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Gomes RMODS, Silva KJGD, Theodoro RC. Group I introns: Structure, splicing and their applications in medical mycology. Genet Mol Biol 2024; 47Suppl 1:e20230228. [PMID: 38525907 DOI: 10.1590/1678-4685-gmb-2023-0228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 02/02/2024] [Indexed: 03/26/2024] Open
Abstract
Group I introns are small RNAs (250-500 nt) capable of catalyzing their own splicing from the precursor RNA. They are widely distributed across the tree of life and have intricate relationships with their host genomes. In this work, we review its basic structure, self-splicing and its mechanisms of gene mobility. As they are widely found in unicellular eukaryotes, especially fungi, we gathered information regarding their possible impact on the physiology of fungal cells and the possible application of these introns in medical mycology.
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Affiliation(s)
| | | | - Raquel Cordeiro Theodoro
- Universidade Federal do Rio Grande do Norte, Instituto de Medicina Tropical do Rio Grande do Norte, Natal, RN, Brazil
- Universidade Federal do Rio Grande do Norte, Centro de Biociências, Departamento de Biologia Celular de Genética, Natal, RN, Brazil
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Degradi L, Tava V, Prigitano A, Esposto MC, Tortorano AM, Saracchi M, Kunova A, Cortesi P, Pasquali M. Exploring Mitogenomes Diversity of Fusarium musae from Banana Fruits and Human Patients. Microorganisms 2022; 10:microorganisms10061115. [PMID: 35744633 PMCID: PMC9227538 DOI: 10.3390/microorganisms10061115] [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] [Received: 05/01/2022] [Revised: 05/21/2022] [Accepted: 05/23/2022] [Indexed: 12/10/2022] Open
Abstract
Fusarium musae has recently been described as a cross-kingdom pathogen causing post-harvest disease in bananas and systemic and superficial infection in humans. The taxonomic identity of fungal cross-kingdom pathogens is essential for confirming the identification of the species on distant infected hosts. Understanding the level of variability within the species is essential to decipher the population homogeneity infecting human and plant hosts. In order to verify that F. musae strains isolated from fruits and patients are part of a common population and to estimate their overall diversity, we assembled, annotated and explored the diversity of the mitogenomes of 18 F. musae strains obtained from banana fruits and human patients. The mitogenomes showed a high level of similarity among strains with different hosts’ origins, with sizes ranging from 56,493 to 59,256 bp. All contained 27 tRNA genes and 14 protein-coding genes, rps3 protein, and small and large ribosomal subunits (rns and rnl). Variations in the number of endonucleases were detected. A comparison of mitochondrial endonucleases distribution with a diverse set of Fusarium mitogenomes allowed us to specifically discriminate F. musae from its sister species F. verticillioides and the other Fusarium species. Despite the diversity in F. musae mitochondria, strains from bananas and strains from human patients group together, indirectly confirming F. musae as a cross-kingdom pathogen.
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Affiliation(s)
- Luca Degradi
- Department of Food, Environmental and Nutritional Science (DeFENS), University of Milan, Via Celoria 2, 20133 Milan, Italy; (L.D.); (V.T.); (M.S.); (A.K.); (P.C.)
| | - Valeria Tava
- Department of Food, Environmental and Nutritional Science (DeFENS), University of Milan, Via Celoria 2, 20133 Milan, Italy; (L.D.); (V.T.); (M.S.); (A.K.); (P.C.)
| | - Anna Prigitano
- Department of Biomedical Sciences for Health, University of Milan, Via Pascal 36, 20133 Milan, Italy; (A.P.); (M.C.E.); (A.M.T.)
| | - Maria Carmela Esposto
- Department of Biomedical Sciences for Health, University of Milan, Via Pascal 36, 20133 Milan, Italy; (A.P.); (M.C.E.); (A.M.T.)
| | - Anna Maria Tortorano
- Department of Biomedical Sciences for Health, University of Milan, Via Pascal 36, 20133 Milan, Italy; (A.P.); (M.C.E.); (A.M.T.)
| | - Marco Saracchi
- Department of Food, Environmental and Nutritional Science (DeFENS), University of Milan, Via Celoria 2, 20133 Milan, Italy; (L.D.); (V.T.); (M.S.); (A.K.); (P.C.)
| | - Andrea Kunova
- Department of Food, Environmental and Nutritional Science (DeFENS), University of Milan, Via Celoria 2, 20133 Milan, Italy; (L.D.); (V.T.); (M.S.); (A.K.); (P.C.)
| | - Paolo Cortesi
- Department of Food, Environmental and Nutritional Science (DeFENS), University of Milan, Via Celoria 2, 20133 Milan, Italy; (L.D.); (V.T.); (M.S.); (A.K.); (P.C.)
| | - Matias Pasquali
- Department of Food, Environmental and Nutritional Science (DeFENS), University of Milan, Via Celoria 2, 20133 Milan, Italy; (L.D.); (V.T.); (M.S.); (A.K.); (P.C.)
- Correspondence:
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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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Valenti I, Degradi L, Kunova A, Cortesi P, Pasquali M, Saracchi M. The First Mitochondrial Genome of Ciborinia camelliae and Its Position in the Sclerotiniaceae Family. FRONTIERS IN FUNGAL BIOLOGY 2022; 2:802511. [PMID: 37744111 PMCID: PMC10512376 DOI: 10.3389/ffunb.2021.802511] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 12/06/2021] [Indexed: 09/26/2023]
Abstract
Ciborinia camelliae is the causal agent of camellia flower blight (CFB). It is a hemibiotrophic pathogen, inoperculate Discomycete of the family Sclerotiniaceae. It shows host and organ specificity infecting only flowers of species belonging to the genus Camellia, causing serious damage to the ornamental component of the plant. In this work, the first mitochondrial genome of Ciborinia camellia is reported. The mitogenome was obtained by combining Illumina short read and Nanopore long read technology. To resolve repetitive elements, specific primers were designed and used for Sanger sequencing. The manually curated mitochondrial DNA (mtDNA) of the Italian strain DSM 112729 is a circular sequence of 114,660 bp, with 29.6% of GC content. It contains two ribosomal RNA genes, 33 transfer RNAs, one RNase P gene, and 62 protein-coding genes. The latter include one gene coding for a ribosomal protein (rps3) and the 14 typical proteins involved in the oxidative metabolism. Moreover, a partial mtDNA assembled from a contig list was obtained from the deposited genome assembly of a New Zealand strain of C. camelliae. The present study contributes to understanding the mitogenome arrangement and the evolution of this phytopathogenic fungus in comparison to other Sclerotiniaceae species and confirms the usefulness of mitochondrial analysis to define phylogenetic positioning of this newly sequenced species.
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Affiliation(s)
| | | | | | | | - Matias Pasquali
- Department of Food, Environmental and Nutritional Sciences, University of Milan, Milan, Italy
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Ali SS, Amoako-Attah I, Shao J, Kumi-Asare E, Meinhardt LW, Bailey BA. Mitochondrial Genomics of Six Cacao Pathogens From the Basidiomycete Family Marasmiaceae. Front Microbiol 2021; 12:752094. [PMID: 34777305 PMCID: PMC8581569 DOI: 10.3389/fmicb.2021.752094] [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: 08/02/2021] [Accepted: 10/01/2021] [Indexed: 11/23/2022] Open
Abstract
Thread blight disease has recently been described as an emerging disease on cacao (Theobroma cacao) in Ghana. In Ghana, thread blight disease is caused by multiple species of the Marasmiaceae family: Marasmius tenuissimus, M. crinis-equi, M. palmivorus, and Marasmiellus scandens. Interestingly, two additional members of the Marasmiaceae; Moniliophthora roreri (frosty pod rot) and Moniliophthora perniciosa (witches’ broom disease), are major pathogens of cacao in the Western hemisphere. It is important to accurately characterize the genetic relationships among these economically important species in support of their disease management. We used data from Illumina NGS-based genome sequencing efforts to study the mitochondrial genomes (mitogenomes) of the four cacao thread blight associated pathogens from Ghana and compared them with published mitogenomes of Mon. roreri and Mon. perniciosa. There is a remarkable interspecies variation in mitogenome size within the six cacao-associated Marasmiaceae species, ranging from 43,121 to 109,103 bp. The differences in genome lengths are primarily due to the number and lengths of introns, differences in intergenic space, and differences in the size and numbers of unidentified ORFs (uORF). Among seven M. tenuissimus mitogenomes sequenced, there is variation in size and sequence pointing to divergent evolution patterns within the species. The intronic regions show a high degree of sequence variation compared to the conserved sequences of the 14 core genes. The intronic ORFs identified, regardless of species, encode GIY-YIG or LAGLIDADG domain-containing homing endonuclease genes. Phylogenetic relationships using the 14 core proteins largely mimic the phylogenetic relationships observed in gene order patterns, grouping M. tenuissimus with M. crinis-equi, and M. palmivorus with Mon. roreri and Mon. perniciosa, leaving Mar. scandens as an outlier. The results from this study provide evidence of independent expansion/contraction events and sequence diversification in each species and establish a foundation for further exploration of the evolutionary trajectory of the fungi in Marasmiaceae family.
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Affiliation(s)
- Shahin S Ali
- Sustainable Perennial Crops Laboratory, U. S. Department of Agriculture (USDA)/Agricultural Research Service (ARS), Beltsville Agricultural Research Center-West, Beltsville, MD, United States.,Department of Viticulture and Enology, University of California, Davis, Davis, CA, United States
| | | | - Jonathan Shao
- U. S. Department of Agriculture (USDA)/Agricultural Research Service (ARS), Beltsville, MD, United States
| | | | - Lyndel W Meinhardt
- Sustainable Perennial Crops Laboratory, U. S. Department of Agriculture (USDA)/Agricultural Research Service (ARS), Beltsville Agricultural Research Center-West, Beltsville, MD, United States
| | - Bryan A Bailey
- Sustainable Perennial Crops Laboratory, U. S. Department of Agriculture (USDA)/Agricultural Research Service (ARS), Beltsville Agricultural Research Center-West, Beltsville, MD, United States
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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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Chen C, Li Q, Fu R, Wang J, Deng G, Chen X, Lu D. Comparative mitochondrial genome analysis reveals intron dynamics and gene rearrangements in two Trametes species. Sci Rep 2021; 11:2569. [PMID: 33510299 PMCID: PMC7843977 DOI: 10.1038/s41598-021-82040-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 01/12/2021] [Indexed: 12/14/2022] Open
Abstract
Trametes species are efficient wood decomposers that are widespread throughout the world. Mitogenomes have been widely used to understand the phylogeny and evolution of fungi. Up to now, two mitogenomes from the Trametes genus have been revealed. In the present study, the complete mitogenomes of two novel Trametes species, Trametes versicolor and T. coccinea, were assembled and compared with other Polyporales mitogenomes. Both species contained circular DNA molecules, with sizes of 67,318 bp and 99,976 bp, respectively. Comparative mitogenomic analysis indicated that the gene number, length and base composition varied between the four Trametes mitogenomes we tested. In addition, all of the core protein coding genes in Trametes species were identified and subjected to purifying selection. The mitogenome of T. coccinea contained the largest number of introns among the four Trametes species tested, and introns were considered the main factors contributing to size variations of Polyporales. Several novel introns were detected in the Trametes species we assembled, and introns identified in Polyporales were found to undergo frequent loss/gain events. Large-scale gene rearrangements were detected between closely related Trametes species, including gene inversions, insertions, and migrations. A well-supported phylogenetic tree for 77 Basidiomycetes was obtained based on the combined mitochondrial gene set using 2 phylogenetic inference methods. The results showed that mitochondrial genes are effective molecular markers for understanding the phylogeny of Basidiomycetes. This study is the first to report the mitogenome rearrangement and intron dynamics of Trametes species, which shed light on the evolution of Trametes and other related species.
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Affiliation(s)
- Cheng Chen
- Institute of Plant Protection, Sichuan Academy of Agricultural Sciences, Key Laboratory of Integrated Pest Management On Crops in Southwest, Ministry of Agriculture, Chengdu, People's Republic of China
| | - Qiang Li
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, School of Food and Biological Engineering, Chengdu University, Chengdu, People's Republic of China
| | - Rongtao Fu
- Institute of Plant Protection, Sichuan Academy of Agricultural Sciences, Key Laboratory of Integrated Pest Management On Crops in Southwest, Ministry of Agriculture, Chengdu, People's Republic of China
| | - Jian Wang
- Institute of Plant Protection, Sichuan Academy of Agricultural Sciences, Key Laboratory of Integrated Pest Management On Crops in Southwest, Ministry of Agriculture, Chengdu, People's Republic of China
| | - Guangmin Deng
- Sichuan Academy of Agricultural Sciences, 20 # Jingjusi Rd, Chengdu, 610066, Sichuan, People's Republic of China
| | - Xiaojuan Chen
- Institute of Plant Protection, Sichuan Academy of Agricultural Sciences, Key Laboratory of Integrated Pest Management On Crops in Southwest, Ministry of Agriculture, Chengdu, People's Republic of China
| | - Daihua Lu
- Institute of Plant Protection, Sichuan Academy of Agricultural Sciences, Key Laboratory of Integrated Pest Management On Crops in Southwest, Ministry of Agriculture, Chengdu, People's Republic of China.
- Sichuan Academy of Agricultural Sciences, 20 # Jingjusi Rd, Chengdu, 610066, Sichuan, People's Republic of China.
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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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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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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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Kulik T, Bilska K, Żelechowski M. Promising Perspectives for Detection, Identification, and Quantification of Plant Pathogenic Fungi and Oomycetes through Targeting Mitochondrial DNA. Int J Mol Sci 2020; 21:E2645. [PMID: 32290169 PMCID: PMC7177237 DOI: 10.3390/ijms21072645] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 04/06/2020] [Accepted: 04/09/2020] [Indexed: 12/11/2022] Open
Abstract
Fungi and oomycetes encompass many pathogens affecting crops worldwide. Their effective control requires screening pathogens across the local and international trade networks along with the monitoring of pathogen inocula in the field. Fundamentals to all of these concerns are their efficient detection, identification, and quantification. The use of molecular markers showed the best promise in the field of plant pathogen diagnostics. However, despite the unquestionable benefits of DNA-based methods, two significant limitations are associated with their use. The first limitation concerns the insufficient level of sensitivity due to the very low and uneven distribution of pathogens in plant material. The second limitation pertains to the inability of widely used diagnostic assays to detect cryptic species. Targeting mtDNA appears to provide a solution to these challenges. Its high copy number in microbial cells makes mtDNA an attractive target for developing highly sensitive assays. In addition, previous studies on different pathogen taxa indicated that mitogenome sequence variation could improve cryptic species delimitation accuracy. This review sheds light on the potential application of mtDNA for pathogen diagnostics. This paper covers a brief description of qPCR and DNA barcoding as two major strategies enabling the diagnostics of plant pathogenic fungi and oomycetes. Both strategies are discussed along with the potential use of mtDNA, including their strengths and weaknesses.
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Affiliation(s)
- Tomasz Kulik
- Department of Botany and Nature Protection, University of Warmia and Mazury in Olsztyn, Plac Łódzki 1, 10-727 Olsztyn, Poland
| | - Katarzyna Bilska
- Department of Botany and Nature Protection, University of Warmia and Mazury in Olsztyn, Plac Łódzki 1, 10-727 Olsztyn, Poland
| | - Maciej Żelechowski
- Department of Botany and Nature Protection, University of Warmia and Mazury in Olsztyn, Plac Łódzki 1, 10-727 Olsztyn, Poland
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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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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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Robicheau BM, Young AP, LaButti K, Grigoriev IV, Walker AK. The complete mitochondrial genome of the conifer needle endophyte, Phialocephala scopiformis DAOMC 229536 confirms evolutionary division within the fungal Phialocephala fortinii s.l. - Acephala appalanata species complex. Fungal Biol 2016; 121:212-221. [PMID: 28215349 DOI: 10.1016/j.funbio.2016.11.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Revised: 11/10/2016] [Accepted: 11/28/2016] [Indexed: 12/15/2022]
Abstract
Despite the recent surge in mitochondrial (mt) genome sequencing, Kingdom Fungi remains underrepresented with respect to mtDNA. We describe the mt genome of the conifer needle endophyte, Phialocephala scopiformis DAOMC 229536 (Helotiales, Ascomycota). This strain is of interest to the Canadian forestry industry as it produces the anti-insectan compound rugulosin. Sequence was obtained from whole genome shotgun sequencing. Comparison to the only other published Phialocephala mt genome, Phialocephala subalpina, indicates that the suite of common mt genes - cox1-3, cob, nad1-6 and 4L, atp6, 8 and 9, as well as rrnL and rrnS - has retained an identical order. Nad4L remains one of the most conserved mitochondrial genes within Phialocephala. Members of the closely related Phialocephala fortinii s.l. - Acephala appalanata species complex (PAC) share too much sequence similarity to properly resolve lineages using ITS barcoding alone. Using P. scopiformis sequence as an outgroup, we determined ancestral gene states that help confirm clades within Phialocephala. Our results show: (1) the complete mt genome of P. scopiformis, representing the 10th complete mt genome for the order Helotiales (containing >3800 species), and (2) how large-scale genomic patterns, such as mitochondrial gene order, can be used to confirm lineages within fungal species complexes.
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Affiliation(s)
- Brent M Robicheau
- Department of Biology, Acadia University, 33 Westwood Ave, Wolfville, NS, B4P 2R6, Canada
| | - Alexander P Young
- Department of Biology, Acadia University, 33 Westwood Ave, Wolfville, NS, B4P 2R6, Canada
| | - Kurt LaButti
- U.S. Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
| | - Igor V Grigoriev
- U.S. Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
| | - Allison K Walker
- Department of Biology, Acadia University, 33 Westwood Ave, Wolfville, NS, B4P 2R6, Canada.
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Leiter É, Park HS, Kwon NJ, Han KH, Emri T, Oláh V, Mészáros I, Dienes B, Vincze J, Csernoch L, Yu JH, Pócsi I. Characterization of the aodA, dnmA, mnSOD and pimA genes in Aspergillus nidulans. Sci Rep 2016; 6:20523. [PMID: 26846452 PMCID: PMC4742808 DOI: 10.1038/srep20523] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Accepted: 01/05/2016] [Indexed: 01/02/2023] Open
Abstract
Mitochondria play key roles in cellular energy generation and lifespan of most eukaryotes. To understand the functions of four nuclear-encoded genes predicted to be related to the maintenance of mitochondrial morphology and function in Aspergillus nidulans, systematic characterization was carried out. The deletion and overexpression mutants of aodA, dnmA, mnSOD and pimA encoding alternative oxidase, dynamin related protein, manganese superoxide dismutase and Lon protease, respectively, were generated and examined for their growth, stress tolerances, respiration, autolysis, cell death, sterigmatocystin production, hyphal morphology and size, and mitochondrial superoxide production as well as development. Overall, genetic manipulation of these genes had less effect on cellular physiology and ageing in A. nidulans than that of their homologs in another fungus Podospora anserina with a well-characterized senescence. The observed interspecial phenotypic differences can be explained by the dissimilar intrinsic stabilities of the mitochondrial genomes in A. nidulans and P. anserina. Furthermore, the marginally altered phenotypes observed in A. nidulans mutants indicate the presence of effective compensatory mechanisms for the complex networks of mitochondrial defense and quality control. Importantly, these findings can be useful for developing novel platforms for heterologous protein production, or on new biocontrol and bioremediation technologies based on Aspergillus species.
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Affiliation(s)
- Éva Leiter
- Department of Biotechnology and Microbiology, Faculty of Science and Technology, University of Debrecen, Debrecen, Hungary
| | - Hee-Soo Park
- Departments of Bacteriology and Genetics, The University of Wisconsin-Madison, Wisconsin, USA
| | - Nak-Jung Kwon
- Departments of Bacteriology and Genetics, The University of Wisconsin-Madison, Wisconsin, USA
| | - Kap-Hoon Han
- Departments of Bacteriology and Genetics, The University of Wisconsin-Madison, Wisconsin, USA.,Department of Pharmaceutical Engineering, Woosuk University, Wanju, Republic of Korea
| | - Tamás Emri
- Department of Biotechnology and Microbiology, Faculty of Science and Technology, University of Debrecen, Debrecen, Hungary
| | - Viktor Oláh
- Department of Botany, Faculty of Science and Technology, University of Debrecen, Debrecen, Hungary
| | - Ilona Mészáros
- Department of Botany, Faculty of Science and Technology, University of Debrecen, Debrecen, Hungary
| | - Beatrix Dienes
- Department of Physiology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - János Vincze
- Department of Physiology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - László Csernoch
- Department of Physiology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Jae-Hyuk Yu
- Departments of Bacteriology and Genetics, The University of Wisconsin-Madison, Wisconsin, USA
| | - István Pócsi
- Department of Biotechnology and Microbiology, Faculty of Science and Technology, University of Debrecen, Debrecen, Hungary
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Joardar V, Abrams NF, Hostetler J, Paukstelis PJ, Pakala S, Pakala SB, Zafar N, Abolude OO, Payne G, Andrianopoulos A, Denning DW, Nierman WC. Sequencing of mitochondrial genomes of nine Aspergillus and Penicillium species identifies mobile introns and accessory genes as main sources of genome size variability. BMC Genomics 2012; 13:698. [PMID: 23234273 PMCID: PMC3562157 DOI: 10.1186/1471-2164-13-698] [Citation(s) in RCA: 92] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2012] [Accepted: 11/29/2012] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND The genera Aspergillus and Penicillium include some of the most beneficial as well as the most harmful fungal species such as the penicillin-producer Penicillium chrysogenum and the human pathogen Aspergillus fumigatus, respectively. Their mitochondrial genomic sequences may hold vital clues into the mechanisms of their evolution, population genetics, and biology, yet only a handful of these genomes have been fully sequenced and annotated. RESULTS Here we report the complete sequence and annotation of the mitochondrial genomes of six Aspergillus and three Penicillium species: A. fumigatus, A. clavatus, A. oryzae, A. flavus, Neosartorya fischeri (A. fischerianus), A. terreus, P. chrysogenum, P. marneffei, and Talaromyces stipitatus (P. stipitatum). The accompanying comparative analysis of these and related publicly available mitochondrial genomes reveals wide variation in size (25-36 Kb) among these closely related fungi. The sources of genome expansion include group I introns and accessory genes encoding putative homing endonucleases, DNA and RNA polymerases (presumed to be of plasmid origin) and hypothetical proteins. The two smallest sequenced genomes (A. terreus and P. chrysogenum) do not contain introns in protein-coding genes, whereas the largest genome (T. stipitatus), contains a total of eleven introns. All of the sequenced genomes have a group I intron in the large ribosomal subunit RNA gene, suggesting that this intron is fixed in these species. Subsequent analysis of several A. fumigatus strains showed low intraspecies variation. This study also includes a phylogenetic analysis based on 14 concatenated core mitochondrial proteins. The phylogenetic tree has a different topology from published multilocus trees, highlighting the challenges still facing the Aspergillus systematics. CONCLUSIONS The study expands the genomic resources available to fungal biologists by providing mitochondrial genomes with consistent annotations for future genetic, evolutionary and population studies. Despite the conservation of the core genes, the mitochondrial genomes of Aspergillus and Penicillium species examined here exhibit significant amount of interspecies variation. Most of this variation can be attributed to accessory genes and mobile introns, presumably acquired by horizontal gene transfer of mitochondrial plasmids and intron homing.
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Affiliation(s)
- Vinita Joardar
- The J. Craig Venter Institute, Rockville, MD 20850, USA.
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Baidyaroy D, Hausner G, Hafez M, Michel F, Fulbright DW, Bertrand H. A 971-bp insertion in the rns gene is associated with mitochondrial hypovirulence in a strain of Cryphonectria parasitica isolated from nature. Fungal Genet Biol 2011; 48:775-83. [DOI: 10.1016/j.fgb.2011.05.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2010] [Revised: 03/18/2011] [Accepted: 05/08/2011] [Indexed: 01/16/2023]
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Santamaria M, Vicario S, Pappadà G, Scioscia G, Scazzocchio C, Saccone C. Towards barcode markers in Fungi: an intron map of Ascomycota mitochondria. BMC Bioinformatics 2009; 10 Suppl 6:S15. [PMID: 19534740 PMCID: PMC2697638 DOI: 10.1186/1471-2105-10-s6-s15] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Background A standardized and cost-effective molecular identification system is now an urgent need for Fungi owing to their wide involvement in human life quality. In particular the potential use of mitochondrial DNA species markers has been taken in account. Unfortunately, a serious difficulty in the PCR and bioinformatic surveys is due to the presence of mobile introns in almost all the fungal mitochondrial genes. The aim of this work is to verify the incidence of this phenomenon in Ascomycota, testing, at the same time, a new bioinformatic tool for extracting and managing sequence databases annotations, in order to identify the mitochondrial gene regions where introns are missing so as to propose them as species markers. Methods The general trend towards a large occurrence of introns in the mitochondrial genome of Fungi has been confirmed in Ascomycota by an extensive bioinformatic analysis, performed on all the entries concerning 11 mitochondrial protein coding genes and 2 mitochondrial rRNA (ribosomal RNA) specifying genes, belonging to this phylum, available in public nucleotide sequence databases. A new query approach has been developed to retrieve effectively introns information included in these entries. Results After comparing the new query-based approach with a blast-based procedure, with the aim of designing a faithful Ascomycota mitochondrial intron map, the first method appeared clearly the most accurate. Within this map, despite the large pervasiveness of introns, it is possible to distinguish specific regions comprised in several genes, including the full NADH dehydrogenase subunit 6 (ND6) gene, which could be considered as barcode candidates for Ascomycota due to their paucity of introns and to their length, above 400 bp, comparable to the lower end size of the length range of barcodes successfully used in animals. Conclusion The development of the new query system described here would answer the pressing requirement to improve drastically the bioinformatics support to the DNA Barcode Initiative. The large scale investigation of Ascomycota mitochondrial introns performed through this tool, allowing to exclude the introns-rich sequences from the barcode candidates exploration, could be the first step towards a mitochondrial barcoding strategy for these organisms, similar to the standard approach employed in metazoans.
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Affiliation(s)
- Monica Santamaria
- CNR - Istituto di Tecnologie Biomediche, Sede di Bari, Via Amendola 122/D, Bari, 70126, Italy.
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Kouvelis VN, Sialakouma A, Typas MA. Mitochondrial gene sequences alone or combined with ITS region sequences provide firm molecular criteria for the classification of Lecanicillium species. ACTA ACUST UNITED AC 2008; 112:829-44. [PMID: 18501578 DOI: 10.1016/j.mycres.2008.01.016] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2007] [Revised: 01/11/2008] [Accepted: 01/24/2008] [Indexed: 11/18/2022]
Abstract
The recent revision of Verticillium sect. Prostrata led to the introduction of the genus Lecanicillium, which comprises the majority of the entomopathogenic strains. Sixty-five strains previously classified as Verticillium lecanii or Verticillium sp. from different geographical regions and hosts were examined and their phylogenetic relationships were determined using sequences from three mitochondrial (mt) genes [the small rRNA subunit (rns), the NADH dehydrogenase subunits 1 (nad1) and 3 (nad3)] and the ITS region. In general, single gene phylogenetic trees differentiated and placed the strains examined in well-supported (by BS analysis) groups of L. lecanii, L. longisporum, L. muscarium, and L. nodulosum, although in some cases a few uncertainties still remained. nad1 was the most informative single gene in phylogenetic analyses and was also found to contain group I introns with putative open reading frames (ORFs) encoding for GIY-YIG endonucleases. The combined use of mt gene sequences resolved taxonomic uncertainties arisen from ITS analysis and, alone or in combination with ITS sequences, helped in placing uncharacterised Verticillium lecanii and Verticillium sp. firmly into Lecanicillium species. Combined gene data from all the mt genes and all the mt genes and the ITS region together, were very similar. Furthermore, a relaxed correlation with host specificity -- at least for Homoptera -- was indicated for the rns and the combined mt gene sequences. Thus, the usefulness of mt gene sequences as a convenient molecular tool in phylogenetic studies of entomopathogenic fungi was demonstrated.
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Affiliation(s)
- Vassili N Kouvelis
- Department of Genetics and Biotechnology, Faculty of Biology, University of Athens, Panepistemiopolis, Athens, Greece
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Seifert KA, Samson RA, Dewaard JR, Houbraken J, Lévesque CA, Moncalvo JM, Louis-Seize G, Hebert PDN. Prospects for fungus identification using CO1 DNA barcodes, with Penicillium as a test case. Proc Natl Acad Sci U S A 2007; 104:3901-6. [PMID: 17360450 PMCID: PMC1805696 DOI: 10.1073/pnas.0611691104] [Citation(s) in RCA: 282] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
DNA barcoding systems employ a short, standardized gene region to identify species. A 648-bp segment of mitochondrial cytochrome c oxidase 1 (CO1) is the core barcode region for animals, but its utility has not been tested in fungi. This study began with an examination of patterns of sequence divergences in this gene region for 38 fungal taxa with full CO1 sequences. Because these results suggested that CO1 could be effective in species recognition, we designed primers for a 545-bp fragment of CO1 and generated sequences for multiple strains from 58 species of Penicillium subgenus Penicillium and 12 allied species. Despite the frequent literature reports of introns in fungal mitochondrial genomes, we detected introns in only 2 of 370 Penicillium strains. Representatives from 38 of 58 species formed cohesive assemblages with distinct CO1 sequences, and all cases of sequence sharing involved known species complexes. CO1 sequence divergences averaged 0.06% within species, less than for internal transcribed spacer nrDNA or beta-tubulin sequences (BenA). CO1 divergences between species averaged 5.6%, comparable to internal transcribed spacer, but less than values for BenA (14.4%). Although the latter gene delivered higher taxonomic resolution, the amplification and alignment of CO1 was simpler. The development of a barcoding system for fungi that shares a common gene target with other kingdoms would be a significant advance.
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Affiliation(s)
- Keith A Seifert
- Biodiversity (Mycology and Botany), Environmental Sciences, Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada K1A 0C6.
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