tonnoidean species were sequenced. All newly sequenced mitogenomes contain 13 protein-coding genes (PCGs), 22 transfer RNA genes and two ribosomal RNA genes, showing similar patterns in genome size, gene order and nucleotide composition. The ratio of nonsynonymous to synonymous of PCGs indicated that NADH complex genes of Tonnoideans were experiencing a more relaxed purifying selection compared with the COX genes. The reconstructed phylogeny based on the combined amino acid sequences of 13 protein-coding genes and the nucleotide sequences of two rRNA genes supported that Ficidae Meek, 1864 (1840) is a sister to Tonnoidea. The monophylies of all Tonnoidean families were recovered and the internal phylogenetic relationships were consistent with the current classification. The phylogeny also revealed that Tutufa rebuta (Linnaeus, 1758) is composed of at least two different species, indicating that the species diversity within Bursidae Thiele, 1925 might be underestimated. The present study contributes to the understanding of the Tonnoidean systematics, and it could provide important information for the revision of Tonnoidean systematics in the future.
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Affiliation(s)
- Jiawen Zheng
- School of Marine Biology and Fisheries, Hainan University, Haikou 570228, China; (J.Z.); (F.L.); (M.F.); (Z.G.); (C.L.); (A.W.)
| | - Fengping Li
- School of Marine Biology and Fisheries, Hainan University, Haikou 570228, China; (J.Z.); (F.L.); (M.F.); (Z.G.); (C.L.); (A.W.)
| | - Mingfu Fan
- School of Marine Biology and Fisheries, Hainan University, Haikou 570228, China; (J.Z.); (F.L.); (M.F.); (Z.G.); (C.L.); (A.W.)
| | - Zhifeng Gu
- School of Marine Biology and Fisheries, Hainan University, Haikou 570228, China; (J.Z.); (F.L.); (M.F.); (Z.G.); (C.L.); (A.W.)
| | - Chunsheng Liu
- School of Marine Biology and Fisheries, Hainan University, Haikou 570228, China; (J.Z.); (F.L.); (M.F.); (Z.G.); (C.L.); (A.W.)
| | - Aimin Wang
- School of Marine Biology and Fisheries, Hainan University, Haikou 570228, China; (J.Z.); (F.L.); (M.F.); (Z.G.); (C.L.); (A.W.)
| | - Yi Yang
- School of Marine Biology and Fisheries, Hainan University, Haikou 570228, China; (J.Z.); (F.L.); (M.F.); (Z.G.); (C.L.); (A.W.)
- Sanya Nanfan Research Institute, Hainan University, Sanya 572025, China
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94
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Zhang F, Kang H, Gao L. Complete Mitochondrial Genome Assembly of an Upland Wild Rice Species, Oryza granulata and Comparative Mitochondrial Genomic Analyses of the Genus Oryza. Life (Basel) 2023; 13:2114. [PMID: 38004254 PMCID: PMC10672236 DOI: 10.3390/life13112114] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Revised: 10/15/2023] [Accepted: 10/18/2023] [Indexed: 11/26/2023] Open
Abstract
Wild upland rice species, including Oryza granulata, possess unique characteristics that distinguish them from other Oryza species. For instance, O. granulata characteristically has a GG genome and is accordingly classified as a basal lineage of the genus Oryza. Here, we deployed a versatile hybrid approach by integrating Illumina and PacBio sequencing data to generate a high-quality mitochondrial genome (mitogenome) assembly for O. granulata. The mitogenome of O. granulata was 509,311 base pairs (bp) with sixty-seven genes comprising two circular chromosomes, five ribosomal RNA (rRNA) coding genes, twenty-five transfer RNA (tRNA) coding genes, and thirty-seven genes coding for proteins. We identified a total of 378 simple sequence repeats (SSRs). The genome also contained 643 pairs of dispersed repeats comprising 340 palindromic and 303 forward. In the O. granulata mitogenome, the length of 57 homologous fragments in the chloroplast genome occupied 5.96% of the mitogenome length. Collinearity analysis of three Oryza mitogenomes revealed high structural variability and frequent rearrangements. Phylogenetic analysis showed that, compared to other related genera, O. granulata had the closest genetic relationship with mitogenomes reported for all members of Oryza, and occupies a position at the base of the Oryza phylogeny. Comparative analysis of complete mitochondrial genome assemblies for Oryza species revealed high levels of mitogenomic diversity, providing a foundation for future conservation and utilization of wild rice biodiversity.
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Affiliation(s)
- Fen Zhang
- College of Agriculture, South China Agricultural University, Guangzhou 510642, China;
| | - Haiqi Kang
- Tropical Biodiversity and Genomics Research Center, Engineering Research Center for Selecting and Breeding New Tropical Crop Varieties, Ministry of Education, Hainan University, Haikou 570228, China;
| | - Lizhi Gao
- College of Agriculture, South China Agricultural University, Guangzhou 510642, China;
- Tropical Biodiversity and Genomics Research Center, Engineering Research Center for Selecting and Breeding New Tropical Crop Varieties, Ministry of Education, Hainan University, Haikou 570228, China;
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95
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Sun H, Wang Z, Shen L, Feng Y, Han L, Qian X, Meng R, Ji K, Liang D, Zhou F, Lou X, Zhang J, Shen B. Developing mitochondrial base editors with diverse context compatibility and high fidelity via saturated spacer library. Nat Commun 2023; 14:6625. [PMID: 37857619 PMCID: PMC10587121 DOI: 10.1038/s41467-023-42359-3] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 10/09/2023] [Indexed: 10/21/2023] Open
Abstract
DddA-derived cytosine base editors (DdCBEs) greatly facilitated the basic and therapeutic research of mitochondrial DNA mutation diseases. Here we devise a saturated spacer library and successfully identify seven DddA homologs by performing high-throughput sequencing based screen. DddAs of Streptomyces sp. BK438 and Lachnospiraceae bacterium sunii NSJ-8 display high deaminase activity with a strong GC context preference, and DddA of Ruminococcus sp. AF17-6 is highly compatible to AC context. We also find that different split sites result in wide divergence on off-target activity and context preference of DdCBEs derived from these DddA homologs. Additionally, we demonstrate the orthogonality between DddA and DddIA, and successfully minimize the nuclear off-target editing by co-expressing corresponding nuclear-localized DddIA. The current study presents a comprehensive and unbiased strategy for screening and characterizing dsDNA cytidine deaminases, and expands the toolbox for mtDNA editing, providing additional insights for optimizing dsDNA base editors.
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Affiliation(s)
- Haifeng Sun
- State Key Laboratory of Reproductive Medicine and Offspring Health, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Center for Global Health, Gusu School, Nanjing Medical University, Nanjing, 211166, China
| | - Zhaojun Wang
- State Key Laboratory of Reproductive Medicine and Offspring Health, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Center for Global Health, Gusu School, Nanjing Medical University, Nanjing, 211166, China
| | - Limini Shen
- State Key Laboratory of Reproductive Medicine and Offspring Health, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Center for Global Health, Gusu School, Nanjing Medical University, Nanjing, 211166, China
| | - Yeling Feng
- State Key Laboratory of Reproductive Medicine and Offspring Health, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Center for Global Health, Gusu School, Nanjing Medical University, Nanjing, 211166, China
| | - Lu Han
- State Key Laboratory of Reproductive Medicine and Offspring Health, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Center for Global Health, Gusu School, Nanjing Medical University, Nanjing, 211166, China
| | - Xuezhen Qian
- State Key Laboratory of Reproductive Medicine and Offspring Health, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Center for Global Health, Gusu School, Nanjing Medical University, Nanjing, 211166, China
| | - Runde Meng
- State Key Laboratory of Reproductive Medicine and Offspring Health, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Center for Global Health, Gusu School, Nanjing Medical University, Nanjing, 211166, China
| | - Kangming Ji
- State Key Laboratory of Reproductive Medicine and Offspring Health, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Center for Global Health, Gusu School, Nanjing Medical University, Nanjing, 211166, China
| | - Dong Liang
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, 210004, China
| | - Fei Zhou
- Cambridge-Suda Genomic Resource Center, Suzhou Medical College of Soochow University, Suzhou, 215123, China
| | - Xin Lou
- Research Institute of Intelligent Computing, Zhejiang Lab, Hangzhou, 311100, China.
| | - Jun Zhang
- State Key Laboratory of Reproductive Medicine and Offspring Health, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Center for Global Health, Gusu School, Nanjing Medical University, Nanjing, 211166, China.
| | - Bin Shen
- State Key Laboratory of Reproductive Medicine and Offspring Health, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Center for Global Health, Gusu School, Nanjing Medical University, Nanjing, 211166, China.
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96
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Wang XG, Wei SY, Qi LL, Yang ZF, Tang J, Liu ZL, Wu SJ. Complete mitochondrial genomic sequence of Auricularia delicata (Auriculariaceae), an edible Chinese mushroom. Mitochondrial DNA B Resour 2023; 8:1109-1113. [PMID: 37859798 PMCID: PMC10583609 DOI: 10.1080/23802359.2023.2268759] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 10/04/2023] [Indexed: 10/21/2023] Open
Abstract
Auricularia delicata (Mont.) Henn. 1893 is an edible and medicinal jelly mushroom popular in China. Here, we report the assembly and annotation of a complete A. delicata mitochondrial genome based on data sequenced using an Illumina NovaSeq 6000 platform. The length of the complete circular A. delicata mitochondrial genome is 189,696 bp, with a GC content of 34.1%. The A. delicata mitochondrial genome contains 60 genes, including 32 protein-coding genes, 26 tRNA genes, and two rRNA genes. Phylogenetic analysis indicated that A. delicata clustered with the Auricularia group, alongside A. auricula-judae and A. heimuer. Additionally, A. delicata was found to be genetically distant from other species of Polyporales, Russulales, and Agaricales. This genome will provide an invaluable reference for the continued study and utilization of A. delicata and other Auricularia species.
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Affiliation(s)
- Xiao-guo Wang
- Microbiology Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, PR China
| | - Shi-yan Wei
- Microbiology Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, PR China
| | - Liang-liang Qi
- Microbiology Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, PR China
| | - Zai-feng Yang
- Agriculture Bureau of Rongshui County, Industrial Crop station of Rongshui, Liuzhou, PR China
| | - Jun Tang
- Microbiology Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, PR China
| | - Zeng-liang Liu
- Microbiology Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, PR China
| | - Sheng-jin Wu
- Microbiology Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, PR China
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97
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Xiong Z, He D, Guang X, Li Q. Novel tRNA Gene Rearrangements in the Mitochondrial Genomes of Poneroid Ants and Phylogenetic Implication of Paraponerinae (Hymenoptera: Formicidae). Life (Basel) 2023; 13:2068. [PMID: 37895449 PMCID: PMC10608118 DOI: 10.3390/life13102068] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 10/04/2023] [Accepted: 10/09/2023] [Indexed: 10/29/2023] Open
Abstract
Ants (Formicidae) are the most diverse eusocial insects in Hymenoptera, distributed across 17 extant subfamilies grouped into 3 major clades, the Formicoid, Leptanilloid, and Poneroid. While the mitogenomes of Formicoid ants have been well studied, there is a lack of published data on the mitogenomes of Poneroid ants, which requires further characterization. In this study, we first present three complete mitogenomes of Poneroid ants: Paraponera clavata, the only extant species from the subfamily Paraponerinae, and two species (Harpegnathos venator and Buniapone amblyops) from the Ponerinae subfamily. Notable novel gene rearrangements were observed in the new mitogenomes, located in the gene blocks CR-trnM-trnI-trnQ-ND2, COX1-trnK-trnD-ATP8, and ND3-trnA-trnR-trnN-trnS1-trnE-trnF-ND5. We reported the duplication of tRNA genes for the first time in Formicidae. An extra trnQ gene was identified in H. venator. These gene rearrangements could be explained by the tandem duplication/random loss (TDRL) model and the slipped-strand mispairing model. Additionally, one large duplicated region containing tandem repeats was identified in the control region of P. clavata. Phylogenetic analyses based on protein-coding genes and rRNA genes via maximum likelihood and Bayes methods supported the monophyly of the Poneroid clade and the sister group relationship between the subfamilies Paraponerinae and Amblyoponinae. However, caution is advised in interpreting the positions of Paraponerinae due to the potential artifact of long-branch attraction.
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Affiliation(s)
- Zijun Xiong
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China;
- BGI Research, Wuhan 430074, China
| | - Ding He
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, 2100 Copenhagen, Denmark;
| | | | - Qiye Li
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China;
- BGI Research, Wuhan 430074, China
- BGI Research, Shenzhen 518083, China;
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98
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Csuzdi C, Koo J, Choi NJ, Szederjesi T, Hong Y. Complete mitochondrial genome of the composting worm Dendrobaena veneta (Clitellata: Oligochaeta, Lumbricidae). Mitochondrial DNA B Resour 2023; 8:1082-1086. [PMID: 37849654 PMCID: PMC10578090 DOI: 10.1080/23802359.2023.2265177] [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] [Received: 06/25/2023] [Accepted: 09/26/2023] [Indexed: 10/19/2023] Open
Abstract
Dendrobaena veneta (Rosa, 1886) is widely distributed all over Europe due to its use as compost worm. The specimen presented here was collected in Tiranë district, Albania. Currently, only two species' complete or nearly complete mitochondrial genome (mitogenome) sequences have been reported in the genus Dendrobaena; D. octaedra (Savigny, 1826) and D. tellermanica Perel, 1966. In this study, the complete mitogenome of D. veneta was sequenced, assembled, and annotated. The mitogenome of D. veneta is a circular DNA molecule, consisting of 15,475 bp with an A + T content of 61.2%. It contains 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes, and 1 non-coding region (control region). Phylogenetic analysis showed that D. veneta is clustered with the other two Dendrobaena species in the well-supported family Lumbricidae.
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Affiliation(s)
- Csaba Csuzdi
- Department of Zoology, Eszterházy Károly Catholic University, Eger, Hungary
| | - Jachoon Koo
- Division of Science Education and Institute of Fusion Science, College of Education, Jeonbuk National University, Jeonju, Korea
| | - Nak jung Choi
- Crop Foundation Research Division, National Institute of Crop Science, Korea
| | - Tímea Szederjesi
- Department of Systematic Zoology, Eötvös Loránd University, Budapest, Hungary
| | - Yong Hong
- Department of Agricultural Biology, College of Agriculture and Life Sciences, Jeonbuk National University, Jeonju, Korea
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99
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Ni Y, Zhang X, Li J, Lu Q, Chen H, Ma B, Liu C. Genetic diversity of Coffea arabica L. mitochondrial genomes caused by repeat- mediated recombination and RNA editing. Front Plant Sci 2023; 14:1261012. [PMID: 37885664 PMCID: PMC10598636 DOI: 10.3389/fpls.2023.1261012] [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] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 09/25/2023] [Indexed: 10/28/2023]
Abstract
Background Coffea arabica L. is one of the most important crops widely cultivated in 70 countries across Asia, Africa, and Latin America. Mitochondria are essential organelles that play critical roles in cellular respiration, metabolism, and differentiation. C. arabica's nuclear and chloroplast genomes have been reported. However, its mitochondrial genome remained unreported. Here, we intended to sequence and characterize its mitochondrial genome to maximize the potential of its genomes for evolutionary studies, molecular breeding, and molecular marker developments. Results We sequenced the total DNA of C. arabica using Illumina and Nanopore platforms. We then assembled the mitochondrial genome with a hybrid strategy using Unicycler software. We found that the mitochondrial genome comprised two circular chromosomes with lengths of 867,678 bp and 153,529 bp, encoding 40 protein-coding genes, 26 tRNA genes, and three rRNA genes. We also detected 270 Simple Sequence Repeats and 34 tandem repeats in the mitochondrial genome. We found 515 high-scoring sequence pairs (HSPs) for a self-to-self similarity comparison using BLASTn. Three HSPs were found to mediate recombination by the mapping of long reads. Furthermore, we predicted 472 using deep-mt with the convolutional neural network model. Then we randomly validated 90 RNA editing events by PCR amplification and Sanger sequencing, with the majority being non-synonymous substitutions and only three being synonymous substitutions. These findings provide valuable insights into the genetic characteristics of the C. arabica mitochondrial genome, which can be helpful for future study on coffee breeding and mitochondrial genome evolution. Conclusion Our study sheds new light on the evolution of C. arabica organelle genomes and their potential use in genetic breeding, providing valuable data for developing molecular markers that can improve crop productivity and quality. Furthermore, the discovery of RNA editing events in the mitochondrial genome of C. arabica offers insights into the regulation of gene expression in this species, contributing to a better understanding of coffee genetics and evolution.
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Affiliation(s)
| | | | | | | | | | | | - Chang Liu
- Center for Bioinformatics, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
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100
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Zheng YT, Chen LL, Zhao K. Complete mitochondrial genome sequence of Lanmaoa macrocarpa (Boletales, Basidiomycota). Mitochondrial DNA B Resour 2023; 8:1067-1070. [PMID: 37829256 PMCID: PMC10566434 DOI: 10.1080/23802359.2023.2266231] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [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: 06/28/2023] [Accepted: 09/28/2023] [Indexed: 10/14/2023] Open
Abstract
Lanmaoa macrocarpa is a boletoid mushroom from the family Boletaceae and was named after its relatively larger basidiocarp and bluish color change when bruised. At present, its mitochondrial genome and phylogenetic relationships with other boletes remain unexplored. In this study, we sequenced the mitochondrial genome of L. macrocarpa using next-generation sequencing technology and found that its mitochondrial genome, a circular DNA molecule of 38,139 bp, comprised 15 core protein-coding genes, 26 transfer RNA genes and two ribosomal RNA genes. The mitochondrial genome had a base composition of A (37.05%), C (12.08%), G (11.42%) and T (39.45%) with a GC content of 23.50%. A phylogenetic tree based on 20 mitochondrial genomes was constructed, which revealed the phylogenetic relationships of this species with related boletes for the first time.
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Affiliation(s)
- Yu-ting Zheng
- College of Life Science, Jiangxi Science and Technology Normal University, Nanchang, China
| | - Liang-liang Chen
- Jiulingshan National Nature Reserve Administration of Jiangxi Province, Jing’an, China
| | - Kuan Zhao
- College of Life Science, Jiangxi Science and Technology Normal University, Nanchang, China
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