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Li Q, Li L, Zhang T, Xiang P, Wu Q, Tu W, Bao Z, Zou L, Chen C. The first two mitochondrial genomes for the genus Ramaria reveal mitochondrial genome evolution of Ramaria and phylogeny of Basidiomycota. IMA Fungus 2022; 13:16. [PMID: 36100951 PMCID: PMC9469536 DOI: 10.1186/s43008-022-00100-7] [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: 04/24/2022] [Accepted: 07/12/2022] [Indexed: 11/10/2022] Open
Abstract
In the present study, we assembled and analyzed the mitogenomes of two Ramaria species. The assembled mitogenomes of Ramaria cfr. rubripermanens and R. rubella were circularized, with sizes of 126,497 bp and 143,271 bp, respectively. Comparative mitogenome analysis showed that intron region contributed the most (contribution rate, 43.74%) to the size variations of Ramaria mitogenomes. The genetic contents, gene length, tRNAs, and codon usages of the two Ramaria mitogenomes varied greatly. In addition, the evolutionary rates of different core protein coding genes (PCGs) in Phallomycetidae mitogenomes varied. We detected large-scale gene rearrangements between Phallomycetidae mitogenomes, including gene displacement and tRNA doubling. A total of 4499 bp and 7746 bp aligned fragments were detected between the mitochondrial and nuclear genomes of R. cfr. rubripermanens and R. rubella, respectively, indicating possible gene transferring events. We further found frequent intron loss/gain and potential intron transfer events in Phallomycetidae mitogenomes during the evolution, and the mitogenomes of R. rubella contained a novel intron P44. Phylogenetic analyses using both Bayesian inference (BI) and Maximum Likelihood (ML) methods based on a combined mitochondrial gene dataset obtained an identical and well-supported phylogenetic tree for Basidiomycota, wherein R. cfr. rubripermanens and Turbinellus floccosus are sister species. This study served as the first report on mitogenomes from the genus Ramaria, which provides a basis for understanding the evolution, genetics, 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, People's Republic of 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, People's Republic of China
| | - Ting Zhang
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, School of Food and Biological Engineering, Chengdu University, Chengdu, Sichuan, People's Republic of China
| | - Peng Xiang
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, School of Food and Biological Engineering, Chengdu University, Chengdu, Sichuan, People's Republic of China
| | - Qian Wu
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, School of Food and Biological Engineering, Chengdu University, Chengdu, Sichuan, People's Republic of 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, People's Republic of 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, People's Republic of China
| | - Liang Zou
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, School of Food and Biological Engineering, Chengdu University, Chengdu, Sichuan, People's Republic of China.
| | - Cheng Chen
- Institute of Plant Protection, Sichuan Academy of Agricultural Sciences, Key Laboratory of Integrated Pest Management on Crops in Southwest, Ministry of Agriculture, 20 # Jingjusi Rd, Chengdu, 610066, Sichuan, People's Republic of China.
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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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