Large inverted repeats identified by intra-specific comparison of mitochondrial genomes provide insights into the evolution of Agrocybe aegerita
Genomic structure and content of Agrocybe aegerita mitochondrial DNA contain essential information regarding the evolution of this gourmet mushroom. In this study, eight isolates of A. aegerita were sequenced and assembled into complete mitochondrial genomes. The mtDNA of the isolate Ag0067 containe...
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Elsevier
2020-01-01
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| Series: | Computational and Structural Biotechnology Journal |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S2001037020303755 |
| _version_ | 1818564614046089216 |
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| author | Xinrui Liu Xiaoping Wu Hao Tan Baogui Xie Youjin Deng |
| author_facet | Xinrui Liu Xiaoping Wu Hao Tan Baogui Xie Youjin Deng |
| author_sort | Xinrui Liu |
| collection | DOAJ |
| description | Genomic structure and content of Agrocybe aegerita mitochondrial DNA contain essential information regarding the evolution of this gourmet mushroom. In this study, eight isolates of A. aegerita were sequenced and assembled into complete mitochondrial genomes. The mtDNA of the isolate Ag0067 contained two genotypes, both of which were quadripartite architecture consisting of two identical inverted repeats, separated by a small single-copy region and a large single-copy region. The only difference was opposite directions of the small single-copy region. The mtDNAs ranged from 116,329 bp to 134,035 bp, harboring two large identical inverted repeats. Genes of plasmid-origin were present in regions flanked by inverted repeat ID2. Most of the core genes evolved at a relatively low rate, whereas five tRNA genes located in corresponding regions of Ag0002:1–14000 and Ag0002:50001–61000 showed higher diversity. A long fragment inversion (10 Kb) was suggested to have occurred during the differentiation of two main clades, leading to two different gene orders. The number and distribution of the introns varied greatly among the A. aegerita mtDNAs. Fast invasion of short insertions likely resulted in the diversity of introns as well as other non-coding regions, increasing the variation of the mtDNAs. We raised a model about the evolution of the large repeats to explain the unusual features of A. aegerita mtDNAs. This study constructed quadripartite architecture of A. aegerita mtDNAs analogous to chloroplast DNA, proposed an interconversion model of the divergent mitochondrial genotypes with large inverted repeats. The findings could increase our knowledge of fungal evolution. |
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| institution | Directory Open Access Journal |
| issn | 2001-0370 |
| language | English |
| last_indexed | 2024-12-14T01:31:06Z |
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| series | Computational and Structural Biotechnology Journal |
| spelling | doaj.art-c728f0e543f44e1f911eefa4ee66b94a2022-12-21T23:22:02ZengElsevierComputational and Structural Biotechnology Journal2001-03702020-01-011824242437Large inverted repeats identified by intra-specific comparison of mitochondrial genomes provide insights into the evolution of Agrocybe aegeritaXinrui Liu0Xiaoping Wu1Hao Tan2Baogui Xie3Youjin Deng4College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, ChinaCollege of Life Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, ChinaMushroom Research Center, Soil and Fertilizer Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610000, China; School of Bioengineering, Jiangnan University, Wuxi 214062, China; Corresponding authors at: College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China (Y. Deng & B. Xie); Mushroom Research Center, Soil and Fertilizer Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610000, China, and School of Bioengineering, Jiangnan University, Wuxi 214062, China (H. Tan).College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China; Corresponding authors at: College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China (Y. Deng & B. Xie); Mushroom Research Center, Soil and Fertilizer Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610000, China, and School of Bioengineering, Jiangnan University, Wuxi 214062, China (H. Tan).College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China; Corresponding authors at: College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China (Y. Deng & B. Xie); Mushroom Research Center, Soil and Fertilizer Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610000, China, and School of Bioengineering, Jiangnan University, Wuxi 214062, China (H. Tan).Genomic structure and content of Agrocybe aegerita mitochondrial DNA contain essential information regarding the evolution of this gourmet mushroom. In this study, eight isolates of A. aegerita were sequenced and assembled into complete mitochondrial genomes. The mtDNA of the isolate Ag0067 contained two genotypes, both of which were quadripartite architecture consisting of two identical inverted repeats, separated by a small single-copy region and a large single-copy region. The only difference was opposite directions of the small single-copy region. The mtDNAs ranged from 116,329 bp to 134,035 bp, harboring two large identical inverted repeats. Genes of plasmid-origin were present in regions flanked by inverted repeat ID2. Most of the core genes evolved at a relatively low rate, whereas five tRNA genes located in corresponding regions of Ag0002:1–14000 and Ag0002:50001–61000 showed higher diversity. A long fragment inversion (10 Kb) was suggested to have occurred during the differentiation of two main clades, leading to two different gene orders. The number and distribution of the introns varied greatly among the A. aegerita mtDNAs. Fast invasion of short insertions likely resulted in the diversity of introns as well as other non-coding regions, increasing the variation of the mtDNAs. We raised a model about the evolution of the large repeats to explain the unusual features of A. aegerita mtDNAs. This study constructed quadripartite architecture of A. aegerita mtDNAs analogous to chloroplast DNA, proposed an interconversion model of the divergent mitochondrial genotypes with large inverted repeats. The findings could increase our knowledge of fungal evolution.http://www.sciencedirect.com/science/article/pii/S2001037020303755Mitochondrial genotypeLinear plasmidShort inverted repeatShort insertion |
| spellingShingle | Xinrui Liu Xiaoping Wu Hao Tan Baogui Xie Youjin Deng Large inverted repeats identified by intra-specific comparison of mitochondrial genomes provide insights into the evolution of Agrocybe aegerita Computational and Structural Biotechnology Journal Mitochondrial genotype Linear plasmid Short inverted repeat Short insertion |
| title | Large inverted repeats identified by intra-specific comparison of mitochondrial genomes provide insights into the evolution of Agrocybe aegerita |
| title_full | Large inverted repeats identified by intra-specific comparison of mitochondrial genomes provide insights into the evolution of Agrocybe aegerita |
| title_fullStr | Large inverted repeats identified by intra-specific comparison of mitochondrial genomes provide insights into the evolution of Agrocybe aegerita |
| title_full_unstemmed | Large inverted repeats identified by intra-specific comparison of mitochondrial genomes provide insights into the evolution of Agrocybe aegerita |
| title_short | Large inverted repeats identified by intra-specific comparison of mitochondrial genomes provide insights into the evolution of Agrocybe aegerita |
| title_sort | large inverted repeats identified by intra specific comparison of mitochondrial genomes provide insights into the evolution of agrocybe aegerita |
| topic | Mitochondrial genotype Linear plasmid Short inverted repeat Short insertion |
| url | http://www.sciencedirect.com/science/article/pii/S2001037020303755 |
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