1
|
Castrillo ML, Bich GÁ, Amerio NS, Barengo MP, Zapata PD, Saparrat MCN, Villalba LL. Trichoderma koningiopsis (Hypocreaceae) has the smallest mitogenome of the genus Trichoderma. Front Microbiol 2023; 14:1141087. [PMID: 37383640 PMCID: PMC10294050 DOI: 10.3389/fmicb.2023.1141087] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 04/24/2023] [Indexed: 06/30/2023] Open
Abstract
Introduction Fungal mitogenomes exhibit remarkable variation in conformation, size, gene content, arrangement and expression, including their intergenic spacers and introns. Methods The complete mitochondrial genome sequence of the mycoparasitic fungus Trichoderma koningiopsis was determined using the Illumina next-generation sequencing technology. We used data from our recent Illumina NGS-based project of T. koningiopsis genome sequencing to study its mitochondrial genome. The mitogenome was assembled, annotated, and compared with other fungal mitogenomes. Results T. koningiopsis strain POS7 mitogenome is a circular molecule of 27,560 bp long with a GC content of 27.80%. It harbors the whole complement of the 14 conserved mitochondrial protein-coding genes (PCG) such as atp6, atp8, atp9, cox1, cox2, cox3, cob, nad1, nad2, nad3, nad4, nad4L, nad5, and nad6, also found in the same gene order to other Hypocreales. The mitogenome also contains 26 transfer RNA genes (tRNAs), 5 of them with more than one copy. Other genes also present in the assembled mitochondrial genome are a small rRNA subunit and a large rRNA subunit containing ribosomal protein S3 gene. Despite the small genome size, two introns were detected in the T. koningiopsis POS7 mitogenome, one of them in cox3 gene and the other in rnl gene, accounting 7.34% of this mitogenome with a total size of 2,024 bp. A phylogenetic analysis was done using the 14 PCGs genes of T. koningiopsis strain POS7 mitogenome to compare them with those from other fungi of the Subphyla Pezizomycotina and Saccharomycotina. T. koningiopsis strain POS7 was clustered together with other representatives of Trichoderma lineage, within the Hypocreales group, which is also supported by previous phylogenetic studies based on nuclear markers. Discussion The mitochondrial genome of T. koningiopsis POS7 will allow further investigations into the taxonomy, phylogenetics, conservation genetics, and evolutionary biology of this important genus as well as other closely related species.
Collapse
Affiliation(s)
- María Lorena Castrillo
- Laboratorio de Biotecnología Molecular, Instituto de Biotecnología Misiones “Dra. María Ebe Reca”-InBioMis, Universidad Nacional de Misiones, Posadas, Misiones, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Gustavo Ángel Bich
- Laboratorio de Biotecnología Molecular, Instituto de Biotecnología Misiones “Dra. María Ebe Reca”-InBioMis, Universidad Nacional de Misiones, Posadas, Misiones, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Natalia Soledad Amerio
- Laboratorio de Biotecnología Molecular, Instituto de Biotecnología Misiones “Dra. María Ebe Reca”-InBioMis, Universidad Nacional de Misiones, Posadas, Misiones, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Marcela Paola Barengo
- Laboratorio de Biotecnología Molecular, Instituto de Biotecnología Misiones “Dra. María Ebe Reca”-InBioMis, Universidad Nacional de Misiones, Posadas, Misiones, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Pedro Darío Zapata
- Laboratorio de Biotecnología Molecular, Instituto de Biotecnología Misiones “Dra. María Ebe Reca”-InBioMis, Universidad Nacional de Misiones, Posadas, Misiones, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Mario Carlos Nazareno Saparrat
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
- Facultad de Ciencias Agrarias y Forestales, Instituto de Fisiología Vegetal, Universidad Nacional de La Plata, La Plata, Buenos Aires, Argentina
- Facultad de Ciencias Naturales y Museo, Instituto de Botánica Carlos Spegazzini, Universidad Nacional de La Plata, La Plata, Buenos Aires, Argentina
- Cátedra de Microbiología Agrícola, Facultad de Ciencias Agrarias y Forestales, Universidad Nacional de La Plata, La Plata, Buenos Aires, Argentina
| | - Laura Lidia Villalba
- Laboratorio de Biotecnología Molecular, Instituto de Biotecnología Misiones “Dra. María Ebe Reca”-InBioMis, Universidad Nacional de Misiones, Posadas, Misiones, Argentina
| |
Collapse
|
2
|
Zhao Z, Zhu K, Tang D, Wang Y, Wang Y, Zhang G, Geng Y, Yu H. Comparative Analysis of Mitochondrial Genome Features among Four Clonostachys Species and Insight into Their Systematic Positions in the Order Hypocreales. Int J Mol Sci 2021; 22:ijms22115530. [PMID: 34073831 PMCID: PMC8197242 DOI: 10.3390/ijms22115530] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 05/10/2021] [Accepted: 05/17/2021] [Indexed: 12/31/2022] Open
Abstract
The mycoparasite fungi of Clonostachys have contributed to the biological control of plant fungal disease and nematodes. The Clonostachys fungi strains were isolated from Ophiocordyceps highlandensis, Ophiocordycepsnigrolla and soil, which identified as Clonostachyscompactiuscula, Clonostachysrogersoniana, Clonostachyssolani and Clonostachys sp. To explore the evolutionary relationship between the mentioned species, the mitochondrial genomes of four Clonostachys species were sequenced and assembled. The four mitogenomes consisted of complete circular DNA molecules, with the total sizes ranging from 27,410 bp to 42,075 bp. The GC contents, GC skews and AT skews of the mitogenomes varied considerably. Mitogenomic synteny analysis indicated that these mitogenomes underwent gene rearrangements. Among the 15 protein-coding genes within the mitogenomes, the nad4L gene exhibited the least genetic distance, demonstrating a high degree of conservation. The selection pressure analysis of these 15 PCGs were all below 1, indicating that PCGs were subject to purifying selection. Based on protein-coding gene calculation of the significantly supported topologies, the four Clonostachys species were divided into a group in the phylogenetic tree. The results supplemented the database of mitogenomes in Hypocreales order, which might be a useful research tool to conduct a phylogenetic analysis of Clonostachys. Additionally, the suitable molecular marker was significant to study phylogenetic relationships in the Bionectriaceae family.
Collapse
Affiliation(s)
- Zhiyuan Zhao
- College of Ecology and Environmental Sciences, Yunnan University, Kunming 650091, China;
- The International Joint Research Center for Sustainable Utilization of Cordyceps Bioresources in China and Southeast Asia, Yunnan University, Kunming 650091, China; (K.Z.); (D.T.); (Y.W.); (Y.W.); (G.Z.)
| | - Kongfu Zhu
- The International Joint Research Center for Sustainable Utilization of Cordyceps Bioresources in China and Southeast Asia, Yunnan University, Kunming 650091, China; (K.Z.); (D.T.); (Y.W.); (Y.W.); (G.Z.)
| | - Dexiang Tang
- The International Joint Research Center for Sustainable Utilization of Cordyceps Bioresources in China and Southeast Asia, Yunnan University, Kunming 650091, China; (K.Z.); (D.T.); (Y.W.); (Y.W.); (G.Z.)
| | - Yuanbing Wang
- The International Joint Research Center for Sustainable Utilization of Cordyceps Bioresources in China and Southeast Asia, Yunnan University, Kunming 650091, China; (K.Z.); (D.T.); (Y.W.); (Y.W.); (G.Z.)
| | - Yao Wang
- The International Joint Research Center for Sustainable Utilization of Cordyceps Bioresources in China and Southeast Asia, Yunnan University, Kunming 650091, China; (K.Z.); (D.T.); (Y.W.); (Y.W.); (G.Z.)
| | - Guodong Zhang
- The International Joint Research Center for Sustainable Utilization of Cordyceps Bioresources in China and Southeast Asia, Yunnan University, Kunming 650091, China; (K.Z.); (D.T.); (Y.W.); (Y.W.); (G.Z.)
| | - Yupeng Geng
- College of Ecology and Environmental Sciences, Yunnan University, Kunming 650091, China;
- Correspondence: (Y.G.); (H.Y.)
| | - Hong Yu
- College of Ecology and Environmental Sciences, Yunnan University, Kunming 650091, China;
- The International Joint Research Center for Sustainable Utilization of Cordyceps Bioresources in China and Southeast Asia, Yunnan University, Kunming 650091, China; (K.Z.); (D.T.); (Y.W.); (Y.W.); (G.Z.)
- Correspondence: (Y.G.); (H.Y.)
| |
Collapse
|
3
|
Wang XC, Zeng ZQ, Zhuang WY. The complete mitochondrial genome of the bambusicolous fungus Fusarium bambusae (Nectriaceae, Ascomycota). Mitochondrial DNA B Resour 2018; 3:1147-1148. [PMID: 33644384 PMCID: PMC7871986 DOI: 10.1080/23802359.2018.1522979] [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] [Indexed: 11/28/2022] Open
Abstract
The complete nucleotide sequence of the mitochondrial genome of the bambusicolous fungus Fusarium bambusae was determined using the next-generation sequencing technology. The circular molecule is 63,593 bp long with a GC content of 31.92%. Gene prediction revealed 44 genes encoding 15 conserved proteins, 27 tRNAs, and the large and small ribosomal RNAs. All genes are located on the same strand. The tRNA genes contain codons for all 20 standard amino acids. It turns out to be similar to the previously sequenced mitochondrial genomes of Fusarium circinatum and F. verticillioides. The differences lie in the number of introns embodied in protein-coding genes. Four introns exist in the mitochondrial genome of F. verticillioides, 10 in F. bambusae, and 14 in F. circinatum. The phylogenetic analysis confirmed F. bambusae as a member of Fusarium (Nectriaceae). The mitochondrial genome of F. bambusae will contribute to the understanding of phylogeny and evolution of the genus and family.
Collapse
Affiliation(s)
- Xin-Cun Wang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, PR China
| | - Zhao-Qing Zeng
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, PR China
| | - Wen-Ying Zhuang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, PR China
| |
Collapse
|