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Tao J, Wang X, Long Y, Gao Z, Zhang G, Guo Z, Wang G, Xu G, Wang Y, Liu H. Determining Gene Order Patterns in the Suillus and Boletales through Comparative Analysis of Their Mitogenomes. Int J Mol Sci 2024; 25:9597. [PMID: 39273542 PMCID: PMC11394714 DOI: 10.3390/ijms25179597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2024] [Revised: 08/27/2024] [Accepted: 08/29/2024] [Indexed: 09/15/2024] Open
Abstract
Suillus is one of the most important genera of ectomycorrhizal fungi. As a model for studying host specificity, its molecular fragments and nuclear genome have been analyzed. However, its mitochondrial genome has not yet been reported. In this study, we assembled five mitogenomes of Suillus and analyzed and compared their basic characteristics. Owing to the large number of introns as well as intergenic regions, the mitogenomic lengths of species of Suillus were greater than those of other species of Boletales. We identified two main patterns of gene order arrangement in the members of the order Boletales. The Ka/Ks values of 15 protein-coding genes were <1 for the mitochondrial genes of 39 Boletales species, indicating their conserved evolution. Phylogenetic trees, reconstructed using the mitogenomes, indicated that the genus Suillus was monophyletic. Phylogenetic results based on the internal transcribed spacer region and mitogenome were used to confirm the distribution of Suillus placidus in China. The results showed that the mitogenome was superior in distinguishing species compared with a single molecular fragment. This is the first study to investigate the mitogenome of Suillus, enriching the mitogenome information and providing basic data for the phylogeny, resource conservation, and genetic diversity of this genus.
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Affiliation(s)
- Jiawei Tao
- School of Public Health, The Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, Guizhou Medical University, Guiyang 561113, China
- Engineering Research Center of Medical Biotechnology, School of Biology and Engineering, Guizhou Medical University, Guiyang 561113, China
| | - Xianyi Wang
- Engineering Research Center of Medical Biotechnology, School of Biology and Engineering, Guizhou Medical University, Guiyang 561113, China
- Engineering Research Center of Health Medicine Biotechnology of Institution of Higher Education of Guizhou Province, Guizhou Medical University, Guiyang 561113, China
- Key Laboratory of Biology and Medical Engineering, Immune Cells and Antibody Engineering Research Center of Guizhou Province, School of Biology and Engineering, Guizhou Medical University, Guiyang 561113, China
| | - Yaohang Long
- Engineering Research Center of Medical Biotechnology, School of Biology and Engineering, Guizhou Medical University, Guiyang 561113, China
- Engineering Research Center of Health Medicine Biotechnology of Institution of Higher Education of Guizhou Province, Guizhou Medical University, Guiyang 561113, China
- Key Laboratory of Biology and Medical Engineering, Immune Cells and Antibody Engineering Research Center of Guizhou Province, School of Biology and Engineering, Guizhou Medical University, Guiyang 561113, China
| | - Zexin Gao
- Engineering Research Center of Medical Biotechnology, School of Biology and Engineering, Guizhou Medical University, Guiyang 561113, China
- Engineering Research Center of Health Medicine Biotechnology of Institution of Higher Education of Guizhou Province, Guizhou Medical University, Guiyang 561113, China
- Key Laboratory of Biology and Medical Engineering, Immune Cells and Antibody Engineering Research Center of Guizhou Province, School of Biology and Engineering, Guizhou Medical University, Guiyang 561113, China
| | - Gongyou Zhang
- Engineering Research Center of Medical Biotechnology, School of Biology and Engineering, Guizhou Medical University, Guiyang 561113, China
- Engineering Research Center of Health Medicine Biotechnology of Institution of Higher Education of Guizhou Province, Guizhou Medical University, Guiyang 561113, China
- Key Laboratory of Biology and Medical Engineering, Immune Cells and Antibody Engineering Research Center of Guizhou Province, School of Biology and Engineering, Guizhou Medical University, Guiyang 561113, China
| | - Zhongyao Guo
- Engineering Research Center of Medical Biotechnology, School of Biology and Engineering, Guizhou Medical University, Guiyang 561113, China
| | - Guoyu Wang
- The High Efficacy Application of Natural Medicinal Resources Engineering Center of Guizhou Province, The Key Laboratory of Optimal Utilization of Natural Medicine Resources, School of Pharmaceutical Sciences, Guizhou Medical University, Guiyang 561113, China
| | - Guangyin Xu
- School of Basic Medicine Science, Guizhou Medical University, Guiyang 561113, China
| | - Yaping Wang
- Engineering Research Center of Medical Biotechnology, School of Biology and Engineering, Guizhou Medical University, Guiyang 561113, China
- Engineering Research Center of Health Medicine Biotechnology of Institution of Higher Education of Guizhou Province, Guizhou Medical University, Guiyang 561113, China
- Key Laboratory of Biology and Medical Engineering, Immune Cells and Antibody Engineering Research Center of Guizhou Province, School of Biology and Engineering, Guizhou Medical University, Guiyang 561113, China
| | - Hongmei Liu
- Engineering Research Center of Medical Biotechnology, School of Biology and Engineering, Guizhou Medical University, Guiyang 561113, China
- Engineering Research Center of Health Medicine Biotechnology of Institution of Higher Education of Guizhou Province, Guizhou Medical University, Guiyang 561113, China
- Key Laboratory of Biology and Medical Engineering, Immune Cells and Antibody Engineering Research Center of Guizhou Province, School of Biology and Engineering, Guizhou Medical University, Guiyang 561113, China
- School of Basic Medicine Science, Guizhou Medical University, Guiyang 561113, China
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Syazwan SA, Mohd-Farid A, Yih Lee S, Mohamed R. Comparative analysis of mitochondrial genomes in Ceratocystis fimbriata complex across diverse hosts. Gene 2024; 921:148539. [PMID: 38710292 DOI: 10.1016/j.gene.2024.148539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 04/16/2024] [Accepted: 05/03/2024] [Indexed: 05/08/2024]
Abstract
The decline ofAcacia mangiumWilld. in Malaysia, especially in Sabah since 2010, is primarily due to Ceratocystiswilt and canker disease (CWCD) caused by theCeratocystis fimbriataEllis & Halst. complex. This study was aimed to investigate the mitochondrial genome architecture of two differentC. fimbriatacomplex isolates from Malaysia: one fromA. mangiumin Pahang (FRIM1162) and another fromEucalyptus pellitain Sarawak (FRIM1441). This research employed Next-Generation Sequencing (NGS) to contrast genomes from diverse hosts with nine additional mitochondrial sequences, identifying significant genetic diversity and mutational hotspots in the mitochondrial genome alignment. The mitochondrial genome-based phylogenetic analysis revealed a significant genetic relationship between the studied isolates and theC. fimbriatacomplex in the South American Subclade, indicating that theC. fimbriatacomplex discovered in Malaysia isC. manginecans. The comparative mitochondrial genome demonstrates the adaptability of the complex due to mobile genetic components and genomic rearrangements in the studiedfungal isolates. This research enhances our knowledge of the genetic diversity and evolutionary patterns within theC. fimbriatacomplex, aiding in a deeper understanding of fungal disease development and host adaption processes. The acquired insights are crucial for creating specific management strategies for CWCD, improving the overall understanding of fungal disease evolution and control.
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Affiliation(s)
- Samsuddin Ahmad Syazwan
- Mycology and Pathology Branch, Forest Health and Conservation Programme, Forest Biodiversity Division, Forest Research Institute Malaysia, 52109 Kepong, Selangor, Malaysia; Department of Forest Science and Biodiversity, Faculty of Forestry and Environment, 43400 Serdang, Selangor, Malaysia.
| | - Ahmad Mohd-Farid
- Mycology and Pathology Branch, Forest Health and Conservation Programme, Forest Biodiversity Division, Forest Research Institute Malaysia, 52109 Kepong, Selangor, Malaysia.
| | - Shiou Yih Lee
- Faculty of Health and Life Sciences, INTI International University, 71800 Nilai, Negeri Sembilan, Malaysia.
| | - Rozi Mohamed
- Department of Forest Science and Biodiversity, Faculty of Forestry and Environment, 43400 Serdang, Selangor, Malaysia.
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Subramaniam R, Kumar VS, Siddiquee S. The complete mitochondrial genome of the basidiomycetous fungus, Tinctoporellus epimiltinus strain RS1. Mitochondrial DNA B Resour 2024; 9:1053-1057. [PMID: 39155914 PMCID: PMC11328819 DOI: 10.1080/23802359.2024.2389914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Accepted: 08/04/2024] [Indexed: 08/20/2024] Open
Abstract
Tinctoporellus epimiltinus is widely known as a wood-decaying fungus. In the present study, we identified the complete mitochondrial genome of this species using next-generation sequencing technology. Our findings revealed that the genomic structure is a circular molecule with a size of 51,878 bp. Consistent with most Basidiomycota species, it consists of 14 core protein-coding genes, one ribosomal protein gene (rps3), 26 transfer RNA genes, and small and large ribosomal RNA (rns and rnl) genes. Seven additional open reading frames were identified. These included two sequences similar to DNA polymerases, an endonuclease-like sequence, and four hypothetical proteins. The mitochondrial genome exhibited a nucleotide composition of A (36.24%), C (12.04%), G (13.18%), and T (38.55%), resulting in a 25.21% GC content. A phylogenetic tree constructed using the combined mitochondrial gene dataset provided insight into the phylogenetic relationships of this species within the context of Basidiomycota and its members.
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Affiliation(s)
- Ranjita Subramaniam
- Biotechnology Research Institute, Universiti Malaysia Sabah, Jalan UMS, Kota Kinabalu, Sabah, Malaysia
| | - Vijay Subbiah Kumar
- Biotechnology Research Institute, Universiti Malaysia Sabah, Jalan UMS, Kota Kinabalu, Sabah, Malaysia
| | - Shafiquzzaman Siddiquee
- Biotechnology Research Institute, Universiti Malaysia Sabah, Jalan UMS, Kota Kinabalu, Sabah, Malaysia
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Dallagnol LC, Cônsoli FL. Evolutionary and phylogenetic insights from the mitochondrial genomic analysis of Diceraeus melacanthus and D. furcatus (Hemiptera: Pentatomidae). Sci Rep 2024; 14:12861. [PMID: 38834792 DOI: 10.1038/s41598-024-63584-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 05/30/2024] [Indexed: 06/06/2024] Open
Abstract
The mitochondrial genomes of D. melacanthus and D. furcatus were sequenced and used to investigate the phylogenetic relationships with 54 species of Pentatomidae. Their mitogenomes are 17,197 and 15,444 bp-long, respectively, including 13 protein-coding genes (PCGs), 2 ribosomal RNA genes, and 22/21 transfer RNA genes, with conserved gene arrangement. Leu, Lys, and Ser were the most common amino acids in their PCGs. PCGs evolutionary analysis indicated their mitogenomes are under purifying selection, and the most conserved genes are from the cytochrome complex, reinforcing their suitability as markers for molecular taxonomy. We identified 490 mtSSRs in 56 Pentatomidae species, with large variation and a positive correlation between mtSSR number and genome size. Three mtSSRs were identified in each Diceraeus species. Only the mtSSR in the nad6 (D. melacanthus) and nad4 (D. furcatus) appear to have application as molecular markers for species characterization. Phylogenetic analysis confirmed the monophyly of Pentatomidae. However, our analysis challenged the monophyly of Pentatominae and Podopinae. We also detected unexpected relationships among some tribes and genera, highlighting the complexity of the internal taxonomic structure of Pentatomidae. Both Diceraeus species were grouped in the same clade with the remaining Carpocorini analyzed.
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Affiliation(s)
- Lilian Cris Dallagnol
- Insect Interactions Laboratory, Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, SP, Brazil
| | - Fernando Luís Cônsoli
- Insect Interactions Laboratory, Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, SP, Brazil.
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Zeb U, Aziz T, Azizullah A, Zan XY, Khan AA, Bacha SAS, Cui FJ. Complete mitochondrial genomes of edible mushrooms: features, evolution, and phylogeny. PHYSIOLOGIA PLANTARUM 2024; 176:e14363. [PMID: 38837786 DOI: 10.1111/ppl.14363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 02/15/2024] [Accepted: 02/27/2024] [Indexed: 06/07/2024]
Abstract
Edible mushrooms are an important food source with high nutritional and medicinal value. They are a useful source for studying phylogenetic evolution and species divergence. The exploration of the evolutionary relationships among these species conventionally involves analyzing sequence variations within their complete mitochondrial genomes, which range from 31,854 bp (Cordyceps militaris) to 197,486 bp (Grifolia frondosa). The study of the complete mitochondrial genomes of edible mushrooms has emerged as a critical field of research, providing important insights into fungal genetic makeup, evolution, and phylogenetic relationships. This review explores the mitochondrial genome structures of various edible mushroom species, highlighting their unique features and evolutionary adaptations. By analyzing these genomes, robust phylogenetic frameworks are constructed to elucidate mushrooms lineage relationships. Furthermore, the exploration of different variations of mitochondrial DNA presents novel opportunities for enhancing mushroom cultivation biotechnology and medicinal applications. The mitochondrial genomic features are essential for improving agricultural practices and ensuring food security through improved crop productivity, disease resistance, and nutritional qualities. The current knowledge about the mitochondrial genomes of edible mushrooms is summarized in this review, emphasising their significance in both scientific research and practical applications in bioinformatics and medicine.
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Affiliation(s)
- Umar Zeb
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, PR China
- Faculty of Biological and Biomedical Science, Department of Biology, The University of Haripur, Khyber Pakhtunkhwa, Pakistan
| | - Tariq Aziz
- Faculty of Civil Engineering and Mechanics, Jiangsu University, Zhenjiang, PR China
| | - Azizullah Azizullah
- Faculty of Biological and Biomedical Science, Department of Biology, The University of Haripur, Khyber Pakhtunkhwa, Pakistan
| | - Xin-Yi Zan
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, PR China
| | - Asif Ali Khan
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, PR China
| | - Syed Asim Shah Bacha
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, PR China
| | - Feng-Jie Cui
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, PR China
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Lu H, Nie Y, Huang B. The second complete mitochondrial genome of Capillidium rhysosporum within the family Capillidiaceae, Entomophthorales. Mitochondrial DNA B Resour 2024; 9:332-337. [PMID: 38476836 PMCID: PMC10930110 DOI: 10.1080/23802359.2024.2324938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Accepted: 02/24/2024] [Indexed: 03/14/2024] Open
Abstract
The complete mitochondrial genome of the entomophthoroid fungus Capillidium rhysosporum (strain no.: ATCC 12588) was sequenced using next-generation sequencing technology. The assembled circular genome has a length of 46,756 base pairs with a GC content of 27.06%. Gene prediction identified 15 core protein-coding genes (PCGs), two rRNA genes, and 27 tRNA genes. Phylogenetic analysis confirmed that C. rhysosporum belongs to the Zoopagomycota clade and is closely related to C. heterosporum. This study presents the second complete mitochondrial genome within the family Capillidiaceae, contributing to the mitochondrial DNA database of entomophthoroid fungi.
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Affiliation(s)
- Hanwen Lu
- Anhui Provincial Key Laboratory for Microbial Pest Control, Anhui Agricultural University, Hefei, China
| | - Yong Nie
- School of Civil Engineering and Architecture, Anhui University of Technology, Ma’anshan, China
| | - Bo Huang
- Anhui Provincial Key Laboratory for Microbial Pest Control, Anhui Agricultural University, Hefei, China
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Anwar G, Mamut R, Wang J. Characterization of Complete Mitochondrial Genomes of the Five Peltigera and Comparative Analysis with Relative Species. J Fungi (Basel) 2023; 9:969. [PMID: 37888225 PMCID: PMC10607270 DOI: 10.3390/jof9100969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 09/15/2023] [Accepted: 09/16/2023] [Indexed: 10/28/2023] Open
Abstract
In the present study, the complete mitochondrial genomes of five Peltigera species (Peltigera elisabethae, Peltigera neocanina, Peltigera canina, Peltigera ponojensis, Peltigera neckeri) were sequenced, assembled and compared with relative species. The five mitogenomes were all composed of circular DNA molecules, and their ranged from 58,132 bp to 69,325 bp. The mitochondrial genomes of the five Peltigera species contain 15 protein-coding genes (PCGs), 2 rRNAs, 26-27 tRNAs and an unidentified open reading frame (ORF). The PCG length, AT skew and GC skew varied among the 15 PCGs in the five mitogenomes. Among the 15 PCGs, cox2 had the least K2P genetic distance, indicating that the gene was highly conserved. The synteny analysis revealed that the coding regions were highly conserved in the Peltigera mitochondrial genomes, but gene rearrangement occurred in the intergenic regions. The phylogenetic analysis based on the 14 PCGs showed that the 11 Peltigera species formed well-supported topologies, indicating that the protein-coding genes in the mitochondrial genome may be used as a reliable molecular tool in the study of the phylogenetic relationship of Peltigera.
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Affiliation(s)
| | - Reyim Mamut
- College of Life Sciences and Technology, Xinjiang University, Urumchi 830017, China; (G.A.); (J.W.)
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Castrillo ML, Bich GÁ, Amerio NS, Barengo MP, Zapata PD, Saparrat MCN, Villalba LL. Trichoderma koningiopsis (Hypocreaceae) has the smallest mitogenome of the genus Trichoderma. Front Microbiol 2023; 14:1141087. [PMID: 37383640 PMCID: PMC10294050 DOI: 10.3389/fmicb.2023.1141087] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 04/24/2023] [Indexed: 06/30/2023] Open
Abstract
Introduction Fungal mitogenomes exhibit remarkable variation in conformation, size, gene content, arrangement and expression, including their intergenic spacers and introns. Methods The complete mitochondrial genome sequence of the mycoparasitic fungus Trichoderma koningiopsis was determined using the Illumina next-generation sequencing technology. We used data from our recent Illumina NGS-based project of T. koningiopsis genome sequencing to study its mitochondrial genome. The mitogenome was assembled, annotated, and compared with other fungal mitogenomes. Results T. koningiopsis strain POS7 mitogenome is a circular molecule of 27,560 bp long with a GC content of 27.80%. It harbors the whole complement of the 14 conserved mitochondrial protein-coding genes (PCG) such as atp6, atp8, atp9, cox1, cox2, cox3, cob, nad1, nad2, nad3, nad4, nad4L, nad5, and nad6, also found in the same gene order to other Hypocreales. The mitogenome also contains 26 transfer RNA genes (tRNAs), 5 of them with more than one copy. Other genes also present in the assembled mitochondrial genome are a small rRNA subunit and a large rRNA subunit containing ribosomal protein S3 gene. Despite the small genome size, two introns were detected in the T. koningiopsis POS7 mitogenome, one of them in cox3 gene and the other in rnl gene, accounting 7.34% of this mitogenome with a total size of 2,024 bp. A phylogenetic analysis was done using the 14 PCGs genes of T. koningiopsis strain POS7 mitogenome to compare them with those from other fungi of the Subphyla Pezizomycotina and Saccharomycotina. T. koningiopsis strain POS7 was clustered together with other representatives of Trichoderma lineage, within the Hypocreales group, which is also supported by previous phylogenetic studies based on nuclear markers. Discussion The mitochondrial genome of T. koningiopsis POS7 will allow further investigations into the taxonomy, phylogenetics, conservation genetics, and evolutionary biology of this important genus as well as other closely related species.
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Affiliation(s)
- María Lorena Castrillo
- Laboratorio de Biotecnología Molecular, Instituto de Biotecnología Misiones “Dra. María Ebe Reca”-InBioMis, Universidad Nacional de Misiones, Posadas, Misiones, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Gustavo Ángel Bich
- Laboratorio de Biotecnología Molecular, Instituto de Biotecnología Misiones “Dra. María Ebe Reca”-InBioMis, Universidad Nacional de Misiones, Posadas, Misiones, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Natalia Soledad Amerio
- Laboratorio de Biotecnología Molecular, Instituto de Biotecnología Misiones “Dra. María Ebe Reca”-InBioMis, Universidad Nacional de Misiones, Posadas, Misiones, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Marcela Paola Barengo
- Laboratorio de Biotecnología Molecular, Instituto de Biotecnología Misiones “Dra. María Ebe Reca”-InBioMis, Universidad Nacional de Misiones, Posadas, Misiones, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Pedro Darío Zapata
- Laboratorio de Biotecnología Molecular, Instituto de Biotecnología Misiones “Dra. María Ebe Reca”-InBioMis, Universidad Nacional de Misiones, Posadas, Misiones, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Mario Carlos Nazareno Saparrat
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
- Facultad de Ciencias Agrarias y Forestales, Instituto de Fisiología Vegetal, Universidad Nacional de La Plata, La Plata, Buenos Aires, Argentina
- Facultad de Ciencias Naturales y Museo, Instituto de Botánica Carlos Spegazzini, Universidad Nacional de La Plata, La Plata, Buenos Aires, Argentina
- Cátedra de Microbiología Agrícola, Facultad de Ciencias Agrarias y Forestales, Universidad Nacional de La Plata, La Plata, Buenos Aires, Argentina
| | - Laura Lidia Villalba
- Laboratorio de Biotecnología Molecular, Instituto de Biotecnología Misiones “Dra. María Ebe Reca”-InBioMis, Universidad Nacional de Misiones, Posadas, Misiones, Argentina
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Fang J, Mamut R, Wang L, Anwar G. De novo mitochondrial genome sequencing of Cladonia subulata and phylogenetic analysis with other dissimilar species. PLoS One 2023; 18:e0285818. [PMID: 37220163 DOI: 10.1371/journal.pone.0285818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 05/01/2023] [Indexed: 05/25/2023] Open
Abstract
In this study, the complete mitochondrial genome of Cladonia subulata (L.) FH Wigg was sequenced and assembled and then compared with those of other Cladonia species. The mitogenome of Cladonia subulata, the type species of Cladonia, consisted of a circular DNA molecule of 58,895 bp 44 genes (15 protein-coding genes, 2 rRNA genes, and 27 tRNA genes). The base composition had shown an obvious AT preference, and all 27 tRNA genes formed a typical clover structure. Comparison with other 7 Cladonia species indicated that the duplication/loss of tRNAs had occurred during evolution, and introns appeared to explain the variation in cox1 genes in Cladonia, the mitochondrial genome tends to be generally conservative and local dynamic changes. Repeat sequences were mainly located in gene intervals, which were mainly distributed among intergenic spacers and may cause rearrangement of the mitogenome. The phylogenetic results showed that Cladonia subulata and C. polycarpoides were assigned to the Cladonia Subclade. The results add to the available mitochondrial genome sequence information of Cladonia subulata, provide basic data for the systematic development, resource protection, and genetic diversity research in Cladonia subulata, and also provide theoretical support for further genomic research of lichens.
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Affiliation(s)
- Jinjin Fang
- College of Life Science and Technology, Xinjiang University, Urumqi, China
| | - Reyim Mamut
- College of Life Science and Technology, Xinjiang University, Urumqi, China
| | - Lidan Wang
- College of Life Science and Technology, Xinjiang University, Urumqi, China
| | - Gulmira Anwar
- College of Life Science and Technology, Xinjiang University, Urumqi, China
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Himmelstrand K, Brandström Durling M, Karlsson M, Stenlid J, Olson Å. Multiple rearrangements and low inter- and intra-species mitogenome sequence variation in the Heterobasidion annosum s.l. species complex. Front Microbiol 2023; 14:1159811. [PMID: 37275157 PMCID: PMC10234125 DOI: 10.3389/fmicb.2023.1159811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 03/16/2023] [Indexed: 06/07/2023] Open
Abstract
Introduction Mitochondria are essential organelles in the eukaryotic cells and responsible for the energy production but are also involved in many other functions including virulence of some fungal species. Although the evolution of fungal mitogenomes have been studied at some taxonomic levels there are still many things to be learned from studies of closely related species. Methods In this study, we have analyzed 60 mitogenomes in the five species of the Heterobasidion annosum sensu lato complex that all are necrotrophic pathogens on conifers. Results and Discussion Compared to other fungal genera the genomic and genetic variation between and within species in the complex was low except for multiple rearrangements. Several translocations of large blocks with core genes have occurred between the five species and rearrangements were frequent in intergenic areas. Mitogenome lengths ranged between 108 878 to 116 176 bp, mostly as a result of intron variation. There was a high degree of homology of introns, homing endonuclease genes, and intergenic ORFs among the five Heterobasidion species. Three intergenic ORFs with unknown function (uORF6, uORF8 and uORF9) were found in all five species and was located in conserved synteny blocks. A 13 bp long GC-containing self-complementary palindrome was discovered in many places in the five species that were optional in presence/absence. The within species variation is very low, among 48 H. parviporum mitogenomes, there was only one single intron exchange, and SNP frequency was 0.28% and indel frequency 0.043%. The overall low variation in the Heterobasidion annosum sensu lato complex suggests a slow evolution of the mitogenome.
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Affiliation(s)
| | | | | | | | - Åke Olson
- Uppsala BioCenter, Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
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Chen WT, Li M, Hu SY, Wang SH, Yuan ML. Comparative mitogenomic and evolutionary analysis of Lycaenidae (Insecta: Lepidoptera): Potential association with high-altitude adaptation. Front Genet 2023; 14:1137588. [PMID: 37144132 PMCID: PMC10151513 DOI: 10.3389/fgene.2023.1137588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 04/03/2023] [Indexed: 05/06/2023] Open
Abstract
Harsh environments (e.g., hypoxia and cold temperatures) of the Qinghai-Tibetan Plateau have a substantial influence on adaptive evolution in various species. Some species in Lycaenidae, a large and widely distributed family of butterflies, are adapted to the Qinghai-Tibetan Plateau. Here, we sequenced four mitogenomes of two lycaenid species in the Qinghai-Tibetan Plateau and performed a detailed comparative mitogenomic analysis including nine other lycaenid mitogenomes (nine species) to explore the molecular basis of high-altitude adaptation. Based on mitogenomic data, Bayesian inference, and maximum likelihood methods, we recovered a lycaenid phylogeny of [Curetinae + (Aphnaeinae + (Lycaeninae + (Theclinae + Polyommatinae)))]. The gene content, gene arrangement, base composition, codon usage, and transfer RNA genes (sequence and structure) were highly conserved within Lycaenidae. TrnS1 not only lacked the dihydrouridine arm but also showed anticodon and copy number diversity. The ratios of non-synonymous substitutions to synonymous substitutions of 13 protein-coding genes (PCGs) were less than 1.0, indicating that all PCGs evolved under purifying selection. However, signals of positive selection were detected in cox1 in the two Qinghai-Tibetan Plateau lycaenid species, indicating that this gene may be associated with high-altitude adaptation. Three large non-coding regions, i.e., rrnS-trnM (control region), trnQ-nad2, and trnS2-nad1, were found in the mitogenomes of all lycaenid species. Conserved motifs in three non-coding regions (trnE-trnF, trnS1-trnE, and trnP-nad6) and long sequences in two non-coding regions (nad6-cob and cob-trnS2) were detected in the Qinghai-Tibetan Plateau lycaenid species, suggesting that these non-coding regions were involved in high-altitude adaptation. In addition to the characterization of Lycaenidae mitogenomes, this study highlights the importance of both PCGs and non-coding regions in high-altitude adaptation.
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Affiliation(s)
- Wen-Ting Chen
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, Lanzhou University, Lanzhou, Gansu, China
- Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Lanzhou, Gansu, China
- College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou, Gansu, China
| | - Min Li
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, Lanzhou University, Lanzhou, Gansu, China
- Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Lanzhou, Gansu, China
- College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou, Gansu, China
| | - Shi-Yun Hu
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, Lanzhou University, Lanzhou, Gansu, China
- College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou, Gansu, China
- National Demonstration Center for Experimental Grassland Science Education, Lanzhou University, Lanzhou, Gansu, China
| | - Su-Hao Wang
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, Lanzhou University, Lanzhou, Gansu, China
- Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Lanzhou, Gansu, China
- College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou, Gansu, China
| | - Ming-Long Yuan
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, Lanzhou University, Lanzhou, Gansu, China
- Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Lanzhou, Gansu, China
- College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou, Gansu, China
- National Demonstration Center for Experimental Grassland Science Education, Lanzhou University, Lanzhou, Gansu, China
- *Correspondence: Ming-Long Yuan,
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12
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Li Q, Zhang T, Li L, Bao Z, Tu W, Xiang P, Wu Q, Li P, Cao M, Huang W. Comparative Mitogenomic Analysis Reveals Intraspecific, Interspecific Variations and Genetic Diversity of Medical Fungus Ganoderma. J Fungi (Basel) 2022; 8:781. [PMID: 35893149 PMCID: PMC9394262 DOI: 10.3390/jof8080781] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 07/21/2022] [Accepted: 07/21/2022] [Indexed: 11/16/2022] Open
Abstract
Ganoderma species are widely distributed in the world with high diversity. Some species are considered to be pathogenic fungi while others are used as traditional medicine in Asia. In this study, we sequenced and assembled four Ganoderma complete mitogenomes, including G. subamboinense s118, G. lucidum s37, G. lingzhi s62, and G. lingzhi s74. The sizes of the four mitogenomes ranged from 50,603 to 73,416 bp. All Ganoderma specimens had a full set of core protein-coding genes (PCGs), and the rps3 gene of Ganoderma species was detected to be under positive or relaxed selection. We found that the non-conserved PCGs, which encode RNA polymerases, DNA polymerases, homing endonucleases, and unknown functional proteins, are dynamic within and between Ganoderma species. Introns were thought to be the main contributing factor in Ganoderma mitogenome size variation (p < 0.01). Frequent intron loss/gain events were detected within and between Ganoderma species. The mitogenome of G. lucidum s26 gained intron P637 in the cox3 gene compared with the other two G. lucidum mitogenomes. In addition, some rare introns in Ganoderma were detected in distinct Basidiomycetes, indicating potential gene transfer events. Comparative mitogenomic analysis revealed that gene arrangements also varied within and between Ganoderma mitogenomes. Using maximum likelihood and Bayesian inference methods with a combined mitochondrial gene dataset, phylogenetic analyses generated identical, well-supported tree topologies for 71 Agaricomycetes species. This study reveals intraspecific and interspecific variations of the Ganoderma mitogenomes, which promotes the understanding of the origin, evolution, and genetic diversity of Ganoderma species.
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Affiliation(s)
- Qiang Li
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Engineering & Technology Research Center of Coarse Cereal Industrialization, School of Food and Biological Engineering, Chengdu University, Chengdu 610106, China; (Q.L.); (T.Z.); (L.L.); (Z.B.); (W.T.); (P.X.); (Q.W.)
| | - Ting Zhang
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Engineering & Technology Research Center of Coarse Cereal Industrialization, School of Food and Biological Engineering, Chengdu University, Chengdu 610106, China; (Q.L.); (T.Z.); (L.L.); (Z.B.); (W.T.); (P.X.); (Q.W.)
| | - Lijiao Li
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Engineering & Technology Research Center of Coarse Cereal Industrialization, School of Food and Biological Engineering, Chengdu University, Chengdu 610106, China; (Q.L.); (T.Z.); (L.L.); (Z.B.); (W.T.); (P.X.); (Q.W.)
| | - Zhijie Bao
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Engineering & Technology Research Center of Coarse Cereal Industrialization, School of Food and Biological Engineering, Chengdu University, Chengdu 610106, China; (Q.L.); (T.Z.); (L.L.); (Z.B.); (W.T.); (P.X.); (Q.W.)
| | - Wenying Tu
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Engineering & Technology Research Center of Coarse Cereal Industrialization, School of Food and Biological Engineering, Chengdu University, Chengdu 610106, China; (Q.L.); (T.Z.); (L.L.); (Z.B.); (W.T.); (P.X.); (Q.W.)
| | - Peng Xiang
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Engineering & Technology Research Center of Coarse Cereal Industrialization, School of Food and Biological Engineering, Chengdu University, Chengdu 610106, China; (Q.L.); (T.Z.); (L.L.); (Z.B.); (W.T.); (P.X.); (Q.W.)
| | - Qian Wu
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Engineering & Technology Research Center of Coarse Cereal Industrialization, School of Food and Biological Engineering, Chengdu University, Chengdu 610106, China; (Q.L.); (T.Z.); (L.L.); (Z.B.); (W.T.); (P.X.); (Q.W.)
| | - Ping Li
- Biotechnology and Nuclear Technology Research Institute, Sichuan Academy of Agricultural Sciences, 106 # Shizishan Rd., Chengdu 610061, China;
| | - Mei Cao
- Core Laboratory, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu 610072, China
- Chinese Academy of Sciences Sichuan Translational Medicine Research Hospital, Chengdu 610072, China
| | - Wenli Huang
- Biotechnology and Nuclear Technology Research Institute, Sichuan Academy of Agricultural Sciences, 106 # Shizishan Rd., Chengdu 610061, China;
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Li Q, Bao Z, Tang K, Feng H, Tu W, Li L, Han Y, Cao M, Zhao C. First two mitochondrial genomes for the order Filobasidiales reveal novel gene rearrangements and intron dynamics of Tremellomycetes. IMA Fungus 2022; 13:7. [PMID: 35501936 PMCID: PMC9059411 DOI: 10.1186/s43008-022-00094-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2021] [Accepted: 04/22/2022] [Indexed: 02/03/2023] Open
Abstract
In the present study, two mitogenomes from the Filobasidium genus were assembled and compared with other Tremellomycetes mitogenomes. The mitogenomes of F. wieringae and F. globisporum both comprised circular DNA molecules, with sizes of 27,861 bp and 71,783 bp, respectively. Comparative mitogenomic analysis revealed that the genetic contents, tRNAs, and codon usages of the two Filobasidium species differed greatly. The sizes of the two Filobasidium mitogenomes varied greatly with the introns being the main factor contributing to mitogenome expansion in F. globisporum. Positive selection was observed in several protein-coding genes (PCGs) in the Agaricomycotina, Pucciniomycotina, and Ustilaginomycotina species, including cob, cox2, nad2, and rps3 genes. Frequent intron loss/gain events were detected to have occurred during the evolution of the Tremellomycetes mitogenomes, and the mitogenomes of 17 species from Agaricomycotina, Pucciniomycotina, and Ustilaginomycotina have undergone large-scale gene rearrangements. Phylogenetic analyses based on Bayesian inference and the maximum likelihood methods using a combined mitochondrial gene set generated identical and well-supported phylogenetic trees, wherein Filobasidium species had close relationships with Trichosporonales species. This study, which is the first report on mitogenomes from the order Filobasidiales, provides a basis for understanding the genomics, evolution, and taxonomy of this important fungal group.
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Affiliation(s)
- Qiang Li
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, School of Food and Biological Engineering, Chengdu University, Chengdu, Sichuan, China
| | - Zhijie Bao
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, School of Food and Biological Engineering, Chengdu University, Chengdu, Sichuan, China
| | - Ke Tang
- School of Public Health, Chengdu Medical College, Chengdu, Sichuan, China
| | - Huiyu Feng
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, School of Food and Biological Engineering, Chengdu University, Chengdu, Sichuan, China
| | - Wenying Tu
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, School of Food and Biological Engineering, Chengdu University, Chengdu, Sichuan, China
| | - Lijiao Li
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, School of Food and Biological Engineering, Chengdu University, Chengdu, Sichuan, China
| | - Yunlei Han
- Department of Pathogenic Biology, Chengdu Medical College, Chengdu, Sichuan, China
| | - Mei Cao
- Core Laboratory, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, Sichuan, China. .,Chinese Academy of Sciences Sichuan Translational Medicine Research Hospital, Chengdu, Sichuan, China.
| | - Changsong Zhao
- School of Public Health, Chengdu Medical College, Chengdu, Sichuan, China.
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14
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Nie Y, Zhao H, Wang Z, Zhou Z, Liu X, Huang B. The Gene Rearrangement, Loss, Transfer, and Deep Intronic Variation in Mitochondrial Genomes of Conidiobolus. Front Microbiol 2021; 12:765733. [PMID: 34858376 PMCID: PMC8632527 DOI: 10.3389/fmicb.2021.765733] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 10/01/2021] [Indexed: 12/22/2022] Open
Abstract
The genus Conidiobolus s.s. was newly delimited from Conidiobolus s.l. In order to gain insight into its mitochondrial genetic background, this study sequenced six mitochondrial genomes of the genus Conidiobolus s.s. These mitogenomes were all composed of circular DNA molecules, ranging from 29,253 to 48,417 bp in size and from 26.61 to 27.90% in GC content. The order and direction for 14 core protein-coding genes (PCGs) were identical, except for the atp8 gene lost in Conidiobolus chlamydosporus, Conidiobolus polyspermus, and Conidiobolus polytocus, and rearranged in the other Conidiobolus s.s. species. Besides, the atp8 gene split the cox1 gene in Conidiobolus taihushanensis. Phylogenomic analysis based on the 14 core PCGs confirmed that all Conidiobolus s.s. species formed a monophyly in the Entomophthoromycotina lineage. The number and length of introns were the main factors contributing to mitogenomic size, and deep variations and potential transfer were detected in introns. In addition, gene transfer occurred between the mitochondrial and nuclear genomes. This study promoted the understanding of the evolution and phylogeny of the Conidiobolus s.s. genus.
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Affiliation(s)
- Yong Nie
- Anhui Provincial Key Laboratory for Microbial Pest Control, Anhui Agricultural University, Hefei, China
- School of Civil Engineering and Architecture, Anhui University of Technology, Ma’anshan, China
| | - Heng Zhao
- School of Ecology and Nature Conservation, Institute of Microbiology, Beijing Forestry University, Beijing, China
- College of Life Sciences, Shandong Normal University, Jinan, China
| | - Zimin Wang
- School of Civil Engineering and Architecture, Anhui University of Technology, Ma’anshan, China
| | - Zhengyu Zhou
- School of Civil Engineering and Architecture, Anhui University of Technology, Ma’anshan, China
| | - Xiaoyong Liu
- College of Life Sciences, Shandong Normal University, Jinan, China
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Bo Huang
- Anhui Provincial Key Laboratory for Microbial Pest Control, Anhui Agricultural University, Hefei, China
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15
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Tan M, Wang Q. Characterization of the complete mitochondrial genome of Dioszegia changbaiensis (Tremellales: Bulleribasidiaceae) with phylogenetic implications. MITOCHONDRIAL DNA PART B-RESOURCES 2021; 6:3315-3317. [PMID: 34746399 PMCID: PMC8567934 DOI: 10.1080/23802359.2021.1915197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
In this study, the complete mitochondrial genome of Dioszegia changbaiensis we sequenced and assembled by the next-generation sequencing. The complete mitochondrial genome of Dioszegia changbaiensis contained 22 protein-coding genes (PCG), two ribosomal RNA (rRNA) genes, and 22 transfer RNA (tRNA) genes. The total length of the Dioszegia changbaiensis mitochondrial genome is 34,853 bp, and the GC content of the mitochondrial genome is 41.88%. Phylogenetic analysis based on a combined mitochondrial gene dataset indicated that the mitochondrial genome of Dioszegia changbaiensis exhibited a close relationship with that of Hannaella oryzae.
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Affiliation(s)
- Maoling Tan
- School of Food and Biological Engineering, Chengdu University, Chengdu, PR China
| | - Qiangfeng Wang
- Biotechnology and Nuclear Technology Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, PR China
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16
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Gou Q, Ren C, Peng C. Characterization of the complete mitochondrial genome of Peniophora lycii (Russulales: Peniophoraceae) with its phylogenetic analysis. Mitochondrial DNA B Resour 2021; 6:2200-2202. [PMID: 34286082 PMCID: PMC8266238 DOI: 10.1080/23802359.2021.1945508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Peniophora lycii is a resupinate lichen-like species distributed all over the world. In the present study, we sequenced and assembled the complete mitochondrial genome of Peniophora lycii. The size of the mitochondrial genome of P. lycii was 38,296 bp, with a GC content of 25.89%. Twenty protein-coding genes, 2 ribosomal RNA genes, and 24 transfer RNA genes were identified in the mitochondrial genome of P. lycii. Phylogenetic analysis based on combined mitochondrial gene dataset indicated that the mitochondrial genome of P. lycii exhibited a close relationship with that of Heterobasidion irregulare.
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Affiliation(s)
- Qiufen Gou
- Leshan Vocational and Technical College, Leshan, Sichuan, China
| | - Chaoqin Ren
- Aba Teachers University, Wenchuan, Sichuan, China
| | - Cong Peng
- School of Food and Biological Engineering, Chengdu University, Chengdu, Sichuan, China
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17
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Wang SR, Zhang JP, He YR, Chang MC, Meng JL. Characterization of the complete mitochondrial genome of Coprinellus micaceus, a wild saprobic mushroom in China. Mitochondrial DNA B Resour 2021; 6:1979-1981. [PMID: 34179487 PMCID: PMC8205013 DOI: 10.1080/23802359.2021.1938717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
The Glistening Inkcap (Coprinellus micaceus) is a wild saprobic mushroom in China. In this study, we assembled and annotated its complete mitochondrial genome using raw data sequenced through Illumina NovaSeq 6000 platform (Illumina, San Diego, CA). The length of the C. micaceus mitochondrial genome is 65,450 bp with 33.05% GC content. Totally, 41 genes, including 14 protein-coding genes, 25 tRNAs and 2 rRNAs were identified in the mitochondrial genome. Phylogenetic analysis showed that the mitochondrial genome relationship between C. micaceus and Coprinopsis cinerea was the closest.
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Affiliation(s)
- Shu-rong Wang
- College of Food Science and Engineering, Shanxi Agricultural University, Taigu, PR China
| | - Jiang-ping Zhang
- Shanxi Forestry Vocational and Technical College, Taiyuan, PR China
| | - Yi-rong He
- College of Food Science and Engineering, Shanxi Agricultural University, Taigu, PR China
| | - Ming-chang Chang
- College of Food Science and Engineering, Shanxi Agricultural University, Taigu, PR China
| | - Jun-long Meng
- College of Food Science and Engineering, Shanxi Agricultural University, Taigu, PR China
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18
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Li Q, Li L, Feng H, Tu W, Bao Z, Xiong C, Wang X, Qing Y, Huang W. Characterization of the Complete Mitochondrial Genome of Basidiomycete Yeast Hannaella oryzae: Intron Evolution, Gene Rearrangement, and Its Phylogeny. Front Microbiol 2021; 12:646567. [PMID: 34122362 PMCID: PMC8193148 DOI: 10.3389/fmicb.2021.646567] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2020] [Accepted: 04/19/2021] [Indexed: 12/24/2022] Open
Abstract
In this study, the mitogenome of Hannaella oryzae was sequenced by next-generation sequencing (NGS) and successfully assembled. The H. oryzae mitogenome comprised circular DNA molecules with a total size of 26,444 bp. We found that the mitogenome of H. oryzae partially deleted the tRNA gene transferring cysteine. Comparative mitogenomic analyses showed that intronic regions were the main factors contributing to the size variations of mitogenomes in Tremellales. Introns of the cox1 gene in Tremellales species were found to have undergone intron loss/gain events, and introns of the H. oryzae cox1 gene may have different origins. Gene arrangement analysis revealed that H. oryzae contained a unique gene order different from other Tremellales species. Phylogenetic analysis based on a combined mitochondrial gene set resulted in identical and well-supported topologies, wherein H. oryzae was closely related to Tremella fuciformis. This study represents the first report of mitogenome for the Hannaella genus, which will allow further study of the population genetics, taxonomy, and evolutionary biology of this important phylloplane yeast and other related species.
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Affiliation(s)
- Qiang Li
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, School of Food and Biological Engineering, Chengdu University, Chengdu, China
| | - Lijiao Li
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, School of Food and Biological Engineering, Chengdu University, Chengdu, China
| | - Huiyu Feng
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, School of Food and Biological Engineering, Chengdu University, Chengdu, China
| | - Wenying Tu
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, School of Food and Biological Engineering, Chengdu University, Chengdu, China
| | - Zhijie Bao
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, School of Food and Biological Engineering, Chengdu University, Chengdu, China
| | - Chuan Xiong
- Biotechnology and Nuclear Technology Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, China
| | - Xu Wang
- College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - Yuan Qing
- Panxi Featured Crops Research and Utilization Key Laboratory of Sichuan Province, Xichang University, Xichang, China
| | - Wenli Huang
- Biotechnology and Nuclear Technology Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, China
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19
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Real-time monitoring of ruminal microbiota reveals their roles in dairy goats during subacute ruminal acidosis. NPJ Biofilms Microbiomes 2021; 7:45. [PMID: 33990613 PMCID: PMC8121909 DOI: 10.1038/s41522-021-00215-6] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 04/09/2021] [Indexed: 02/08/2023] Open
Abstract
Ruminal microbiota changes frequently with high grain diets and the occurrence of subacute ruminal acidosis (SARA). A grain-induced goat model of SARA, with durations of a significant decrease in the rumen pH value to less than 5.6 and an increase in the rumen lipopolysaccharides concentration, is constructed for real-time monitoring of bacteria alteration. Using 16 S rRNA gene sequencing, significant bacterial differences between goats from the SARA and healthy groups are identified at every hour for six continuous hours after feeding. Moreover, 29 common differential genera between two groups over 6 h after feeding are all related to the altered pH and lipopolysaccharides. Transplanting the microbiota from donor goats with SARA could induce colonic inflammation in antibiotic-pretreated mice. Overall, significant differences in the bacterial community and rumen fermentation pattern between the healthy and SARA dairy goats are real-time monitored, and then tested using ruminal microbe transplantation to antibiotic-treated mice.
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20
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Liu Q, Wang X. Characterization and phylogenetic analysis of the complete mitochondrial genome of pathogen Trichosporon inkin (Trichosporonales: Trichosporonaceae). MITOCHONDRIAL DNA PART B-RESOURCES 2021; 6:803-805. [PMID: 33763584 PMCID: PMC7954414 DOI: 10.1080/23802359.2021.1882912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
In the present study, the complete mitochondrial genome of Trichosporon inkin was sequenced and assembled. The complete mitochondrial genome of T. inkin contained 22 protein-coding genes (PCG), 2 ribosomal RNA (rRNA) genes, and 24 transfer RNA (tRNA) genes. The total size of the T. inkin mitochondrial genome is 39,466 bp, with the GC content of 27.56%. Phylogenetic analysis based on combined mitochondrial gene dataset indicated that the T. inkin exhibited a close relationship with Trichosporon asahii.
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Affiliation(s)
- Qiaofeng Liu
- Department of Pathology and Pathophysiology, Chengdu Medical College, Chengdu, China
| | - Xin Wang
- Department of Pathogenic Biology, Chengdu Medical College, Chengdu, China
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21
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Huang W, Feng H, Tu W, Xiong C, Jin X, Li P, Wang X, Li Q. Comparative Mitogenomic Analysis Reveals Dynamics of Intron Within and Between Tricholoma Species and Phylogeny of Basidiomycota. Front Genet 2021; 12:534871. [PMID: 33659021 PMCID: PMC7917209 DOI: 10.3389/fgene.2021.534871] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 01/18/2021] [Indexed: 01/28/2023] Open
Abstract
The genus of Tricholoma is a group of important ectomycorrhizal fungi. The overlapping of morphological characteristics often leads to the confusion of Tricholoma species classification. In this study, the mitogenomes of five Tricholoma species were sequenced based on the next-generation sequencing technology, including T. matsutake SCYJ1, T. bakamatsutake, T. terreum, T. flavovirens, and T. saponaceum. These five mitogenomes were all composed of circular DNA molecules, with sizes ranging from 49,480 to 103,090 bp. Intergenic sequences were considered to be the main factor contributing to size variations of Tricholoma mitogenomes. Comparative mitogenomic analysis showed that the introns of the Agaricales mitogenome experienced frequent loss/gain events. In addition, potential gene transfer was detected between the mitochondrial and nuclear genomes of the five species of Tricholoma. Evolutionary analysis showed that the rps3 gene of the Tricholoma species was under positive selection or relaxed selection in the evolutionary process. In addition, large-scale gene rearrangements were detected between some Tricholoma species. Phylogenetic analysis using the Bayesian inference and maximum likelihood methods based on a combined mitochondrial gene set yielded identical and well-supported tree topologies. This study promoted the understanding of the genetics, evolution, and phylogeny of the Tricholoma genus and related species.
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Affiliation(s)
- Wenli Huang
- Biotechnology and Nuclear Technology Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, China
| | - Huiyu Feng
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, School of Food and Biological Engineering, Chengdu University, Chengdu, China
| | - Wenying Tu
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, School of Food and Biological Engineering, Chengdu University, Chengdu, China
| | - Chuan Xiong
- Biotechnology and Nuclear Technology Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, China
| | - Xin Jin
- Biotechnology and Nuclear Technology Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, China
| | - Ping Li
- Biotechnology and Nuclear Technology Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, China
| | - Xu Wang
- College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - Qiang Li
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, School of Food and Biological Engineering, Chengdu University, Chengdu, China
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Araújo DS, De-Paula RB, Tomé LMR, Quintanilha-Peixoto G, Salvador-Montoya CA, Del-Bem LE, Badotti F, Azevedo VAC, Brenig B, Aguiar ERGR, Drechsler-Santos ER, Fonseca PLC, Góes-Neto A. Comparative mitogenomics of Agaricomycetes: Diversity, abundance, impact and coding potential of putative open-reading frames. Mitochondrion 2021; 58:1-13. [PMID: 33582235 DOI: 10.1016/j.mito.2021.02.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 01/31/2021] [Accepted: 02/01/2021] [Indexed: 02/07/2023]
Abstract
The mitochondrion is an organelle found in eukaryote organisms, and it is vital for different cellular pathways. The mitochondrion has its own DNA molecule and, because its genetic content is relatively conserved, despite the variation of size and structure, mitogenome sequences have been widely used as a promising molecular biomarker for taxonomy and evolution in fungi. In this study, the mitogenomes of two fungal species of Agaricomycetes class, Phellinotus piptadeniae and Trametes villosa, were assembled and annotated for the first time. We used these newly sequenced mitogenomes for comparative analyses with other 55 mitogenomes of Agaricomycetes available in public databases. Mitochondrial DNA (mtDNA) size and content are highly variable and non-coding and intronic regions, homing endonucleases (HEGs), and unidentified ORFs (uORFs) significantly contribute to the total size of the mitogenome. Furthermore, accessory genes (most of them as HEGs) are shared between distantly related species, most likely as a consequence of horizontal gene transfer events. Conversely, uORFs are only shared between taxonomically related species, most probably as a result of vertical evolutionary inheritance. Additionally, codon usage varies among mitogenomes and the GC content of mitochondrial features may be used to distinguish coding from non-coding sequences. Our results also indicated that transposition events of mitochondrial genes to the nuclear genome are not common. Despite the variation of size and content of the mitogenomes, mitochondrial genes seemed to be reliable molecular markers in our time-divergence analysis, even though the nucleotide substitution rates of mitochondrial and nuclear genomes of fungi are quite different. We also showed that many events of mitochondrial gene shuffling probably happened amongst the Agaricomycetes during evolution, which created differences in the gene order among species, even those of the same genus. Altogether, our study revealed new information regarding evolutionary dynamics in Agaricomycetes.
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Affiliation(s)
- Daniel S Araújo
- Molecular and Computational Biology of Fungi Laboratory, Department of Microbiology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Ruth B De-Paula
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Luiz M R Tomé
- Molecular and Computational Biology of Fungi Laboratory, Department of Microbiology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Gabriel Quintanilha-Peixoto
- Molecular and Computational Biology of Fungi Laboratory, Department of Microbiology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | | | - Luiz-Eduardo Del-Bem
- Department of Botany, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil; Program of Bioinformatics, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Fernanda Badotti
- Department of Chemistry, Centro Federal de Educação Tecnológica de Minas Gerais, Belo Horizonte, Brazil
| | - Vasco A C Azevedo
- Program of Bioinformatics, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Bertram Brenig
- Institute of Veterinary Medicine, Burckhardtweg, University of Göttingen, Göttingen, Germany
| | - Eric R G R Aguiar
- Department of Biological Science, Center of Biotechnology and Genetics, Universidade Estadual de Santa Cruz, Ilhéus, Brazil
| | | | - Paula L C Fonseca
- Molecular and Computational Biology of Fungi Laboratory, Department of Microbiology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.
| | - Aristóteles Góes-Neto
- Molecular and Computational Biology of Fungi Laboratory, Department of Microbiology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil; Program of Bioinformatics, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.
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Panorama of intron dynamics and gene rearrangements in the phylum Basidiomycota as revealed by the complete mitochondrial genome of Turbinellus floccosus. Appl Microbiol Biotechnol 2021; 105:2017-2032. [PMID: 33555361 DOI: 10.1007/s00253-021-11153-w] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 01/18/2021] [Accepted: 01/28/2021] [Indexed: 01/26/2023]
Abstract
In the present study, the complete mitogenome of Turbinellus floccosus was sequenced, assembled, and compared with other basidiomycete mitogenomes. The mitogenome of T. floccosus consists of a circular DNA molecule, with a size of 62,846 bp. Gene arrangement analysis indicated that large-scale gene rearrangements occurred in the levels of family and genus of basidiomycete species, and the mitogenome of T. floccosus contained a unique gene order. A significant correlation between the number of introns and the mitochondrial genome size of Basidiomycota were detected (P < 0.01). A total of 896 introns were detected in the core protein-coding genes (PCGs) of 74 basidiomycete species, and the cox1 gene was the largest host gene of basidiomycete introns. Intron position class (Pcls) P383 in the cox1 gene was the most common intron in Basidiomycota, which distributed in 40 of 74 basidiomycete species. In addition, frequent intron loss/gain events were detected in basidiomycete species. More than 50% of bases around insertion sites (- 15 bp to 15 bp) of Pcls from different species were conservative, indicating site preferences of intron insertions in Basidiomycota. Further analysis showed that 76.09% of introns tended to insert downstream to a T base in Basidiomycota. Phylogenetic analysis for 74 basidiomycetes indicated mitochondrial genes are effective molecular markers for phylogeny of basidiomycetes. The study served as the first report on the mitogenome from the family Gomphaceae, which will help to understand the intron origin and evolution in Basidiomycota. KEY POINTS: • The mitogenome of Turbinellus floccosus had a unique gene arrangement. • Intron loss/gain events were detected in the 74 basidiomycete species. • Introns tend to insert downstream of a T base in basidiomycete mitogenomes.
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The first eleven mitochondrial genomes from the ectomycorrhizal fungal genus (Boletus) reveal intron loss and gene rearrangement. Int J Biol Macromol 2021; 172:560-572. [PMID: 33476615 DOI: 10.1016/j.ijbiomac.2021.01.087] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 01/13/2021] [Accepted: 01/13/2021] [Indexed: 12/12/2022]
Abstract
In the present study, eleven novel complete mitogenomes of Boletus were assembled and compared. The eleven complete mitogenomes were all composed of circular DNA molecules, with sizes ranging from 32,883 bp to 48,298 bp. The mitochondrial gene arrangement of Boletus varied greatly from other Boletales mitogenomes, and gene position reversal were observed frequently in the evolution of Boletus. Across the 15 core protein-coding genes (PCGs) tested, atp9 had the least and rps3 had the largest genetic distances among the eleven Boletus species, indicating varied evolution rates of core PCGs. In addition, the Ka/Ks value for nad3 gene was >1, suggesting that this gene was subject to possible positive selection pressure. Comparative mitogenomic analysis indicated that the intronic region was significantly correlated with the size of mitogenomes in Boletales. Two large-scale intron loss events were detected in the evolution of Boletus. Phylogenetic analyses based on a combined mitochondrial gene dataset yielded a well-supported (BPP ≥ 0.99; BS =100) phylogenetic tree for 72 Agaricomycetes, and the Boletus species had a close relationship with Paxillus. This study served as the first report on complete mitogenomes in Boletus, which will further promote investigations of the genetics, evolution and phylogeny of the Boletus genus.
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Wu P, Bao Z, Tu W, Li L, Xiong C, Jin X, Li P, Gui M, Huang W, Li Q. The mitogenomes of two saprophytic Boletales species ( Coniophora) reveals intron dynamics and accumulation of plasmid-derived and non-conserved genes. Comput Struct Biotechnol J 2020; 19:401-414. [PMID: 33489009 PMCID: PMC7804350 DOI: 10.1016/j.csbj.2020.12.041] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 12/25/2020] [Accepted: 12/26/2020] [Indexed: 02/02/2023] Open
Abstract
The order Boletales is a group of fungi with complex life styles, which include saprophytic and ectomycorrhizal mushroom-forming fungi. In the present study, the complete mitogenomes of two saprophytic Boletales species, Coniophora olivacea, and C. puteana, were assembled and compared with mitogenomes of ectomycorrhizal Boletales. Both mitogenomes comprised circular DNA molecules with sizes of 78,350 bp and 79,655 bp, respectively. Comparative mitogenomic analysis indicated that the two saprophytic Boletales species contained more plasmid-derived (7 on average) and unknown functional genes (12 on average) than the four ectomycorrhizal Boletales species previously reported. In addition, the core protein coding genes, nad2 and rps3, were found to be subjected to positive selection pressure between some Boletales species. Frequent intron gain/loss events were detected in Boletales and Basidiomycetes, and several novel intron classes were found in two Coniophora species. A total of 33 introns were detected in C. olivacea, and most were found to have undergone contraction in the C. olivacea mitogenome. Mitochondrial genes of Coniophora species were found to have undergone large-scale gene rearrangements, and the accumulation of intra-genomic repeats in the mitogenome was considered as one of the main contributing factors. Based on combined mitochondrial gene sets, we obtained a well-supported phylogenetic tree for 76 Basidiomycetes, demonstrating the utility of mitochondrial gene analysis for inferring Basidiomycetes phylogeny. The study served as the first report on the mitogenomes of the family Coniophorineae, which will help to understand the origin and evolution patterns of Boletales species with complex lifestyles.
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Affiliation(s)
- Peng Wu
- Yunnan Plateau Characteristic Agricultural Industry Research Institute, Yunan Agricultural University, Kunming, Yunnan, China
| | - Zhijie Bao
- School of Food and Biological Engineering, Chengdu University, Chengdu, Sichuan, China
| | - Wenying Tu
- School of Food and Biological Engineering, Chengdu University, Chengdu, Sichuan, China
| | - Lijiao Li
- School of Food and Biological Engineering, Chengdu University, Chengdu, Sichuan, China
| | - Chuan Xiong
- Biotechnology and Nuclear Technology Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan, China
| | - Xin Jin
- Biotechnology and Nuclear Technology Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan, China
| | - Ping Li
- Biotechnology and Nuclear Technology Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan, China
| | - Mingying Gui
- Yunnan Plateau Characteristic Agricultural Industry Research Institute, Yunan Agricultural University, Kunming, Yunnan, China
| | - Wenli Huang
- Biotechnology and Nuclear Technology Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan, China
| | - Qiang Li
- School of Food and Biological Engineering, Chengdu University, Chengdu, Sichuan, China
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Li X, Li L, Bao Z, Tu W, He X, Zhang B, Ye L, Wang X, Li Q. The 287,403 bp Mitochondrial Genome of Ectomycorrhizal Fungus Tuber calosporum Reveals Intron Expansion, tRNA Loss, and Gene Rearrangement. Front Microbiol 2020; 11:591453. [PMID: 33362740 PMCID: PMC7756005 DOI: 10.3389/fmicb.2020.591453] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 11/09/2020] [Indexed: 02/02/2023] Open
Abstract
In the present study, the mitogenome of Tuber calosporum was assembled and analyzed. The mitogenome of T. calosporum comprises 15 conserved protein-coding genes, two rRNA genes, and 14 tRNAs, with a total size of 287,403 bp. Fifty-eight introns with 170 intronic open reading frames were detected in the T. calosporum mitogenome. The intronic region occupied 69.41% of the T. calosporum mitogenome, which contributed to the T. calosporum mitogenome significantly expand relative to most fungal species. Comparative mitogenomic analysis revealed large-scale gene rearrangements occurred in the mitogenome of T. calosporum, involving gene relocations and position exchanges. The mitogenome of T. calosporum was found to have lost several tRNA genes encoding for cysteine, aspartate, histidine, etc. In addition, a pair of fragments with a total length of 32.91 kb in both the nuclear and mitochondrial genomes of T. calosporum was detected, indicating possible gene transfer events. A total of 12.83% intragenomic duplications were detected in the T. calosporum mitogenome. Phylogenetic analysis based on mitochondrial gene datasets obtained well-supported tree topologies, indicating that mitochondrial genes could be reliable molecular markers for phylogenetic analyses of Ascomycota. This study served as the first report on mitogenome in the family Tuberaceae, thereby laying the groundwork for our understanding of the evolution, phylogeny, and population genetics of these important ectomycorrhizal fungi.
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Affiliation(s)
- Xiaolin Li
- Soil and Fertilizer Institute, Sichuan Academy of Agricultural Sciences, Chengdu, China
| | - Lijiao Li
- School of Food and Biological Engineering, Chengdu University, Chengdu, China
| | - Zhijie Bao
- School of Food and Biological Engineering, Chengdu University, Chengdu, China
| | - Wenying Tu
- School of Food and Biological Engineering, Chengdu University, Chengdu, China
| | - Xiaohui He
- School of Food and Biological Engineering, Chengdu University, Chengdu, China
| | - Bo Zhang
- Soil and Fertilizer Institute, Sichuan Academy of Agricultural Sciences, Chengdu, China
| | - Lei Ye
- Soil and Fertilizer Institute, Sichuan Academy of Agricultural Sciences, Chengdu, China
| | - Xu Wang
- College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - Qiang Li
- School of Food and Biological Engineering, Chengdu University, Chengdu, China
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27
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Chen C, Wang J, Li Q, Fu R, Jin X, Huang W, Lu D. Mitogenomes of Two Phallus Mushroom Species Reveal Gene Rearrangement, Intron Dynamics, and Basidiomycete Phylogeny. Front Microbiol 2020; 11:573064. [PMID: 33193177 PMCID: PMC7644776 DOI: 10.3389/fmicb.2020.573064] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 10/05/2020] [Indexed: 11/13/2022] Open
Abstract
Phallus indusiatus and Phallus echinovolvatus are edible bamboo mushrooms with pharmacological properties. We sequenced, assembled, annotated, and compared the mitogenomes of these species. Both mitogenomes were composed of circular DNA molecules, with sizes of 89,139 and 50,098 bp, respectively. Introns were the most important factor in mitogenome size variation within the genus Phallus. Phallus indusiatus, P. echinovolvatus, and Turbinellus floccosus in the subclass Phallomycetidae have conservative gene arrangements. Large-scale gene rearrangements were observed in species representing 42 different genera of Basidiomycetes. A variety of intron position classes were found in the 44 Basidiomycete species analyzed. A novel group II intron from the P. indusiatus mitogenome was compared with other fungus species containing the same intron, and we demonstrated that the insertion sites of the intron had a base preference. Phylogenetic analyses based on combined gene datasets yielded well-supported Bayesian posterior probability (BPP = 1) topologies. This indicated that mitochondrial genes are reliable molecular markers for analyzing the phylogenetic relationships of the Basidiomycetes. This is the first study of the mitogenome of the genus Phallus, and it increases our understanding of the population genetics and evolution of bamboo mushrooms and related species.
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Affiliation(s)
- Cheng Chen
- Institute of Plant Protection, Sichuan Academy of Agricultural Sciences, Chengdu, China.,Key Laboratory of Integrated Pest Management on Crops in Southwest, Ministry of Agriculture, Chengdu, China
| | - Jian Wang
- Institute of Plant Protection, Sichuan Academy of Agricultural Sciences, Chengdu, China.,Key Laboratory of Integrated Pest Management on Crops in Southwest, Ministry of Agriculture, Chengdu, China
| | - Qiang Li
- School of Food and Biological Engineering, Chengdu University, Chengdu, China
| | - Rongtao Fu
- Institute of Plant Protection, Sichuan Academy of Agricultural Sciences, Chengdu, China.,Key Laboratory of Integrated Pest Management on Crops in Southwest, Ministry of Agriculture, Chengdu, China
| | - Xin Jin
- Biotechnology and Nuclear Technology Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, China
| | - Wenli Huang
- Biotechnology and Nuclear Technology Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, China
| | - Daihua Lu
- Institute of Plant Protection, Sichuan Academy of Agricultural Sciences, Chengdu, China.,Key Laboratory of Integrated Pest Management on Crops in Southwest, Ministry of Agriculture, Chengdu, China
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Wang X, Wang Y, Yao W, Shen J, Chen M, Gao M, Ren J, Li Q, Liu N. The 256 kb mitochondrial genome of Clavaria fumosa is the largest among phylum Basidiomycota and is rich in introns and intronic ORFs. IMA Fungus 2020; 11:26. [PMID: 33292749 PMCID: PMC7666478 DOI: 10.1186/s43008-020-00047-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 10/22/2020] [Indexed: 11/10/2022] Open
Abstract
In the present study, the complete mitogenome of Clavaria fumosa, was sequenced, assembled, and compared. The complete mitogenome of C. fumosa is 256,807 bp in length and is the largest mitogenomes among all Basidiomycota mitogenomes reported. Comparative mitogenomic analysis indicated that the C. fumosa mitogenome contained the most introns and intronic ORFs among all fungal mitogenomes. Large intergenic regions, intronic regions, accumulation of repeat sequences and plasmid-derived genes together promoted the size expansion of the C. fumosa mitogenome. In addition, the rps3 gene was found subjected to positive selection between some Agaricales species. We found frequent intron gain/loss events in Agaricales mitogenomes, and four novel intron classes were detected in the C. fumosa mitogenome. Large-scale gene rearrangements were found occurred in Agaricales species and the C. fumosa mitogenome had a unique gene arrangement which differed from other Agaricales species. Phylogenetic analysis for 76 Basidiomycetes based on combined mitochondrial gene sets indicated that mitochondrial genes could be used as effective molecular markers for reconstructing evolution of Basidiomycota. The study served as the first report on the mitogenomes of the family Clavariaceae, which will promote the understanding of the genetics, evolution and taxonomy of C. fumosa and related species.
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Affiliation(s)
- Xu Wang
- Present Address: College of Life Sciences, Henan Agricultural University, Zhengzhou, 450002, Henan, China
| | - Yajie Wang
- Present Address: College of Life Sciences, Henan Agricultural University, Zhengzhou, 450002, Henan, China
| | - Wen Yao
- Present Address: College of Life Sciences, Henan Agricultural University, Zhengzhou, 450002, Henan, China
| | - Jinwen Shen
- Present Address: College of Life Sciences, Henan Agricultural University, Zhengzhou, 450002, Henan, China
| | - Mingyue Chen
- Present Address: College of Life Sciences, Henan Agricultural University, Zhengzhou, 450002, Henan, China
| | - Ming Gao
- Present Address: College of Life Sciences, Henan Agricultural University, Zhengzhou, 450002, Henan, China
| | - Jiening Ren
- Present Address: College of Life Sciences, Henan Agricultural University, Zhengzhou, 450002, Henan, China
| | - Qiang Li
- School of Food and Biological Engineering, Chengdu University, Chengdu, 610106, Sichuan, China.
| | - Na Liu
- Present Address: College of Life Sciences, Henan Agricultural University, Zhengzhou, 450002, Henan, China.
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The 206 kbp mitochondrial genome of Phanerochaete carnosa reveals dynamics of introns, accumulation of repeat sequences and plasmid-derived genes. Int J Biol Macromol 2020; 162:209-219. [DOI: 10.1016/j.ijbiomac.2020.06.142] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 06/14/2020] [Accepted: 06/15/2020] [Indexed: 01/14/2023]
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Wang X, Jia L, Wang M, Yang H, Chen M, Li X, Liu H, Li Q, Liu N. The complete mitochondrial genome of medicinal fungus Taiwanofungus camphoratus reveals gene rearrangements and intron dynamics of Polyporales. Sci Rep 2020; 10:16500. [PMID: 33020532 PMCID: PMC7536210 DOI: 10.1038/s41598-020-73461-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 09/08/2020] [Indexed: 12/31/2022] Open
Abstract
Taiwanofungus camphoratus is a highly valued medicinal mushroom that is endemic to Taiwan, China. In the present study, the mitogenome of T. camphoratus was assembled and compared with other published Polyporales mitogenomes. The T. camphoratus mitogenome was composed of circular DNA molecules, with a total size of 114,922 bp. Genome collinearity analysis revealed large-scale gene rearrangements between the mitogenomes of Polyporales, and T. camphoratus contained a unique gene order. The number and classes of introns were highly variable in 12 Polyporales species we examined, which proved that numerous intron loss or gain events occurred in the evolution of Polyporales. The Ka/Ks values for most core protein coding genes in Polyporales species were less than 1, indicating that these genes were subject to purifying selection. However, the rps3 gene was found under positive or relaxed selection between some Polyporales species. Phylogenetic analysis based on the combined mitochondrial gene set obtained a well-supported topology, and T. camphoratus was identified as a sister species to Laetiporus sulphureus. This study served as the first report on the mitogenome in the Taiwanofungus genus, which will provide a basis for understanding the phylogeny and evolution of this important fungus.
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Affiliation(s)
- Xu Wang
- College of Life Sciences, Henan Agricultural University, Zhengzhou, 450002, Henan, China
| | - Lihua Jia
- College of Life Sciences, Henan Agricultural University, Zhengzhou, 450002, Henan, China
| | - Mingdao Wang
- College of Life Sciences, Henan Agricultural University, Zhengzhou, 450002, Henan, China
| | - Hao Yang
- College of Life Sciences, Henan Agricultural University, Zhengzhou, 450002, Henan, China
| | - Mingyue Chen
- College of Life Sciences, Henan Agricultural University, Zhengzhou, 450002, Henan, China
| | - Xiao Li
- College of Life Sciences, Henan Agricultural University, Zhengzhou, 450002, Henan, China
| | - Hanyu Liu
- College of Life Sciences, Henan Agricultural University, Zhengzhou, 450002, Henan, China
| | - Qiang Li
- School of Food and Biological Engineering, Chengdu University, Chengdu, 610106, Sichuan, China.
- College of Life Sciences, Henan Agricultural University, Zhengzhou, 450002, Henan, China.
| | - Na Liu
- College of Life Sciences, Henan Agricultural University, Zhengzhou, 450002, Henan, China.
- College of Life Sciences, Henan Agricultural University, Zhengzhou, 450002, Henan, China.
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Sarkar I, Dey P, Sharma SK, Ray SD, Kochiganti VHS, Singh R, Pramod P, Singh RP. Turdoides affinis mitogenome reveals the translational efficiency and importance of NADH dehydrogenase complex-I in the Leiothrichidae family. Sci Rep 2020; 10:16202. [PMID: 33004841 PMCID: PMC7530654 DOI: 10.1038/s41598-020-72674-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2020] [Accepted: 08/24/2020] [Indexed: 01/01/2023] Open
Abstract
Mitochondrial genome provides useful information about species concerning its evolution and phylogenetics. We have taken the advantage of high throughput next-generation sequencing technique to sequence the complete mitogenome of Yellow-billed babbler (Turdoides affinis), a species endemic to Peninsular India and Sri Lanka. Both, reference-based and de-novo assemblies of mitogenome were performed and observed that de-novo assembled mitogenome was most appropriate. The complete mitogenome of yellow-billed babbler (assembled de-novo) was 17,672 bp in length with 53.2% AT composition. Thirteen protein-coding genes along with two rRNAs and 22 tRNAs were detected. The arrangement pattern of these genes was found conserved among Leiothrichidae family mitogenomes. Duplicated control regions were found in the newly sequenced mitogenome. Downstream bioinformatics analysis revealed the effect of translational efficiency and purifying selection pressure over thirteen protein-coding genes in yellow-billed babbler mitogenome. Ka/Ks analysis indicated the highest synonymous substitution rate in the nad6 gene. Evolutionary analysis revealed the conserved nature of all the protein-coding genes across Leiothrichidae family mitogenomes. Our limited phylogeny results placed T. affinis in a separate group, a sister group of Garrulax. Overall, our results provide a useful information for future studies on the evolutionary and adaptive mechanisms of birds belong to the Leiothrichidae family.
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Affiliation(s)
- Indrani Sarkar
- National Avian Forensic Laboratory, Sálim Ali Centre for Ornithology and Natural History, Anaikatty, Coimbatore, Tamil Nadu, 641108, India
| | - Prateek Dey
- National Avian Forensic Laboratory, Sálim Ali Centre for Ornithology and Natural History, Anaikatty, Coimbatore, Tamil Nadu, 641108, India
| | - Sanjeev Kumar Sharma
- National Avian Forensic Laboratory, Sálim Ali Centre for Ornithology and Natural History, Anaikatty, Coimbatore, Tamil Nadu, 641108, India.
| | - Swapna Devi Ray
- National Avian Forensic Laboratory, Sálim Ali Centre for Ornithology and Natural History, Anaikatty, Coimbatore, Tamil Nadu, 641108, India
| | | | - Renu Singh
- Central Avian Research Institute, Bareilly, Uttar Pradesh, 243122, India
| | - Padmanabhan Pramod
- National Avian Forensic Laboratory, Sálim Ali Centre for Ornithology and Natural History, Anaikatty, Coimbatore, Tamil Nadu, 641108, India
| | - Ram Pratap Singh
- National Avian Forensic Laboratory, Sálim Ali Centre for Ornithology and Natural History, Anaikatty, Coimbatore, Tamil Nadu, 641108, India.
- Department of Life Science, Central University of South Bihar, Gaya, Bihar, 824236, India.
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32
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Tan M, Wang Q. Characterization of the complete mitochondrial genome of Sterigmatomyces hyphaenes (Agaricostilbales: Agaricostilbaceae) and implications for its phylogeny. MITOCHONDRIAL DNA PART B-RESOURCES 2020; 5:3331-3333. [PMID: 33367015 PMCID: PMC7717615 DOI: 10.1080/23802359.2020.1815602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
In this study, the complete mitochondrial genome of Sterigmatomyces hyphaenes was sequenced by the next-generation sequencing. The complete mitochondrial genome of S. hyphaenes contained 17 protein-coding genes (PCG), 2 ribosomal RNA (rRNA) genes, and 23 transfer RNA (tRNA) genes. The total size of the S. hyphaenes mitochondrial genome is 26,198 bp, and the GC content of the mitochondrial genome is 42.08%. Phylogenetic analysis based on the combined mitochondrial gene dataset indicated that the mitochondrial genome of S. hyphaenes exhibited a close relationship with that of Rhodotorula mucilaginosa.
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Affiliation(s)
- Maoling Tan
- College of Food and Biological Engineering, Chengdu University, Chengdu, Sichuan, P.R. China
| | - Qiangfeng Wang
- Biotechnology and Nuclear Technology Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan, P.R. China
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Ye J, Cheng J, Ren Y, Liao W, Li Q. The First Mitochondrial Genome for Geastrales ( Sphaerobolus stellatus) Reveals Intron Dynamics and Large-Scale Gene Rearrangements of Basidiomycota. Front Microbiol 2020; 11:1970. [PMID: 32849488 PMCID: PMC7432440 DOI: 10.3389/fmicb.2020.01970] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 07/24/2020] [Indexed: 12/19/2022] Open
Abstract
In this study, the mitogenome of artillery fungus, Sphaerobolus stellatus, was assembled and compared with other Basidiomycota mitogenomes. The Sphaerobolus stellatus mitogenome was composed of circular DNA molecules, with a total size of 152,722 bp. Accumulation of intergenic and intronic sequences contributed to the Sphaerobolus stellatus mitogenome becoming the fourth largest mitogenome among Basidiomycota. We detected large-scale gene rearrangements in Basidiomycota mitogenomes, and the Sphaerobolus stellatus mitogenome contains a unique gene order. The quantity and position classes of intron varied between 75 Basidiomycota species we tested, indicating frequent intron loss/gain events occurred in the evolution of Basidiomycota. A novel intron position classes (P1281) was detected in the Sphaerobolus stellatus mitogenome, without any homologous introns from other Basidiomycota species. A pair of fragments with a total length of 9.12 kb in both the nuclear and mitochondrial genomes of Sphaerobolus stellatus was detected, indicating possible gene transferring events. Phylogenetic analysis based on the combined mitochondrial gene set obtained well-supported tree topologies (Bayesian posterior probabilities ≥ 0.99; bootstrap values ≥98). This study served as the first report on the mitogenome from the order Geastrales, which will promote the understanding of the phylogeny, population genetics, and evolution of the artillery fungus, Sphaerobolus stellatus.
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Affiliation(s)
- Jinghua Ye
- College of Information Science & Technology, Chengdu University, Chengdu, China
| | - Jie Cheng
- College of Food and Biological Engineering, Chengdu University, Chengdu, China
| | - Yuanhang Ren
- College of Food and Biological Engineering, Chengdu University, Chengdu, China
| | - Wenlong Liao
- College of Food and Biological Engineering, Chengdu University, Chengdu, China
| | - Qiang Li
- College of Food and Biological Engineering, Chengdu University, Chengdu, China
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34
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Huang J, Qu H, Shen X. Characterization of the complete mitochondrial genome of biocontrol yeast Sporobolomyces sp. (Sporidiobolales: Sporidiobolaceae) with phylogenetic analysis. Mitochondrial DNA B Resour 2020; 5:3039-3041. [PMID: 33458049 PMCID: PMC7782182 DOI: 10.1080/23802359.2020.1797581] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
In this study, we obtained the complete mitochondrial genome of Sporobolomyces sp. using next-generation sequencing. The complete mitochondrial genome of Sporobolomyces sp. contained 15 protein-coding genes (PCG), two ribosomal RNA (rRNA) genes, and 25 transfer RNA (tRNA) genes. The total length of the Sporobolomyces sp. mitochondrial genome is 26,430 bp, and the GC content of the mitochondrial genome is 39.32%. Phylogenetic analysis based on combined mitochondrial gene dataset indicated that the mitochondrial genome of Sporobolomyces sp. exhibited a close relationship with that of Rhodotorula mucilaginosa.
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Affiliation(s)
- Jingwei Huang
- College of Medicine (School of Nursing), Chengdu University, Chengdu, P.R. China.,Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Chengdu University, Chengdu, P.R. China
| | - Huijuan Qu
- Sichuan Academy of Agricultural Sciences, Chengdu, P.R. China
| | - Xueshan Shen
- Sichuan Academy of Agricultural Sciences, Chengdu, P.R. China
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Ren Y, Lu L, Tan M, Cao Y, Peng L. Characterization of the complete mitochondrial genome of Meira sp. (Exobasidiales: Brachybasidiaceae) with phylogenetic analysis. Mitochondrial DNA B Resour 2020; 5:2607-2608. [PMID: 33457878 PMCID: PMC7781881 DOI: 10.1080/23802359.2020.1781576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
In this study, the complete mitochondrial genome of Meira sp. was sequenced and assembled. The complete mitochondrial genome of Meira sp. has 15 protein-coding (PCG) genes, 2 ribosomal RNA (rRNA) genes, and 22 transfer RNA (tRNA) genes. The mitochondrial genome of Meira sp. has a total size of 23,353 bp, with the base composition as follows: A (30.62%), T (32.82%), G (17.84%) and C (18.73%). Phylogenetic analysis indicated that the mitogenome of Meira sp. exhibited a close relationship with the mitogenome of Jaminaea angkorensis.
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Affiliation(s)
- Yuanhang Ren
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, College of Pharmacy and Biological Engineering, Chengdu University, Chengdu, Sichuan, P. R. China
| | - Lidan Lu
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, College of Pharmacy and Biological Engineering, Chengdu University, Chengdu, Sichuan, P. R. China
| | - Maoling Tan
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, College of Pharmacy and Biological Engineering, Chengdu University, Chengdu, Sichuan, P. R. China
| | - Yanan Cao
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, College of Pharmacy and Biological Engineering, Chengdu University, Chengdu, Sichuan, P. R. China
| | - Lianxin Peng
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, College of Pharmacy and Biological Engineering, Chengdu University, Chengdu, Sichuan, P. R. China
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36
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Li Q, Ren Y, Xiang D, Shi X, Zhao J, Peng L, Zhao G. Comparative mitogenome analysis of two ectomycorrhizal fungi ( Paxillus) reveals gene rearrangement, intron dynamics, and phylogeny of basidiomycetes. IMA Fungus 2020; 11:12. [PMID: 32670777 PMCID: PMC7333402 DOI: 10.1186/s43008-020-00038-8] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 06/23/2020] [Indexed: 02/07/2023] Open
Abstract
In this study, the mitogenomes of two Paxillus species were assembled, annotated and compared. The two mitogenomes of Paxillus involutus and P. rubicundulus comprised circular DNA molecules, with the size of 39,109 bp and 41,061 bp, respectively. Evolutionary analysis revealed that the nad4L gene had undergone strong positive selection in the two Paxillus species. In addition, 10.64 and 36.50% of the repetitive sequences were detected in the mitogenomes of P. involutus and P. rubicundulus, respectively, which might transfer between mitochondrial and nuclear genomes. Large-scale gene rearrangements and frequent intron gain/loss events were detected in 61 basidiomycete species, which revealed large variations in mitochondrial organization and size in Basidiomycota. In addition, the insertion sites of the basidiomycete introns were found to have a base preference. Phylogenetic analysis of the combined mitochondrial gene set gave identical and well-supported tree topologies, indicating that mitochondrial genes were reliable molecular markers for analyzing the phylogenetic relationships of Basidiomycota. This study is the first report on the mitogenomes of Paxillus, which will promote a better understanding of their contrasted ecological strategies, molecular evolution and phylogeny of these important ectomycorrhizal fungi and related basidiomycete species.
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Affiliation(s)
- Qiang Li
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, College of Pharmacy and Biological Engineering, Chengdu University, Chengdu, 610106 Sichuan China
| | - Yuanhang Ren
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, College of Pharmacy and Biological Engineering, Chengdu University, Chengdu, 610106 Sichuan China
| | - Dabing Xiang
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, College of Pharmacy and Biological Engineering, Chengdu University, Chengdu, 610106 Sichuan China
| | - Xiaodong Shi
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, College of Pharmacy and Biological Engineering, Chengdu University, Chengdu, 610106 Sichuan China
| | - Jianglin Zhao
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, College of Pharmacy and Biological Engineering, Chengdu University, Chengdu, 610106 Sichuan China
| | - Lianxin Peng
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, College of Pharmacy and Biological Engineering, Chengdu University, Chengdu, 610106 Sichuan China
- Present address: Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, 2025 # Chengluo Avenue, Chengdu, 610106 Sichuan China
| | - Gang Zhao
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, College of Pharmacy and Biological Engineering, Chengdu University, Chengdu, 610106 Sichuan China
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Shao SC, Luo Y, Yu WB. The complete mitochondrial genome sequence of Lactarius trivialis (Russulalles, Basidiomycota). Mitochondrial DNA B Resour 2020; 5:2078-2079. [PMID: 33457749 PMCID: PMC7782267 DOI: 10.1080/23802359.2020.1765217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Lactarius trivialis is a very common species and widely distributes in north temperate. In this study, a complete mitogenome of L. trivialis was assembled and annotated. The whole mitogenome of L. trivialis was a circular molecule with 42,366 bp in length, encoding 44 genes as follows: 19 coding genes, two rRNAs, and 23 tRNAs. The contents of four bases in mtDNA were A (39.65%), T (38.82%), C (11.30%), and G (21.53%), respectively. Phylogenetic analysis recovered that it is nested with other Lactarius spp. in the order Russulalles.
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Affiliation(s)
- Shi-Cheng Shao
- Gardening and Horticulture Department, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, China
| | - Yan Luo
- Gardening and Horticulture Department, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Mengla, China
| | - Wen-Bin Yu
- Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Mengla, China
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38
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Tan M, Zhao G. Characterization and phylogenetic analysis of the complete mitochondrial genome of Clavulina sp. (Cantharellales: Clavulinaceae). Mitochondrial DNA B Resour 2020; 5:2944-2945. [PMID: 33458013 PMCID: PMC7781943 DOI: 10.1080/23802359.2020.1790327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
In this study, the complete mitochondrial genome of Clavulina sp. was sequenced and assembled. The complete mitochondrial genome of Clavulina sp. contains 20 protein-coding (PCG) genes, 2 ribosomal RNA (rRNA) genes, and 25 transfer RNA (tRNA) genes. The total size of the Clavulina sp. complete mitochondrial genome is 31,816 bp, with the GC content of 27.72%. Phylogenetic analysis indicated that the mitochondrial genome of Clavulina sp. exhibited a close relationship with that of the genus Cantharellus.
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Affiliation(s)
- Maoling Tan
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, College of Food and Biological Engineering, Chengdu University, Chengdu, PR China
| | - Gang Zhao
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, College of Food and Biological Engineering, Chengdu University, Chengdu, PR China
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39
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Wang X, Liu N. Mitochondrial genome characterization and phylogenetic analysis of bird schistosome Trichobilharzia szidati. MITOCHONDRIAL DNA PART B-RESOURCES 2020; 5:2592-2594. [PMID: 33457871 PMCID: PMC7781922 DOI: 10.1080/23802359.2020.1715299] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
In the present study, the complete mitochondrial genome of T. szidati was assembled by next generation sequencing (NGS). We found that the complete mitochondrial genome of T.szidati is 14, 303 bp in length and consists of 3023 (21.1%) adenine, 1153 (8.1%) cytosine, 3432 (24.0%) guanosine and 6695 (46.8%) thymine. The genome contains 12 conserved core protein-coding genes (atp6, cox1, cox2, cox3, nad1, nad2, nad3, nad4, nad4L, nad5, nad6, CYTB), 21 tRNA genes, 2 rRNA genes and 1 D-loop region. Phylogenetic analysis showed that T. szidati has a close relationship with T. regent. Knowledge of mitochondrial genome of T. szidati could provide useful information for the further studies of evolutionary biology, epidemiology and species identification.
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Affiliation(s)
- Xu Wang
- College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - Na Liu
- College of Life Sciences, Henan Agricultural University, Zhengzhou, China
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40
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Li Q, He X, Ren Y, Xiong C, Jin X, Peng L, Huang W. Comparative Mitogenome Analysis Reveals Mitochondrial Genome Differentiation in Ectomycorrhizal and Asymbiotic Amanita Species. Front Microbiol 2020; 11:1382. [PMID: 32636830 PMCID: PMC7318869 DOI: 10.3389/fmicb.2020.01382] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 05/28/2020] [Indexed: 11/19/2022] Open
Abstract
In this present study, we assembled and analyzed the mitogenomes of two asymbiotic and six ectomycorrhizal Amanita species based on next-generation sequencing data. The size of the eight Amanita mitogenomes ranged from 37,341 to 137,428 bp, and we considered introns to be one of the main factors contributing to the size variation of Amanita. The introns of the cox1 gene experienced frequent gain/loss events in Amanita; and the intron position class cox1P386 was lost in the six ectomycorrhizal Amanita species. In addition, ectomycorrhizal Amanita species had more repetitive sequences and fewer intergenic sequences than asymbiotic Amanita species in their mitogenomes. Large-scale gene rearrangements were detected in the Amanita species we tested, including gene displacements and inversions. On the basis of the combined mitochondrial gene set, we reconstructed the phylogenetic relationships of 66 Basidiomycetes. The six ectomycorrhizal Amanita species were of single origin, and the two saprophytic Amanita species formed two distinct clades. This study is the first to elucidate the functions of the mitogenome in the evolution and ecological adaptation of Amanita species.
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Affiliation(s)
- Qiang Li
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, College of Pharmacy and Biological Engineering, Chengdu University, Chengdu, China
- Biotechnology and Nuclear Technology Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, China
| | - Xiaohui He
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, College of Pharmacy and Biological Engineering, Chengdu University, Chengdu, China
| | - Yuanhang Ren
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, College of Pharmacy and Biological Engineering, Chengdu University, Chengdu, China
| | - Chuan Xiong
- Biotechnology and Nuclear Technology Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, China
| | - Xin Jin
- Biotechnology and Nuclear Technology Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, China
| | - Lianxin Peng
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, College of Pharmacy and Biological Engineering, Chengdu University, Chengdu, China
| | - Wenli Huang
- Biotechnology and Nuclear Technology Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, China
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41
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Liu Q, Wang X. Characterization and phylogenetic analysis of the complete mitochondrial genome of a basidiomycetous yeast Cystobasidium sp. (Cystobasidiales: Cystobasidiaceae). MITOCHONDRIAL DNA PART B-RESOURCES 2020; 5:2449-2450. [PMID: 33457822 PMCID: PMC7783051 DOI: 10.1080/23802359.2020.1777910] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
In the present study, the complete mitochondrial genome of a basidiomycetous yeast Cystobasidium sp. was assembled and obtained. The mitochondrial genome of Cystobasidium sp. contains 16 protein-coding genes, 2 ribosomal RNA genes (rRNA), and 24 transfer RNA (tRNA) genes. The complete mitogenome of Cystobasidium sp. has a total length of 24,914 bp, with the base composition as follows: A (30.82), T (32.88%), C (18.37%) and G (17.93%). The Cystobasidium sp. mitogenome exhibited a close relationship with the mitogenome of Microbotryum cf. violaceum, M. lychnidis-dioicae, and Rhodotorula mucilaginosa.
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Affiliation(s)
- Qiaofeng Liu
- Department of Pathology and Pathophysiology, Chengdu Medical College, Chengdu, China
| | - Xin Wang
- Department of Pathogenic Biology, Chengdu Medical College, Chengdu, China
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42
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Yang M, Zhang H, van der Lee TAJ, Waalwijk C, van Diepeningen AD, Feng J, Brankovics B, Chen W. Population Genomic Analysis Reveals a Highly Conserved Mitochondrial Genome in Fusarium asiaticum. Front Microbiol 2020; 11:839. [PMID: 32431686 PMCID: PMC7214670 DOI: 10.3389/fmicb.2020.00839] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 04/07/2020] [Indexed: 11/26/2022] Open
Abstract
Fusarium asiaticum is one of the pivotal members of the Fusarium graminearum species complex (FGSC) causing Fusarium head blight (FHB) on wheat, barley and rice in large parts of Asia. Besides resulting in yield losses, FHB also causes the accumulation of mycotoxins such as nivalenol (NIV) and deoxynivalenol (DON). The aim of this study was to conduct population studies on F. asiaticum from Southern China through mitochondrial genome analyses. All strains were isolated from wheat or rice from several geographic areas in seven provinces in Southern China. Based on geographic location and host, 210 isolates were selected for next generation sequencing, and their mitogenomes were assembled by GRAbB and annotated to explore the mitochondrial genome variability of F. asiaticum. The F. asiaticum mitogenome proves extremely conserved and variation is mainly caused by absence/presence of introns harboring homing endonuclease genes. These variations could be utilized to develop molecular markers for track and trace of migrations within and between populations. This study illustrates how mitochondrial introns can be used as markers for population genetic analysis. SNP analysis demonstrate the occurrence of mitochondrial recombination in F. asiaticum as was previously found for F. oxysporum and implied for F. graminearum. Furthermore, varying degrees of genetic diversity and recombination showed a high association with different geographic regions as well as with cropping systems. The mitogenome of F. graminearum showed a much higher SNP diversity while the interspecies intron variation showed no evidence of gene flow between the two closely related and sexual compatible species.
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Affiliation(s)
- Meixin Yang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agriculture Sciences, Beijing, China.,Biointeractions and Plant Health, Wageningen Plant Research, Wageningen, Netherlands
| | - Hao Zhang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agriculture Sciences, Beijing, China
| | - Theo A J van der Lee
- Biointeractions and Plant Health, Wageningen Plant Research, Wageningen, Netherlands
| | - Cees Waalwijk
- Biointeractions and Plant Health, Wageningen Plant Research, Wageningen, Netherlands
| | | | - Jie Feng
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agriculture Sciences, Beijing, China
| | - Balázs Brankovics
- Biointeractions and Plant Health, Wageningen Plant Research, Wageningen, Netherlands
| | - Wanquan Chen
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agriculture Sciences, Beijing, China
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Wang X, Liu N. Mitochondrial genome characterization and phylogenetic analysis of Blastocladiella sp. (Blastocladiales: Blastocladiaceae). Mitochondrial DNA B Resour 2020; 5:800-801. [PMID: 33366757 PMCID: PMC7748703 DOI: 10.1080/23802359.2020.1715859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
In the present study, the complete mitochondrial genome of an early diverging fungus Blastocladiella sp. was assembled by the next-generation sequencing. The complete mitochondrial genome of Blastocladiella sp. is 33, 800 bp in length and consists of 11,620 (34.38%) adenine, 5,047 (14.93%) cytosine, 6,025 (17.83%) guanosine and 11,108 (32.86%) thymine. The genome contains 19 protein-coding genes, 24 tRNA genes and 2 rRNA genes. Phylogenetic analysis based on the combined mitochondrial gene set showed that Blastocladiella sp. has a close relationship with Allomyces macrogynus and Blastocladiella emersonii.
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Affiliation(s)
- Xu Wang
- College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - Na Liu
- College of Life Sciences, Henan Agricultural University, Zhengzhou, China
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44
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Wang X, Wang M, Liu X, Tan A, Liu N. Mitochondrial genome characterization and phylogenetic analysis of arbuscular mycorrhizal fungus Rhizophagus sp. Mitochondrial DNA B Resour 2020; 5:810-811. [PMID: 33366762 PMCID: PMC7748601 DOI: 10.1080/23802359.2020.1715868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/30/2022] Open
Abstract
In the present study, the complete mitochondrial genome of Rhizophagus sp. was assembled by the next-generation sequencing. We found that the complete mitochondrial genome of Rhizophagus sp. is 50,449 bp in length and consists of 14,741 (29.22%) adenine, 9427 (18.69%) cytosine, 9248 (18.33%) guanosine, and 17,033 (33.76%) thymine. The genome contains 24 conserved core protein-coding genes, 25 tRNA genes, and 2 rRNA genes. Phylogenetic analysis based on the combined mitochondrial gene set showed that Rhizophagus sp. has a close relationship with Rhizophagus fasciculatus, Glomus irregular, and G. intratadices.
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Affiliation(s)
- Xu Wang
- College of Life Sciences, Henan Agricultural University, Zhengzhou, Henan, China
| | - Mingdao Wang
- College of Life Sciences, Henan Agricultural University, Zhengzhou, Henan, China
| | - Xinyu Liu
- College of Life Sciences, Henan Agricultural University, Zhengzhou, Henan, China
| | - Ailing Tan
- College of Life Sciences, Henan Agricultural University, Zhengzhou, Henan, China
| | - Na Liu
- College of Life Sciences, Henan Agricultural University, Zhengzhou, Henan, China
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45
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He MQ, Zhao RL, Hyde KD, Begerow D, Kemler M, Yurkov A, McKenzie EHC, Raspé O, Kakishima M, Sánchez-Ramírez S, Vellinga EC, Halling R, Papp V, Zmitrovich IV, Buyck B, Ertz D, Wijayawardene NN, Cui BK, Schoutteten N, Liu XZ, Li TH, Yao YJ, Zhu XY, Liu AQ, Li GJ, Zhang MZ, Ling ZL, Cao B, Antonín V, Boekhout T, da Silva BDB, De Crop E, Decock C, Dima B, Dutta AK, Fell JW, Geml J, Ghobad-Nejhad M, Giachini AJ, Gibertoni TB, Gorjón SP, Haelewaters D, He SH, Hodkinson BP, Horak E, Hoshino T, Justo A, Lim YW, Menolli N, Mešić A, Moncalvo JM, Mueller GM, Nagy LG, Nilsson RH, Noordeloos M, Nuytinck J, Orihara T, Ratchadawan C, Rajchenberg M, Silva-Filho AGS, Sulzbacher MA, Tkalčec Z, Valenzuela R, Verbeken A, Vizzini A, Wartchow F, Wei TZ, Weiß M, Zhao CL, Kirk PM. Notes, outline and divergence times of Basidiomycota. FUNGAL DIVERS 2019. [DOI: 10.1007/s13225-019-00435-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
AbstractThe Basidiomycota constitutes a major phylum of the kingdom Fungi and is second in species numbers to the Ascomycota. The present work provides an overview of all validly published, currently used basidiomycete genera to date in a single document. An outline of all genera of Basidiomycota is provided, which includes 1928 currently used genera names, with 1263 synonyms, which are distributed in 241 families, 68 orders, 18 classes and four subphyla. We provide brief notes for each accepted genus including information on classification, number of accepted species, type species, life mode, habitat, distribution, and sequence information. Furthermore, three phylogenetic analyses with combined LSU, SSU, 5.8s, rpb1, rpb2, and ef1 datasets for the subphyla Agaricomycotina, Pucciniomycotina and Ustilaginomycotina are conducted, respectively. Divergence time estimates are provided to the family level with 632 species from 62 orders, 168 families and 605 genera. Our study indicates that the divergence times of the subphyla in Basidiomycota are 406–430 Mya, classes are 211–383 Mya, and orders are 99–323 Mya, which are largely consistent with previous studies. In this study, all phylogenetically supported families were dated, with the families of Agaricomycotina diverging from 27–178 Mya, Pucciniomycotina from 85–222 Mya, and Ustilaginomycotina from 79–177 Mya. Divergence times as additional criterion in ranking provide additional evidence to resolve taxonomic problems in the Basidiomycota taxonomic system, and also provide a better understanding of their phylogeny and evolution.
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46
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Chen C, Li Q, Fu R, Wang J, Xiong C, Fan Z, Hu R, Zhang H, Lu D. Characterization of the mitochondrial genome of the pathogenic fungus Scytalidium auriculariicola (Leotiomycetes) and insights into its phylogenetics. Sci Rep 2019; 9:17447. [PMID: 31768013 PMCID: PMC6877775 DOI: 10.1038/s41598-019-53941-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Accepted: 10/17/2019] [Indexed: 12/26/2022] Open
Abstract
Scytalidium auriculariicola is the causative pathogen of slippery scar disease in the cultivated cloud ear fungus, Auricularia polytricha. In the present study, the mitogenome of S. auriculariicola was sequenced and assembled by next-generation sequencing technology. The circular mitogenome is 96,857 bp long and contains 56 protein-coding genes, 2 ribosomal RNA genes, and 30 transfer RNA genes (tRNAs). The high frequency of A and T used in codons contributed to the high AT content (73.70%) of the S. auriculariicola mitogenome. Comparative analysis indicated that the base composition and the number of introns and protein-coding genes in the S. auriculariicola mitogenome varied from that of other Leotiomycetes mitogenomes, including a uniquely positive AT skew. Five distinct groups were found in the gene arrangements of Leotiomycetes. Phylogenetic analyses based on combined gene datasets (15 protein-coding genes) yielded well-supported (BPP = 1) topologies. A single-gene phylogenetic tree indicated that the nad4 gene may be useful as a molecular marker to analyze the phylogenetic relationships of Leotiomycetes species. This study is the first report on the mitochondrial genome of the genus Scytalidium, and it will contribute to our understanding of the population genetics and evolution of S. auriculariicola and related species.
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Affiliation(s)
- Cheng Chen
- Institute of plant protection, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, Sichuan, P.R. China
- Key Laboratory of Integrated Pest Management on Crops in Southwest, Ministry of Agriculture, Chengdu, 610066, Sichuan, P.R. China
| | - Qiang Li
- College of Pharmacy and Biological Engineering, Chengdu University, Chengdu, 610106, Sichuan, P.R. China
| | - Rongtao Fu
- Institute of plant protection, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, Sichuan, P.R. China
| | - Jian Wang
- Institute of plant protection, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, Sichuan, P.R. China
| | - Chuan Xiong
- Biotechnology and Nuclear Technology Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610061, Sichuan, P.R. China
| | - Zhonghan Fan
- Institute of plant protection, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, Sichuan, P.R. China
| | - Rongping Hu
- Institute of plant protection, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, Sichuan, P.R. China
| | - Hong Zhang
- Institute of plant protection, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, Sichuan, P.R. China
| | - Daihua Lu
- Institute of plant protection, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, Sichuan, P.R. China.
- Sichuan Academy of Agricultural Sciences, 20 # Jingjusi Rd, Chengdu, 610066, Sichuan, P.R. China.
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47
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Li Q, Yang L, Xiang D, Wan Y, Wu Q, Huang W, Zhao G. The complete mitochondrial genomes of two model ectomycorrhizal fungi (Laccaria): features, intron dynamics and phylogenetic implications. Int J Biol Macromol 2019; 145:974-984. [PMID: 31669472 DOI: 10.1016/j.ijbiomac.2019.09.188] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2019] [Revised: 07/10/2019] [Accepted: 09/20/2019] [Indexed: 10/25/2022]
Abstract
Laccaria amethystine and L. bicolor have served as model species for studying the life history and genetics of ectomycorrhizal fungi. However, the characterizations and variations of their mitogenomes are still unknown. In the present study, the mitogenomes of the two Laccaria species were assembled, annotated, and compared. The two mitogenomes of L. amethystine and L. bicolor comprised circular DNA molecules, with the sizes of 65,156 bp and 95,304 bp, respectively. Genome collinearity analysis revealed large-scale gene rearrangements between the two Laccaria species. Comparative mitogenome analysis indicated the introns of cox1 genes in Agaricales experienced frequent lost/gain eveants, which promoted the organization and size variations in Agaricales mitogenomes. Evolutionary analysis indicated the core protein-coding genes in the two mitogenomes were subject to strong pressure of purifying selection. Phylogenetic analysis using the Bayesian inference (BI) and Maximum likelihood (ML) methods based on a combined mitochondrial gene set resulted in identical and well-supported tree topologies, wherein the two Laccaria species were most closely related to Coprinopsis cinerea. This study severed as the first study on the mitogenomes of Laccaria species, which promoted a comprehensive understanding of the genetics and evolution of the model ectomycorrhizal fungi.
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Affiliation(s)
- Qiang Li
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, College of Pharmacy and Biological Engineering, Chengdu University, Chengdu, Sichuan, China; Biotechnology and Nuclear Technology Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan, China
| | - Luxi Yang
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, College of Pharmacy and Biological Engineering, Chengdu University, Chengdu, Sichuan, China
| | - Dabing Xiang
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, College of Pharmacy and Biological Engineering, Chengdu University, Chengdu, Sichuan, China
| | - Yan Wan
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, College of Pharmacy and Biological Engineering, Chengdu University, Chengdu, Sichuan, China
| | - Qi Wu
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, College of Pharmacy and Biological Engineering, Chengdu University, Chengdu, Sichuan, China
| | - Wenli Huang
- Biotechnology and Nuclear Technology Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan, China.
| | - Gang Zhao
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, College of Pharmacy and Biological Engineering, Chengdu University, Chengdu, Sichuan, China.
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48
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Li Q, Ren Y, Shi X, Peng L, Zhao J, Song Y, Zhao G. Comparative Mitochondrial Genome Analysis of Two Ectomycorrhizal Fungi ( Rhizopogon) Reveals Dynamic Changes of Intron and Phylogenetic Relationships of the Subphylum Agaricomycotina. Int J Mol Sci 2019; 20:E5167. [PMID: 31635252 PMCID: PMC6829451 DOI: 10.3390/ijms20205167] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 10/12/2019] [Accepted: 10/17/2019] [Indexed: 01/12/2023] Open
Abstract
In the present study, we assembled and compared two mitogenomes from the Rhizopogon genus. The two mitogenomes of R. salebrosus and R. vinicolor comprised circular DNA molecules, with the sizes of 66,704 bp and 77,109 bp, respectively. Comparative mitogenome analysis indicated that the length and base composition of protein coding genes (PCGs), rRNA genes and tRNA genes varied between the two species. Large fragments aligned between the mitochondrial and nuclear genomes of both R. salebrosus (43.41 kb) and R. vinicolor (12.83 kb) indicated that genetic transfer between mitochondrial and nuclear genomes has occurred over evolutionary time of Rhizopogon species. Intronic regions were found to be the main factors contributing to mitogenome expansion in R. vinicolor. Variations in the number and type of introns in the two mitogenomes indicated that frequent intron loss/gain events occurred during the evolution of Rhizopogon species. Phylogenetic analyses based on Bayesian inference (BI) and Maximum likelihood (ML) methods using a combined mitochondrial gene set yielded identical and well-supported tree topologies, wherein Rhizopogon species showed close relationships with Agaricales species. This is the first study of mitogenomes within the genus Rhizopogon, and it provides a basis for understanding the evolution and differentiation of mitogenomes from the ectomycorrhizal fungal genus.
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Affiliation(s)
- Qiang Li
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, College of Pharmacy and Biological Engineering, Chengdu University, Chengdu 610106, Sichuan, China.
| | - Yuanhang Ren
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, College of Pharmacy and Biological Engineering, Chengdu University, Chengdu 610106, Sichuan, China.
| | - Xiaodong Shi
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, College of Pharmacy and Biological Engineering, Chengdu University, Chengdu 610106, Sichuan, China.
| | - Lianxin Peng
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, College of Pharmacy and Biological Engineering, Chengdu University, Chengdu 610106, Sichuan, China.
| | - Jianglin Zhao
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, College of Pharmacy and Biological Engineering, Chengdu University, Chengdu 610106, Sichuan, China.
| | - Yu Song
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, College of Pharmacy and Biological Engineering, Chengdu University, Chengdu 610106, Sichuan, China.
| | - Gang Zhao
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, College of Pharmacy and Biological Engineering, Chengdu University, Chengdu 610106, Sichuan, China.
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