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Mukhopadhyay J, Wai A, Hutchison LJ, Hausner G. The mitogenome of Urnula craterium. Can J Microbiol 2022; 68:561-568. [PMID: 35623096 DOI: 10.1139/cjm-2022-0012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Urnula craterium (Schwein.) Fr. (1851) has been reported from North America, Europe, and Asia, and can be a pathogen on various hardwood species. In this study we investigated the mitochondrial genome of U. craterium. The biology and taxonomy of this fungus is poorly studied and there are no mitogenomes currently available for any member of the Sarcosomataceae (Order Pezizales). The complete mitogenome of U. craterium comprises 43 967 bps and encodes 14 protein-coding genes, a complete set of tRNAs and rRNA genes. A novel feature of the mitogenome is the presence of a single subunit DNA polymerase coding region that is typically associated with linear invertron-type plasmids. The mitogenome may offer insights into the evolution of mitogenomes among members of the Pezizales with regards to gene content and order, mobile elements, and genome sizes.
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Affiliation(s)
| | - Alvan Wai
- University of Manitoba, 8664, Winnipeg, Canada;
| | - Leonard J Hutchison
- Lakehead University Faculty of Natural Resources Management, 157776, Thunder Bay, Ontario, Canada;
| | - Georg Hausner
- University of Manitoba, 8664, Buller Building 213, Winnipeg, Manitoba, Canada;
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2
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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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3
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Song N, Geng Y, Li X. The Mitochondrial Genome of the Phytopathogenic Fungus Bipolaris sorokiniana and the Utility of Mitochondrial Genome to Infer Phylogeny of Dothideomycetes. Front Microbiol 2020; 11:863. [PMID: 32457727 PMCID: PMC7225605 DOI: 10.3389/fmicb.2020.00863] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Accepted: 04/09/2020] [Indexed: 12/01/2022] Open
Abstract
A number of species in Bipolaris are important plant pathogens. Due to a limited number of synapomorphic characters, it is difficult to perform species identification and to estimate phylogeny of Bipolaris based solely on morphology. In this study, we sequenced the complete mitochondrial genome of Bipolaris sorokiniana, and presented the detailed annotation of the genome. The B. sorokiniana mitochondrial genome is 137,775 bp long, and contains two ribosomal RNA genes, 12 core protein-coding genes, 38 tRNA genes. In addition, two ribosomal protein genes (rps3 gene and rps5 gene) and the fungal mitochondrial RNase P gene (rnpB) are identified. The large genome size is mostly determined by the presence of numerous intronic and intergenic regions. A total of 28 introns are inserted in eight core protein-coding genes. Together with the published mitochondrial genome sequences, we conducted a preliminary phylogenetic inference of Dothideomycetes under various datasets and substitution models. The monophyly of Capnodiales, Botryosphaeriales and Pleosporales are consistently supported in all analyses. The Venturiaceae forms an independent lineage, with a distant phylogenetic relationship to Pleosporales. At the family level, the Mycosphaerellaceae, Botryosphaeriaceae. Phaeosphaeriaceae, and Pleosporaceae are recognized in the majority of trees.
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Affiliation(s)
- Nan Song
- College of Plant Protection, Henan Agricultural University, Zhengzhou, China
| | - Yuehua Geng
- College of Plant Protection, Henan Agricultural University, Zhengzhou, China
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Lee HH, Ke HM, Lin CYI, Lee TJ, Chung CL, Tsai IJ. Evidence of Extensive Intraspecific Noncoding Reshuffling in a 169-kb Mitochondrial Genome of a Basidiomycetous Fungus. Genome Biol Evol 2020; 11:2774-2788. [PMID: 31418013 PMCID: PMC6786477 DOI: 10.1093/gbe/evz181] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/13/2019] [Indexed: 12/19/2022] Open
Abstract
Comparative genomics of fungal mitochondrial genomes (mitogenomes) have revealed a remarkable pattern of rearrangement between and within major phyla owing to horizontal gene transfer and recombination. The role of recombination was exemplified at a finer evolutionary time scale in basidiomycetes group of fungi as they display a diversity of mitochondrial DNA inheritance patterns. Here, we assembled mitogenomes of six species from the Hymenochaetales order of basidiomycetes and examined 59 mitogenomes from 2 genetic lineages of Phellinus noxius. Gene order is largely collinear, while intergene regions are major determinants of mitogenome size variation. Substantial sequence divergence was found in shared introns consistent with high horizontal gene transfer frequency observed in yeasts, but we also identified a rare case where an intron was retained in five species since speciation. In contrast to the hyperdiversity observed in nuclear genomes of Phellinus noxius, mitogenomes’ intraspecific polymorphisms at protein-coding sequences are extremely low. Phylogeny network based on introns revealed turnover as well as exchange of introns between two lineages. Strikingly, some strains harbor a mosaic origin of introns from both lineages. Analysis of intergenic sequence indicated substantial differences between and within lineages, and an expansion may be ongoing as a result of exchange between distal intergenes. These findings suggest that the evolution in mitochondrial DNAs is usually lineage specific but chimeric mitotypes are frequently observed, thus capturing the possible evolutionary processes shaping mitogenomes in a basidiomycete. The large mitogenome sizes reported in various basidiomycetes appear to be a result of interspecific reshuffling of intergenes.
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Affiliation(s)
- Hsin-Han Lee
- Biodiversity Research Center, Academia Sinica, Taipei City, Taiwan
| | - Huei-Mien Ke
- Biodiversity Research Center, Academia Sinica, Taipei City, Taiwan
| | - Chan-Yi Ivy Lin
- Biodiversity Research Center, Academia Sinica, Taipei City, Taiwan
| | - Tracy J Lee
- Biodiversity Research Center, Academia Sinica, Taipei City, Taiwan.,Biodiversity Program, Taiwan International Graduate Program, Academia Sinica and National Taiwan Normal University, Taipei City, Taiwan.,Department of Life Science, National Taiwan Normal University, Taipei City, Taiwan
| | - Chia-Lin Chung
- Department of Plant Pathology and Microbiology, National Taiwan University, Taipei City, Taiwan
| | - Isheng J Tsai
- Biodiversity Research Center, Academia Sinica, Taipei City, Taiwan
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Liu W, Cai Y, Zhang Q, Chen L, Shu F, Ma X, Bian Y. The mitochondrial genome of Morchella importuna (272.2 kb) is the largest among fungi and contains numerous introns, mitochondrial non-conserved open reading frames and repetitive sequences. Int J Biol Macromol 2019; 143:373-381. [PMID: 31830457 DOI: 10.1016/j.ijbiomac.2019.12.056] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 12/06/2019] [Accepted: 12/07/2019] [Indexed: 12/11/2022]
Abstract
The complete mitochondrial genome of Morchella importuna, the famous edible and medicinal mushroom, was assembled as a 272,238 bp single circular dsDNA. As the largest mitogenome among fungi, it exhibits several distinct characteristics. The mitogenome of M. importuna encoded 14 core conserved mitochondrial protein-coding genes and 151 mitochondrial non-conserved open reading frames (ncORFs) were predicted, of which 61 were annotated as homing endonuclease genes, and 108 were confirmed to be expressed during the vegetative growth stages of M. importuna. In addition, 34 introns were identified in seven core genes (cob, cox1, cox2, cox3, nad1, nad4 and nad5) and two rRNA genes (rrnS and rrnL) with a length from 383 bp to 7453 bp, and eight large introns with a length range of 2340 bp to 7453 bp contained multiple intronic mtORFs. Moreover, 34 group I (IA, IB, IC1, IC2, ID and derived group I introns) and four group II intron domains were identified for the 34 introns, including five hybrid ones. Furthermore, the M. importuna mitogenome showed the presence of about 18.7% mitogenomic interspersed repeats. These and the aforementioned ncORFs and introns, contributed to the enlarged size of the mitogenome.
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Affiliation(s)
- Wei Liu
- Institute of Applied Mycology, Huazhong Agricultural University, Wuhan 430070, China
| | - Yingli Cai
- Institute of Vegetable, Wuhan Academy of Agricultural Sciences, Wuhan 430070, China
| | - Qianqian Zhang
- Institute of Applied Mycology, Huazhong Agricultural University, Wuhan 430070, China
| | - Lianfu Chen
- Institute of Applied Mycology, Huazhong Agricultural University, Wuhan 430070, China
| | - Fang Shu
- Institute of Applied Mycology, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiaolong Ma
- Institute of Vegetable, Wuhan Academy of Agricultural Sciences, Wuhan 430070, China
| | - Yinbing Bian
- Institute of Applied Mycology, Huazhong Agricultural University, Wuhan 430070, China.
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6
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Deng Y, Hsiang T, Li S, Lin L, Wang Q, Chen Q, Xie B, Ming R. Comparison of the Mitochondrial Genome Sequences of Six Annulohypoxylon stygium Isolates Suggests Short Fragment Insertions as a Potential Factor Leading to Larger Genomic Size. Front Microbiol 2018; 9:2079. [PMID: 30250455 PMCID: PMC6140425 DOI: 10.3389/fmicb.2018.02079] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Accepted: 08/14/2018] [Indexed: 12/22/2022] Open
Abstract
Mitochondrial DNA (mtDNA) is a core non-nuclear genetic material found in all eukaryotic organisms, the size of which varies extensively in the eumycota, even within species. In this study, mitochondrial genomes of six isolates of Annulohypoxylon stygium (Lév.) were assembled from raw reads from PacBio and Illumina sequencing. The diversity of genomic structures, conserved genes, intergenic regions and introns were analyzed and compared. Genome sizes ranged from 132 to 147 kb and contained the same sets of conserved protein-coding, tRNA and rRNA genes and shared the same gene arrangements and orientation. In addition, most intergenic regions were homogeneous and had similar sizes except for the region between cytochrome b (cob) and cytochrome c oxidase I (cox1) genes which ranged from 2,998 to 8,039 bp among the six isolates. Sixty-five intron insertion sites and 99 different introns were detected in these genomes. Each genome contained 45 or more introns, which varied in distribution and content. Introns from homologous insertion sites also showed high diversity in size, type and content. Comparison of introns at the same loci showed some complex introns, such as twintrons and ORF-less introns. There were 44 short fragment insertions detected within introns, intergenic regions, or as introns, some of them located at conserved domain regions of homing endonuclease genes. Insertions of short fragments such as small inverted repeats might affect or hinder the movement of introns, and these allowed for intron accumulation in the mitochondrial genomes analyzed, and enlarged their size. This study showed that the evolution of fungal mitochondrial introns is complex, and the results suggest short fragment insertions as a potential factor leading to larger mitochondrial genomes in A. stygium.
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Affiliation(s)
- Youjin Deng
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China.,Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Tom Hsiang
- Environmental Sciences, University of Guelph, Guelph, ON, Canada
| | - Shuxian Li
- USDA-Agricultural Research Service, Crop Genetics Research Unit, Stoneville, MS, United States
| | - Longji Lin
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Qingfu Wang
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Qinghe Chen
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China.,Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Baogui Xie
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Ray Ming
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China.,Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, United States
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