1
|
Yu Y, Liu T, Wang Y, Liu L, He X, Li J, Martin FM, Peng W, Tan H. Comparative analyses of Pleurotus pulmonarius mitochondrial genomes reveal two major lineages of mini oyster mushroom cultivars. Comput Struct Biotechnol J 2024; 23:905-917. [PMID: 38370975 PMCID: PMC10869244 DOI: 10.1016/j.csbj.2024.01.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 01/29/2024] [Accepted: 01/29/2024] [Indexed: 02/20/2024] Open
Abstract
Pleurotus pulmonarius, commonly known as the mini oyster mushroom, is highly esteemed for its crisp texture and umami flavor. Limited genetic diversity among P. pulmonarius cultivars raises concerns regarding its sustainable industrial production. To delve into the maternal genetic diversity of the principal P. pulmonarius cultivars, 36 cultivars and five wild isolates were subjected to de novo sequencing and assembly to generate high-quality mitogenome sequences. The P. pulmonarius mitogenomes had lengths ranging from 69,096 to 72,905 base pairs. The mitogenome sizes of P. pulmonarius and those of other mushroom species in the Pleurotus genus showed a significant positive correlation with the counts of LAGLIDAG and GIY-YIG homing endonucleases encoded by intronic open reading frames. A comparison of gene arrangements revealed an inversion of a fragment containing atp9-nad3-nad2 between P. pulmonarius and P. ostreatus. The mitogenomes of P. pulmonarius were clustered into three distinct clades, two of which were crowded with commercial cultivars. Clade I, all of which possess an inserted dpo gene, shared a maternal origin linked to an ancestral cultivar from Taiwan. Primers were designed to target the dpo gene, potentially safeguarding intellectual property rights. The wild isolates in Clade III exhibited more divergent mitogenomes, rendering them valuable for breeding.
Collapse
Affiliation(s)
- Yang Yu
- Sichuan Institute of Edible Fungi, Sichuan Academy of Agricultural Sciences, Chengdu 610000, China
| | - Tianhai Liu
- Sichuan Institute of Edible Fungi, Sichuan Academy of Agricultural Sciences, Chengdu 610000, China
- Sichuan Agricultural University, Chengdu 610000, China
| | - Yong Wang
- Sichuan Institute of Edible Fungi, Sichuan Academy of Agricultural Sciences, Chengdu 610000, China
| | - Lixu Liu
- Sichuan Institute of Edible Fungi, Sichuan Academy of Agricultural Sciences, Chengdu 610000, China
| | - Xiaolan He
- Sichuan Institute of Edible Fungi, Sichuan Academy of Agricultural Sciences, Chengdu 610000, China
| | - Jianwei Li
- Sichuan Academy of Agricultural Sciences, Chengdu 610000, China
| | - Francis M. Martin
- Université de Lorraine, INRAE, UMR Interactions Arbres/Microorganismes, Centre INRAE Grand Est, Nancy, Champenoux 54280, France
| | - Weihong Peng
- Sichuan Institute of Edible Fungi, Sichuan Academy of Agricultural Sciences, Chengdu 610000, China
| | - Hao Tan
- Sichuan Institute of Edible Fungi, Sichuan Academy of Agricultural Sciences, Chengdu 610000, China
- Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
| |
Collapse
|
2
|
Deng Y, Chen G, Bao X, He J. Characterization and phylogenetic analysis of the complete mitochondrial genome of Saccharomycopsis fibuligera (lindner) Klocker 1907 (saccharomycetales: saccharomycopsidaceae). Mitochondrial DNA B Resour 2024; 9:743-747. [PMID: 38887218 PMCID: PMC11182061 DOI: 10.1080/23802359.2024.2364756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2024] [Accepted: 05/31/2024] [Indexed: 06/20/2024] Open
Abstract
Saccharomycopsis fibuligera (Lindner) Klocker 1907 is frequently employed in the fermentation of metabolites such as citric acid, ethanol, mannitol, and pyruvate. Its heat tolerance and alcohol-producing capabilities during fermentation make it a desirable option for bread and wine production. To date, the mitochondrial genome of S. fibuligera has not been sequenced. In the present study, we obtained the full mitochondrial genome of S. fibuligera, which is 57,302 bp long and has a GC content of 24.40%. This genome contained 14 core protein-coding genes, 3 independent ORFs, 21 intronic ORFs, 25 tRNAs, and 2 rRNA genes. By utilizing the Bayesian inference phylogenetic method, we constructed phylogenetic trees for 24 Saccharomycotina fungi, which indicated that S. fibuligera is closely related to S. capsularis.
Collapse
Affiliation(s)
- Yue Deng
- Luzhou Vocational and Technical College, Luzhou, Sichuan, China
| | - Guangjiu Chen
- Luzhou Vocational and Technical College, Luzhou, Sichuan, China
| | - Xuedong Bao
- Luzhou Vocational and Technical College, Luzhou, Sichuan, China
| | - Jie He
- Luzhou Vocational and Technical College, Luzhou, Sichuan, China
| |
Collapse
|
3
|
Song X, Geng Y, Xu C, Li J, Guo Y, Shi Y, Ma Q, Li Q, Zhang M. The complete mitochondrial genomes of five critical phytopathogenic Bipolaris species: features, evolution, and phylogeny. IMA Fungus 2024; 15:15. [PMID: 38863028 PMCID: PMC11167856 DOI: 10.1186/s43008-024-00149-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 05/28/2024] [Indexed: 06/13/2024] Open
Abstract
In the present study, three mitogenomes from the Bipolaris genus (Bipolaris maydis, B. zeicola, and B. oryzae) were assembled and compared with the other two reported Bipolaris mitogenomes (B. oryzae and B. sorokiniana). The five mitogenomes were all circular DNA molecules, with lengths ranging from 106,403 bp to 135,790 bp. The mitogenomes of the five Bipolaris species mainly comprised the same set of 13 core protein-coding genes (PCGs), two rRNAs, and a certain number of tRNAs and unidentified open reading frames (ORFs). The PCG length, AT skew and GC skew showed large variability among the 13 PCGs in the five mitogenomes. Across the 13 core PCGs tested, nad6 had the least genetic distance among the 16 Pleosporales species we investigated, indicating that this gene was highly conserved. In addition, the Ka/Ks values for all 12 core PCGs (excluding rps3) were < 1, suggesting that these genes were subject to purifying selection. Comparative mitogenomic analyses indicate that introns were the main factor contributing to the size variation of Bipolaris mitogenomes. The introns of the cox1 gene experienced frequent gain/loss events in Pleosporales species. The gene arrangement and collinearity in the mitogenomes of the five Bipolaris species were almost highly conserved within the genus. Phylogenetic analysis based on combined mitochondrial gene datasets showed that the five Bipolaris species formed well-supported topologies. This study is the first report on the mitogenomes of B. maydis and B. zeicola, as well as the first comparison of mitogenomes among Bipolaris species. The findings of this study will further advance investigations into the population genetics, evolution, and genomics of Bipolaris species.
Collapse
Affiliation(s)
- Xinzheng Song
- Department of Plant Pathology, Henan Agricultural University, Zhengzhou, Henan, China
| | - Yuehua Geng
- Department of Plant Pathology, Henan Agricultural University, Zhengzhou, Henan, China
| | - Chao Xu
- Department of Plant Pathology, Henan Agricultural University, Zhengzhou, Henan, China
| | - Jiaxin Li
- Department of Plant Pathology, Henan Agricultural University, Zhengzhou, Henan, China
| | - Yashuang Guo
- Department of Plant Pathology, Henan Agricultural University, Zhengzhou, Henan, China
| | - Yan Shi
- Department of Plant Pathology, Henan Agricultural University, Zhengzhou, Henan, China
| | - Qingzhou Ma
- Department of Plant Pathology, Henan Agricultural University, Zhengzhou, Henan, China.
| | - Qiang Li
- School of Food and Biological Engineering, Chengdu University, Chengdu, Sichuan, China.
| | - Meng Zhang
- Department of Plant Pathology, Henan Agricultural University, Zhengzhou, Henan, China.
| |
Collapse
|
4
|
Malik M, Malik F, Fatma T, Qasim Hayat M, Jamal A, Gul A, Faraz Bhatti M. The complete mitochondrial genome of Penicillium expansum: Insights into the fungal evolution and phylogeny. Gene 2024; 910:148315. [PMID: 38417689 DOI: 10.1016/j.gene.2024.148315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Revised: 02/19/2024] [Accepted: 02/21/2024] [Indexed: 03/01/2024]
Abstract
Penicillium expansum is an important phytopathogenic fungus that causes blue mold disease. In this study, the novel mitochondrial genome of P. expansum was sequenced, assembled, annotated, and compared with the previously published Penicillium mitogenomes. P. expansum mitogenome is composed of circular DNA molecules with a genome size of 25,496 bp. It encodes 16 protein-encoding genes (PCGs), two rRNA genes, and 25 tRNA genes. Comparative analysis with six other Penicillium species revealed that gene length, GC content, AT skew, and GC skew were variable among the core protein-coding genes. The Penicillium species' gene synteny analysis identified several gene rearrangements. Among the core 15 PCGs, atp8 had the lowest K2P genetic distance, which shows that this gene is highly conserved. The Ka/Ks value of most PCGs was less than 1, which shows that these genes have undergone purifying selection. Phylogenetic analysis based on 14 concatenated core mitochondrial genes revealed that P. expansum shares a close relationship with P. solitum. This study served as a first report on the complete mitochondrial genome of P. expansum and its comparative analysis that will contribute to population genetics and rapid evolutionary studies among Penicillium species.
Collapse
Affiliation(s)
- Mahnoor Malik
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), 44000 Islamabad, Pakistan.
| | - Fatima Malik
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), 44000 Islamabad, Pakistan.
| | - Tehsin Fatma
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), 44000 Islamabad, Pakistan.
| | - Muhammad Qasim Hayat
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), 44000 Islamabad, Pakistan.
| | - Atif Jamal
- Crop Diseases Research Institute, National Agricultural Research Centre, Islamabad, Pakistan
| | - Alvina Gul
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), 44000 Islamabad, Pakistan
| | - Muhammad Faraz Bhatti
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), 44000 Islamabad, Pakistan.
| |
Collapse
|
5
|
Deng Y, Chen G, Bao X, He J, Li Q. Mitochondrial genomic characteristics and phylogenetic analysis of a brewing fungus, Rhizopus microsporus Tiegh. 1875 (Mucorales: Rhizopodaceae). Mitochondrial DNA B Resour 2024; 9:657-662. [PMID: 38774188 PMCID: PMC11107855 DOI: 10.1080/23802359.2024.2356133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 05/12/2024] [Indexed: 05/24/2024] Open
Abstract
Rhizopus microsporus Tiegh. 1875 is widely used in a variety of industries, such as brewing, wine making, baking, and medicine production, as it has the capability to break down proteins and generate surface-active agents. To date, the mitochondrial genome features of early evolved fungi from the Rhizopus genus have not been extensively studied. Our research obtained a full mitochondrial genome of R. microsporus species, which was 43,837 bp in size and had a GC content of 24.93%. This genome contained 14 core protein-coding genes, 3 independent ORFs, 7 intronic ORFs, 24 tRNAs, and 2 rRNA genes. Through the use of the BI phylogenetic inference method, we were able to create phylogenetic trees for 25 early differentiation fungi which strongly supported the major clades; this indicated that R. microsporus is most closely related to Rhizopus oryzae.
Collapse
Affiliation(s)
- Yue Deng
- Luzhou Vocational and Technical College, Luzhou, Sichuan, P. R. China
| | - Guangjiu Chen
- Luzhou Vocational and Technical College, Luzhou, Sichuan, P. R. China
| | - Xuedong Bao
- Luzhou Vocational and Technical College, Luzhou, Sichuan, P. R. China
| | - Jie He
- Luzhou Vocational and Technical College, Luzhou, Sichuan, P. R. China
| | - Qiang Li
- School of Food and Biological Engineering, Chengdu University, Chengdu, Sichuan, P. R. China
| |
Collapse
|
6
|
Özkale E, Doğan Ö, Budak M, Mahir Korkmaz E. Mitogenome evolution in Trichoderma afroharzianum strains: for a better understanding of distinguishing genus. Genome 2024; 67:139-150. [PMID: 38118129 DOI: 10.1139/gen-2022-0092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2023]
Abstract
Trichoderma afroharzianum (Hypocreales) is known as an important mycoparasite and biocontrol fungus and feeds on fungal material by parasitizing other fungi. Recent studies indicate that this species is also an ear rot pathogen in Europe. Here, the complete mitochondrial genome of three T. afroharzianum strains was sequenced using next-generation sequencing and comparatively characterized by the reported Trichoderma mitogenomes. T. afroharzianum mitogenomes were varying between 29 511 bp and 29 517 bp in length, with an average A + T content of 72.32%. These mitogenomes contain 14 core protein coding genes (PCGs), 22 tRNAs, two rRNAs, one gene encoding the ribosomal protein S3, and three or four genes including conserved domains for the homing endonucleases (HEGs; GIY-YIG type and LAGLIDADG type). All PCGs are initiated by ATG codons, except for atp8, and all are terminated with TAA. A significant correlation was observed between nucleotide composition and codon preference. Four introns belonging to the group I intron class were predicted, accounting for about 14.54% of the size of the mitogenomes. Phylogenetic analyses confirmed the positions of T. afroharzianum strains within the genus of Trichoderma and supported a sister group relationship between T. afroharzianum and T. simmonsii. The recovered trees also supported the monophyly of all included families and of the genus of Acremonium. The characterization of mitochondrial genome of T. afroharzianum contributes to the understanding of phylogeny and evolution of Hypocreales.
Collapse
Affiliation(s)
- Evrim Özkale
- Faculty of Engineering and Natural Sciences, Department of Biology, Manisa Celal Bayar University, Manisa 45140, Turkiye
| | - Özgül Doğan
- Vocational School of Health Services, Sivas Cumhuriyet University, Sivas 58140, Turkiye
| | - Mahir Budak
- Faculty of Science, Department of Molecular Biology and Genetics, Sivas Cumhuriyet University, Sivas 58140, Turkiye
- Institute of Science, Department of Bioinformatics, Sivas Cumhuriyet University, Sivas 58140, Turkiye
| | - Ertan Mahir Korkmaz
- Faculty of Science, Department of Molecular Biology and Genetics, Sivas Cumhuriyet University, Sivas 58140, Turkiye
- Institute of Science, Department of Bioinformatics, Sivas Cumhuriyet University, Sivas 58140, Turkiye
| |
Collapse
|
7
|
Zhang YJ, Fan XP, Li JN, Zhang S. Mitochondrial genome of Cordyceps blackwelliae: organization, transcription, and evolutionary insights into Cordyceps. IMA Fungus 2023; 14:13. [PMID: 37415259 DOI: 10.1186/s43008-023-00118-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 06/20/2023] [Indexed: 07/08/2023] Open
Abstract
Cordyceps is a diverse genus of insect pathogenic fungi, with about 180 accepted species, including some well-known ones used as ethnic medicine and/or functional food. Nevertheless, mitogenomes are only available for four members of the genus. The current study reports the mitogenome of Cordyceps blackwelliae, a newly described entomopathogenic fungus. The 42,257-bp mitogenome of the fungus encoded genes typically found in fungal mitogenomes, and a total of 14 introns inserted into seven genes, including cob (1 intron), cox1 (4), cox3 (3), nad1 (1), nad4 (1), nad5 (1), and rnl (3). RNA-Seq analysis revealed differential expression of mitochondrial genes and supported annotations resulting from in silico analysis. There was clear evidence for polycistronic transcription and alternative splicing of mitochondrial genes. Comparison among mitogenomes of five different Cordyceps species (i.e., C. blackwelliae, C. chanhua, C. militaris, C. pruinosa, and C. tenuipes) revealed a high synteny, with mitogenome size expansion correlating with intron insertions. Different mitochondrial protein-coding genes showed variable degrees of genetic differentiation among these species, but they were all under purifying selection. Mitochondrial phylogeny based on either nucleotide or amino acid sequences confirmed the taxonomic position of C. blackwelliae in Cordycipitaceae, clustering together with C. chanhua. This study promotes our understanding of fungal evolution in Cordyceps.
Collapse
Affiliation(s)
- Yong-Jie Zhang
- School of Life Science, Shanxi University, Taiyuan, 030006, China.
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Shanxi University, Taiyuan, 030006, China.
| | - Xiang-Ping Fan
- School of Life Science, Shanxi University, Taiyuan, 030006, China
| | - Jia-Ni Li
- School of Life Science, Shanxi University, Taiyuan, 030006, China
| | - Shu Zhang
- School of Life Science, Shanxi University, Taiyuan, 030006, China.
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture and Rural Affairs, Beijing, 100081, China.
| |
Collapse
|
8
|
Tan H, Yu Y, Fu Y, Liu T, Wang Y, Peng W, Wang B, Chen J. Comparative analyses of Flammulina filiformis mitochondrial genomes reveal high length polymorphism in intergenic regions and multiple intron gain/loss in cox1. Int J Biol Macromol 2022; 221:1593-1605. [PMID: 36116598 DOI: 10.1016/j.ijbiomac.2022.09.110] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 08/23/2022] [Accepted: 09/10/2022] [Indexed: 11/30/2022]
Abstract
The golden-needle mushroom Flammulina filiformis is one of the bulk mushroom products in the world. This study obtained complete mitogenomes of 44 wild isolates collected from nine provinces and two artificially bred cultivars of F. filiformis, together with three Flammulina rossica isolates and one Flammulina fennae isolate for comparison. The mitogenome of F. filiformis ranged from 83,540 bp to 90,938 bp, consisting of 14 conserved protein-coding genes (PCGs), two rRNA genes, and 25 tRNA genes. To the best of our knowledge, it contained the highest proportion of intergenic regions compared to the other known Basidiomycota mitogenomes. Introns and intergenic regions were two major contributing factors to the total size of the F. filiformis mitogenome. The conserved PCG cox3 is located in an intron of another conserved PCG, nad5. This is a unique phenomenon in all known fungal mitogenomes. Gain/loss of introns was observed in cox1, nad5, and rnl. Length polymorphism was widely observed in intergenic regions. Accordingly, primers were designed as useful markers for rapid identification of F. filiformis isolates with differentiated mitogenomes. Our findings provide a basis for further studies related to variety identification and population genetics of this economically important mushroom.
Collapse
Affiliation(s)
- Hao Tan
- School of Bioengineering, Jiangnan University, Wuxi, China; Sichuan Institute of Edible Fungi, Sichuan Academy of Agricultural Sciences, Chengdu, China
| | - Yang Yu
- Sichuan Institute of Edible Fungi, Sichuan Academy of Agricultural Sciences, Chengdu, China
| | - Yu Fu
- Sichuan Institute of Edible Fungi, Sichuan Academy of Agricultural Sciences, Chengdu, China; College of Life Sciences, Sichuan University, Chengdu, China
| | - Tianhai Liu
- Sichuan Institute of Edible Fungi, Sichuan Academy of Agricultural Sciences, Chengdu, China
| | - Yong Wang
- Sichuan Institute of Edible Fungi, Sichuan Academy of Agricultural Sciences, Chengdu, China
| | - Weihong Peng
- Sichuan Institute of Edible Fungi, Sichuan Academy of Agricultural Sciences, Chengdu, China
| | - Bo Wang
- Sichuan Institute of Edible Fungi, Sichuan Academy of Agricultural Sciences, Chengdu, China.
| | - Jian Chen
- School of Bioengineering, Jiangnan University, Wuxi, China.
| |
Collapse
|
9
|
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.
Collapse
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.
| |
Collapse
|
10
|
Zhang S, Wang S, Fang Z, Lang BF, Zhang YJ. Characterization of the mitogenome of Gongronella sp. w5 reveals substantial variation in Mucoromycota. Appl Microbiol Biotechnol 2022; 106:2587-2601. [PMID: 35318523 DOI: 10.1007/s00253-022-11880-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Revised: 02/24/2022] [Accepted: 03/06/2022] [Indexed: 11/02/2022]
Abstract
Gongronella is a genus of fungi in Mucorales (Mucoromycota). Some of its members have important biotechnological applications, but until now, not a single mitogenome has been characterized in Gongronella. Here, we present the complete mitogenome assembly of Gongronella sp. w5, a soil isolate known to interact with plants and several fungi. Its 36,593-bp circular mitogenome encodes the large and small subunit rRNAs, 14 standard mitochondrial proteins, 24 tRNAs, three free-standing ORF proteins, and the RNA subunit of RNase P (rnpB). These genes arrange in an order novel to known fungal mitogenomes. Three group I introns are present in the cob, cox1, and nad5 genes, respectively, and they are probably acquired by horizontal gene transfer. Phylogenetic analysis based on mitochondrion-encoded proteins supports the grouping of Gongronella sp. w5 with Absidia glauca, forming the Cunninghamellaceae clade within Mucoromycota. Gongronella and most other Mucoromycota species are predicted to use the standard genetic code in mitochondrial translation, rather than code 4 assigned by GenBank. A comparison among seven publicly available mitogenomes in Mucoromycota reveals the presence of the same 14 typical protein-coding genes plus rnpB, yet substantial variation in mitogenome size, intron number, gene order, and orientation. In this comparison, the uniqueness of Gongronella is evident from similarly large differences to its closest phylogenetic neighbor, A. glauca. This study promotes our understanding of fungal evolution in Mucoromycota. KEY POINTS: • This study reports the first mitogenome in Gongronella, which presents a novel gene order. • Different Mucoromycota mitogenomes show substantial variation of gene organizations. • Most Mucoromycota species use the standard genetic code to translate mitochondrial genes.
Collapse
Affiliation(s)
- Shu Zhang
- School of Life Science, Shanxi University, Taiyuan, 030006, China
| | - Shuang Wang
- School of Life Science, Shanxi University, Taiyuan, 030006, China
| | - Zemin Fang
- School of Life Sciences, Anhui University, Hefei, 230601, China.
| | - B Franz Lang
- Département de Biochimie, Centre Robert Cedergren, Université de Montréal, Montreal, Québec, H3T 1J4, Canada.
| | - Yong-Jie Zhang
- School of Life Science, Shanxi University, Taiyuan, 030006, China.
| |
Collapse
|