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Suryanarayanan TS. Crowdsourcing for mining new fungal sources for addressing the need for novel antibiotics against multidrug resistant pathogens. J Antibiot (Tokyo) 2024; 77:335-337. [PMID: 38632393 DOI: 10.1038/s41429-024-00723-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2024] [Revised: 03/18/2024] [Accepted: 03/22/2024] [Indexed: 04/19/2024]
Abstract
There are a limited number of new antibiotics to manage the health crisis caused by the evolution and spread of antimicrobial resistant (AMR) bacteria including multidrug resistant (MDR), extensively drug-resistant (XDR) and pan-drug-resistant (PDR) ones. Bioprospecting fungi of less studied and extreme environments using new and less used older approaches could reveal novel antibiotics to manage MDR pathogens. Furthermore, I posit a crowdsourcing model which could substantially increase the chances of discovering novel antibiotics as well as new chemotypes for other therapeutic areas and considerably reduce the cost and time of this exercise.
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Affiliation(s)
- T S Suryanarayanan
- Vivekananda Institute of Tropical Mycology, Ramakrishna Mission Vidyapith, Chennai, India.
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2
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Bao Y, Deng J, Akbar S, Duan Z, Zhang C, Lin W, Wu S, Yue Y, Yao W, Xu J, Zhang M. Genome-Wide Identification and Characterization of Homeobox Transcription Factors in Phoma sorghina var. saccharum Causing Sugarcane Twisted Leaf Disease. Int J Mol Sci 2024; 25:5346. [PMID: 38791383 PMCID: PMC11121360 DOI: 10.3390/ijms25105346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Revised: 05/07/2024] [Accepted: 05/10/2024] [Indexed: 05/26/2024] Open
Abstract
A homeobox transcription factor is a conserved transcription factor, ubiquitous in eukaryotes, that regulates the tissue formation of structure, cell differentiation, proliferation, and cancer. This study identified the homeobox transcription factor family and its distribution in Phoma sorghina var. saccharum at the whole genome level. It elucidated the gene structures and evolutionary characteristics of this family. Additionally, knockout experiments were carried out and the preliminary function of these transcription factors was studied. Through bioinformatics approaches, nine homeobox transcription factors (PsHOX1-PsHOX9) were identified in P. sorghina var. saccharum, and these contained HOX-conserved domains and helix-turn-helix secondary structures. Nine homeobox gene deletion mutants were obtained using the homologous recombinant gene knockout technique. Protoplast transformation was mediated by polyethylene glycol (PEG) and the transformants were identified using PCR. The knockouts of PsHOX1, PsHOX2, PsHOX3, PsHOX4, PsHOX6, PsHOX8, and PsHOX9 genes resulted in a smaller growth diameter in P. sorghina var. saccharum. In contrast, the knockouts of the PsHOX3, PsHOX6, and PsHOX9 genes inhibited the formation of conidia and led to a significant decrease in the pathogenicity. This study's results will provide insights for understanding the growth and development of P. sorghina var. saccharum. The pathogenic mechanism of the affected sugarcane will provide an essential theoretical basis for preventing and controlling sugarcane twisted leaf disease.
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Affiliation(s)
- Yixue Bao
- State Key Lab for Conservation and Utilization of Subtropical Agric-Biological Resources & Guangxi Key Lab for Sugarcane Biology, Guangxi University, Nanning 530004, China; (Y.B.)
| | - Jinlan Deng
- State Key Lab for Conservation and Utilization of Subtropical Agric-Biological Resources & Guangxi Key Lab for Sugarcane Biology, Guangxi University, Nanning 530004, China; (Y.B.)
| | - Sehrish Akbar
- State Key Lab for Conservation and Utilization of Subtropical Agric-Biological Resources & Guangxi Key Lab for Sugarcane Biology, Guangxi University, Nanning 530004, China; (Y.B.)
| | - Zhenzhen Duan
- State Key Lab for Conservation and Utilization of Subtropical Agric-Biological Resources & Guangxi Key Lab for Sugarcane Biology, Guangxi University, Nanning 530004, China; (Y.B.)
| | - Chi Zhang
- State Key Lab for Conservation and Utilization of Subtropical Agric-Biological Resources & Guangxi Key Lab for Sugarcane Biology, Guangxi University, Nanning 530004, China; (Y.B.)
| | - Wenfeng Lin
- State Key Lab for Conservation and Utilization of Subtropical Agric-Biological Resources & Guangxi Key Lab for Sugarcane Biology, Guangxi University, Nanning 530004, China; (Y.B.)
| | - Suyan Wu
- State Key Lab for Conservation and Utilization of Subtropical Agric-Biological Resources & Guangxi Key Lab for Sugarcane Biology, Guangxi University, Nanning 530004, China; (Y.B.)
| | - Yabing Yue
- State Key Lab for Conservation and Utilization of Subtropical Agric-Biological Resources & Guangxi Key Lab for Sugarcane Biology, Guangxi University, Nanning 530004, China; (Y.B.)
| | - Wei Yao
- State Key Lab for Conservation and Utilization of Subtropical Agric-Biological Resources & Guangxi Key Lab for Sugarcane Biology, Guangxi University, Nanning 530004, China; (Y.B.)
| | - Jianlong Xu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Muqing Zhang
- State Key Lab for Conservation and Utilization of Subtropical Agric-Biological Resources & Guangxi Key Lab for Sugarcane Biology, Guangxi University, Nanning 530004, China; (Y.B.)
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3
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Castañeda-Casasola CC, Nieto-Jacobo MF, Soares A, Padilla-Padilla EA, Anducho-Reyes MA, Brown C, Soth S, Esquivel-Naranjo EU, Hampton J, Mendoza-Mendoza A. Unveiling a Microexon Switch: Novel Regulation of the Activities of Sugar Assimilation and Plant-Cell-Wall-Degrading Xylanases and Cellulases by Xlr2 in Trichoderma virens. Int J Mol Sci 2024; 25:5172. [PMID: 38791210 PMCID: PMC11121469 DOI: 10.3390/ijms25105172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 05/02/2024] [Accepted: 05/06/2024] [Indexed: 05/26/2024] Open
Abstract
Functional microexons have not previously been described in filamentous fungi. Here, we describe a novel mechanism of transcriptional regulation in Trichoderma requiring the inclusion of a microexon from the Xlr2 gene. In low-glucose environments, a long mRNA including the microexon encodes a protein with a GAL4-like DNA-binding domain (Xlr2-α), whereas in high-glucose environments, a short mRNA that is produced encodes a protein lacking this DNA-binding domain (Xlr2-β). Interestingly, the protein isoforms differ in their impact on cellulase and xylanase activity. Deleting the Xlr2 gene reduced both xylanase and cellulase activity and growth on different carbon sources, such as carboxymethylcellulose, xylan, glucose, and arabinose. The overexpression of either Xlr2-α or Xlr2-β in T. virens showed that the short isoform (Xlr2-β) caused higher xylanase activity than the wild types or the long isoform (Xlr2-α). Conversely, cellulase activity did not increase when overexpressing Xlr2-β but was increased with the overexpression of Xlr2-α. This is the first report of a novel transcriptional regulation mechanism of plant-cell-wall-degrading enzyme activity in T. virens. This involves the differential expression of a microexon from a gene encoding a transcriptional regulator.
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Affiliation(s)
- Cynthia Coccet Castañeda-Casasola
- Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln 7647, New Zealand; (C.C.C.-C.); (A.S.); (E.A.P.-P.); (S.S.); (E.U.E.-N.); (J.H.)
- Laboratorio de AgroBiotecnología, Universidad Politécnica de Pachuca, Carretera Pachuca-Cd. Sahagún, km 20, ExHacienda de Santa Bárbara, Zempoala 43830, Mexico;
- Servicio Nacional de Sanidad, Inocuidad y Calidad Agroalimentaria, Centro Nacional de Referencia Fitosanitaria, Tecamac 55740, Mexico
| | | | - Amanda Soares
- Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln 7647, New Zealand; (C.C.C.-C.); (A.S.); (E.A.P.-P.); (S.S.); (E.U.E.-N.); (J.H.)
| | - Emir Alejandro Padilla-Padilla
- Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln 7647, New Zealand; (C.C.C.-C.); (A.S.); (E.A.P.-P.); (S.S.); (E.U.E.-N.); (J.H.)
- Department of Biochemistry, School of Biomedical Sciences, University of Otago, Dunedin 9054, New Zealand;
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca 04510, Mexico
| | - Miguel Angel Anducho-Reyes
- Laboratorio de AgroBiotecnología, Universidad Politécnica de Pachuca, Carretera Pachuca-Cd. Sahagún, km 20, ExHacienda de Santa Bárbara, Zempoala 43830, Mexico;
| | - Chris Brown
- Department of Biochemistry, School of Biomedical Sciences, University of Otago, Dunedin 9054, New Zealand;
| | - Sereyboth Soth
- Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln 7647, New Zealand; (C.C.C.-C.); (A.S.); (E.A.P.-P.); (S.S.); (E.U.E.-N.); (J.H.)
| | - Edgardo Ulises Esquivel-Naranjo
- Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln 7647, New Zealand; (C.C.C.-C.); (A.S.); (E.A.P.-P.); (S.S.); (E.U.E.-N.); (J.H.)
- Unit for Basic and Applied Microbiology, Faculty of Natural Sciences, Autonomous University of Queretaro, Queretaro 76230, Mexico
| | - John Hampton
- Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln 7647, New Zealand; (C.C.C.-C.); (A.S.); (E.A.P.-P.); (S.S.); (E.U.E.-N.); (J.H.)
| | - Artemio Mendoza-Mendoza
- Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln 7647, New Zealand; (C.C.C.-C.); (A.S.); (E.A.P.-P.); (S.S.); (E.U.E.-N.); (J.H.)
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4
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Hariri Akbari F, Song Z, Turk M, Gunde-Cimerman N, Gostinčar C. Experimental evolution of extremotolerant and extremophilic fungi under osmotic stress. IUBMB Life 2024. [PMID: 38647201 DOI: 10.1002/iub.2825] [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: 12/29/2023] [Accepted: 03/15/2024] [Indexed: 04/25/2024]
Abstract
Experimental evolution was carried out to investigate the adaptive responses of extremotolerant fungi to a stressful environment. For 12 cultivation cycles, the halotolerant black yeasts Aureobasidium pullulans and Aureobasidium subglaciale were grown at high NaCl or glycerol concentrations, and the halophilic basidiomycete Wallemia ichthyophaga was grown close to its lower NaCl growth limit. All evolved Aureobasidium spp. accelerated their growth at low water activity. Whole genomes of the evolved strains were sequenced. No aneuploidies were detected in any of the genomes, contrary to previous studies on experimental evolution at high salinity with other species. However, several hundred single-nucleotide polymorphisms were identified compared with the genomes of the progenitor strains. Two functional groups of genes were overrepresented among the genes presumably affected by single-nucleotide polymorphisms: voltage-gated potassium channels in A. pullulans at high NaCl concentration, and hydrophobins in W. ichthyophaga at low NaCl concentration. Both groups of genes were previously associated with adaptation to high salinity. Finally, most evolved Aureobasidium spp. strains were found to have increased intracellular and decreased extracellular glycerol concentrations at high salinity, suggesting that the strains have optimised their management of glycerol, their most important compatible solute. Experimental evolution therefore not only confirmed the role of potassium transport, glycerol management, and cell wall in survival at low water activity, but also demonstrated that fungi from extreme environments can further improve their growth rates under constant extreme conditions in a relatively short time and without large scale genomic rearrangements.
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Affiliation(s)
- Farhad Hariri Akbari
- Biotechnical Faculty, Department of Biology, University of Ljubljana, Ljubljana, Slovenia
| | - Zewei Song
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Martina Turk
- Biotechnical Faculty, Department of Biology, University of Ljubljana, Ljubljana, Slovenia
| | - Nina Gunde-Cimerman
- Biotechnical Faculty, Department of Biology, University of Ljubljana, Ljubljana, Slovenia
| | - Cene Gostinčar
- Biotechnical Faculty, Department of Biology, University of Ljubljana, Ljubljana, Slovenia
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Karamad V, Sogutlu F, Ozkaya FC, Shademan B, Ebrahim W, El-Neketi M, Avci CB. Investigation of iso-propylchaetominine anticancer activity on apoptosis, cell cycle and Wnt signaling pathway in different cancer models. Fitoterapia 2024; 173:105789. [PMID: 38158162 DOI: 10.1016/j.fitote.2023.105789] [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: 08/03/2023] [Revised: 11/29/2023] [Accepted: 12/20/2023] [Indexed: 01/03/2024]
Abstract
Dysregulation of the Wnt signaling pathway contributes to the development of many cancer types. Natural compounds produced with biotechnological systems have been the focus of research for being a new drug candidate both with unlimited resources and cost-effective production. In this study, it was aimed to reveal the effects of isopropylchaetominine on cytotoxic, cytostatic, apoptotic and Wnt signaling pathways in brain, pancreatic and prostate cancer. The IC50 values of isopropylchaetominine in U-87 MG, PANC1, PC3 and LNCaP cells were calculated as 91.94 μM, 41.68 μM, 54.54 μM and 7.86 μM in 72nd h, respectively. The metabolite arrests the cell cycle in G0/G1 phase in each cancer cells. Iso-propylchaetominine induced a 4.3-fold and 1.9-fold increase in apoptosis in PC3 and PANC1 cells, respectively. The toxicity of isopropylchaetominine in healthy fibroblast cells was assessed using the annexin V method, and no significant apoptotic activity was observed between the groups treated with the active substance and untreated. In U-87 MG, PANC1, PC3, and LNCaP cells under treatment with isopropylchaetominin, the expression levels of DKK3, TLE1, AES, DKK1, FRZB, DAB2, AXIN1/2, PPARD, SFRP4, APC and SOX17 tumor suppressor genes increased significantly. Decreases in expression of Wnt1, Wnt2, Wnt3, Wnt4, Wnt5, Wnt6, Wnt10, Wnt11, FRZ2, FRZ3, FRZ7, TCF7L1, BCL9, PYGO, CCND2, c-MYC, WISP1 and CTNNB1 oncogenic genes were detected. All these result shows that isopropylchaetominine can present promising new treatment strategy in different cancer types.
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Affiliation(s)
- Vahidreza Karamad
- Department of Medical Biology, Faculty of Medicine, Ege University, Izmir 35100, Turkey
| | - Fatma Sogutlu
- Department of Medical Biology, Faculty of Medicine, Ege University, Izmir 35100, Turkey
| | - Ferhat Can Ozkaya
- Aliaga Industrial Zone Technology Transfer Office, Aliaga, İzmir 35800, Turkey
| | - Behrouz Shademan
- Stem cell Research Center, Tabriz University of Medical Sciences, Tabriz 51666-16471, Iran
| | - Weaam Ebrahim
- Department of Pharmacognosy, Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt
| | - Mona El-Neketi
- Department of Pharmacognosy, Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt
| | - Cigir Biray Avci
- Department of Medical Biology, Faculty of Medicine, Ege University, Izmir 35100, Turkey.
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6
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Erdos Z, Studholme DJ, Sharma MD, Chandler D, Bass C, Raymond B. Manipulating multi-level selection in a fungal entomopathogen reveals social conflicts and a method for improving biocontrol traits. PLoS Pathog 2024; 20:e1011775. [PMID: 38527086 PMCID: PMC10994555 DOI: 10.1371/journal.ppat.1011775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 04/04/2024] [Accepted: 03/09/2024] [Indexed: 03/27/2024] Open
Abstract
Changes in parasite virulence are commonly expected to lead to trade-offs in other life history traits that can affect fitness. Understanding these trade-offs is particularly important if we want to manipulate the virulence of microbial biological control agents. Theoretically, selection across different spatial scales, i.e. between- and within-hosts, shapes these trade-offs. However, trade-offs are also dependent on parasite biology. Despite their applied importance the evolution of virulence in fungal parasites is poorly understood: virulence can be unstable in culture and commonly fails to increase in simple passage experiments. We hypothesized that manipulating selection intensity at different scales would reveal virulence trade-offs in a fungal pathogen of aphids, Akanthomyces muscarius. Starting with a genetically diverse stock we selected for speed of kill, parasite yield or infectivity by manipulating competition within and between hosts and between-populations of hosts over 7 rounds of infection. We characterized ancestral and evolved lineages by whole genome sequencing and by measuring virulence, growth rate, sporulation and fitness. While several lineages showed increases in virulence, we saw none of the trade-offs commonly found in obligately-killing parasites. Phenotypically similar lineages within treatments often shared multiple single-nucleotide variants, indicating strong convergent evolution. The most dramatic phenotypic changes were in timing of sporulation and spore production in vitro. We found that early sporulation led to reduced competitive fitness but could increase yield of spores on media, a trade-off characteristic of social conflict. Notably, the selection regime with strongest between-population competition and lowest genetic diversity produced the most consistent shift to early sporulation, as predicted by social evolution theory. Multi-level selection therefore revealed social interactions novel to fungi and showed that these biocontrol agents have the genomic flexibility to improve multiple traits-virulence and spore production-that are often in conflict in other parasites.
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Affiliation(s)
- Zoltan Erdos
- Centre for Ecology and Conservation, University of Exeter, Penryn, United Kingdom
| | | | - Manmohan D. Sharma
- Centre for Ecology and Conservation, University of Exeter, Penryn, United Kingdom
| | - David Chandler
- School of Life Sciences, The University of Warwick, Coventry, United Kingdom
| | - Chris Bass
- Centre for Ecology and Conservation, University of Exeter, Penryn, United Kingdom
| | - Ben Raymond
- Centre for Ecology and Conservation, University of Exeter, Penryn, United Kingdom
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Gupta A, Kang K, Pathania R, Saxton L, Saucedo B, Malik A, Torres-Tiji Y, Diaz CJ, Dutra Molino JV, Mayfield SP. Harnessing genetic engineering to drive economic bioproduct production in algae. Front Bioeng Biotechnol 2024; 12:1350722. [PMID: 38347913 PMCID: PMC10859422 DOI: 10.3389/fbioe.2024.1350722] [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: 12/05/2023] [Accepted: 01/16/2024] [Indexed: 02/15/2024] Open
Abstract
Our reliance on agriculture for sustenance, healthcare, and resources has been essential since the dawn of civilization. However, traditional agricultural practices are no longer adequate to meet the demands of a burgeoning population amidst climate-driven agricultural challenges. Microalgae emerge as a beacon of hope, offering a sustainable and renewable source of food, animal feed, and energy. Their rapid growth rates, adaptability to non-arable land and non-potable water, and diverse bioproduct range, encompassing biofuels and nutraceuticals, position them as a cornerstone of future resource management. Furthermore, microalgae's ability to capture carbon aligns with environmental conservation goals. While microalgae offers significant benefits, obstacles in cost-effective biomass production persist, which curtails broader application. This review examines microalgae compared to other host platforms, highlighting current innovative approaches aimed at overcoming existing barriers. These approaches include a range of techniques, from gene editing, synthetic promoters, and mutagenesis to selective breeding and metabolic engineering through transcription factors.
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Affiliation(s)
- Abhishek Gupta
- Mayfield Laboratory, Department of Molecular Biology, School of Biological Sciences, University of California San Diego, San Diego, CA, United States
| | - Kalisa Kang
- Mayfield Laboratory, Department of Molecular Biology, School of Biological Sciences, University of California San Diego, San Diego, CA, United States
| | - Ruchi Pathania
- Mayfield Laboratory, Department of Molecular Biology, School of Biological Sciences, University of California San Diego, San Diego, CA, United States
| | - Lisa Saxton
- Mayfield Laboratory, Department of Molecular Biology, School of Biological Sciences, University of California San Diego, San Diego, CA, United States
| | - Barbara Saucedo
- Mayfield Laboratory, Department of Molecular Biology, School of Biological Sciences, University of California San Diego, San Diego, CA, United States
| | - Ashleyn Malik
- Mayfield Laboratory, Department of Molecular Biology, School of Biological Sciences, University of California San Diego, San Diego, CA, United States
| | - Yasin Torres-Tiji
- Mayfield Laboratory, Department of Molecular Biology, School of Biological Sciences, University of California San Diego, San Diego, CA, United States
| | - Crisandra J. Diaz
- Mayfield Laboratory, Department of Molecular Biology, School of Biological Sciences, University of California San Diego, San Diego, CA, United States
| | - João Vitor Dutra Molino
- Mayfield Laboratory, Department of Molecular Biology, School of Biological Sciences, University of California San Diego, San Diego, CA, United States
| | - Stephen P. Mayfield
- Mayfield Laboratory, Department of Molecular Biology, School of Biological Sciences, University of California San Diego, San Diego, CA, United States
- California Center for Algae Biotechnology, University of California San Diego, San Diego, CA, United States
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8
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Qi Z, Lu P, Long X, Cao X, Wu M, Xin K, Xue T, Gao X, Huang Y, Wang Q, Jiang C, Xu JR, Liu H. Adaptive advantages of restorative RNA editing in fungi for resolving survival-reproduction trade-offs. SCIENCE ADVANCES 2024; 10:eadk6130. [PMID: 38181075 PMCID: PMC10776026 DOI: 10.1126/sciadv.adk6130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 12/05/2023] [Indexed: 01/07/2024]
Abstract
RNA editing in various organisms commonly restores RNA sequences to their ancestral state, but its adaptive advantages are debated. In fungi, restorative editing corrects premature stop codons in pseudogenes specifically during sexual reproduction. We characterized 71 pseudogenes and their restorative editing in Fusarium graminearum, demonstrating that restorative editing of 16 pseudogenes is crucial for germ tissue development in fruiting bodies. Our results also revealed that the emergence of premature stop codons is facilitated by restorative editing and that premature stop codons corrected by restorative editing are selectively favored over ancestral amino acid codons. Furthermore, we found that ancestral versions of pseudogenes have antagonistic effects on reproduction and survival. Restorative editing eliminates the survival costs of reproduction caused by antagonistic pleiotropy and provides a selective advantage in fungi. Our findings highlight the importance of restorative editing in the evolution of fungal complex multicellularity and provide empirical evidence that restorative editing serves as an adaptive mechanism enabling the resolution of genetic trade-offs.
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Affiliation(s)
- Zhaomei Qi
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Ping Lu
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xinyuan Long
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xinyu Cao
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Mengchun Wu
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Kaiyun Xin
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Tuan Xue
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xinlong Gao
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yi Huang
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Qinhu Wang
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Cong Jiang
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Jin-Rong Xu
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907, USA
| | - Huiquan Liu
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
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9
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McLaughlin JF, Brock KM, Gates I, Pethkar A, Piattoni M, Rossi A, Lipshutz SE. Multivariate Models of Animal Sex: Breaking Binaries Leads to a Better Understanding of Ecology and Evolution. Integr Comp Biol 2023; 63:891-906. [PMID: 37156506 PMCID: PMC10563656 DOI: 10.1093/icb/icad027] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 04/28/2023] [Accepted: 05/05/2023] [Indexed: 05/10/2023] Open
Abstract
"Sex" is often used to describe a suite of phenotypic and genotypic traits of an organism related to reproduction. However, these traits-gamete type, chromosomal inheritance, physiology, morphology, behavior, etc.-are not necessarily coupled, and the rhetorical collapse of variation into a single term elides much of the complexity inherent in sexual phenotypes. We argue that consideration of "sex" as a constructed category operating at multiple biological levels opens up new avenues for inquiry in our study of biological variation. We apply this framework to three case studies that illustrate the diversity of sex variation, from decoupling sexual phenotypes to the evolutionary and ecological consequences of intrasexual polymorphisms. We argue that instead of assuming binary sex in these systems, some may be better categorized as multivariate and nonbinary. Finally, we conduct a meta-analysis of terms used to describe diversity in sexual phenotypes in the scientific literature to highlight how a multivariate model of sex can clarify, rather than cloud, studies of sexual diversity within and across species. We argue that such an expanded framework of "sex" better equips us to understand evolutionary processes, and that as biologists, it is incumbent upon us to push back against misunderstandings of the biology of sexual phenotypes that enact harm on marginalized communities.
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Affiliation(s)
- J F McLaughlin
- Department of Environmental Science, Policy, and Management, College of Natural Resources, University of California, Berkeley, CA 94720, USA
| | - Kinsey M Brock
- Department of Environmental Science, Policy, and Management, College of Natural Resources, University of California, Berkeley, CA 94720, USA
- Museum of Vertebrate Zoology, University of California, Berkeley, CA 94720, USA
- Department of Biology, San Diego State University, San Diego, CA 92182, USA
| | - Isabella Gates
- Department of Biology, Loyola University Chicago, Chicago, IL 60660, USA
| | - Anisha Pethkar
- Department of Biology, Loyola University Chicago, Chicago, IL 60660, USA
| | - Marcus Piattoni
- Department of Biology, Loyola University Chicago, Chicago, IL 60660, USA
| | - Alexis Rossi
- Department of Biology, Loyola University Chicago, Chicago, IL 60660, USA
| | - Sara E Lipshutz
- Department of Biology, Loyola University Chicago, Chicago, IL 60660, USA
- Department of Biology, Duke University, Durham, NC 27708, USA
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10
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Aanen DK, van ’t Padje A, Auxier B. Longevity of Fungal Mycelia and Nuclear Quality Checks: a New Hypothesis for the Role of Clamp Connections in Dikaryons. Microbiol Mol Biol Rev 2023; 87:e0002221. [PMID: 37409939 PMCID: PMC10521366 DOI: 10.1128/mmbr.00022-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/07/2023] Open
Abstract
This paper addresses the stability of mycelial growth in fungi and differences between ascomycetes and basidiomycetes. Starting with general evolutionary theories of multicellularity and the role of sex, we then discuss individuality in fungi. Recent research has demonstrated the deleterious consequences of nucleus-level selection in fungal mycelia, favoring cheaters with a nucleus-level benefit during spore formation but a negative effect on mycelium-level fitness. Cheaters appear to generally be loss-of-fusion (LOF) mutants, with a higher propensity to form aerial hyphae developing into asexual spores. Since LOF mutants rely on heterokaryosis with wild-type nuclei, we argue that regular single-spore bottlenecks can efficiently select against such cheater mutants. We then zoom in on ecological differences between ascomycetes being typically fast-growing but short-lived with frequent asexual-spore bottlenecks and basidiomycetes being generally slow-growing but long-lived and usually without asexual-spore bottlenecks. We argue that these life history differences have coevolved with stricter nuclear quality checks in basidiomycetes. Specifically, we propose a new function for clamp connections, structures formed during the sexual stage in ascomycetes and basidiomycetes but during somatic growth only in basidiomycete dikaryons. During dikaryon cell division, the two haploid nuclei temporarily enter a monokaryotic phase, by alternatingly entering a retrograde-growing clamp cell, which subsequently fuses with the subapical cell to recover the dikaryotic cell. We hypothesize that clamp connections act as screening devices for nuclear quality, with both nuclei continuously testing each other for fusion ability, a test that LOF mutants will fail. By linking differences in longevity of the mycelial phase to ecology and stringency of nuclear quality checks, we propose that mycelia have a constant and low lifetime cheating risk, irrespective of their size and longevity.
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Affiliation(s)
- Duur K. Aanen
- Department of Plant Sciences, Laboratory of Genetics, Wageningen University, Wageningen, The Netherlands
| | - Anouk van ’t Padje
- Department of Plant Sciences, Laboratory of Genetics, Wageningen University, Wageningen, The Netherlands
| | - Benjamin Auxier
- Department of Plant Sciences, Laboratory of Genetics, Wageningen University, Wageningen, The Netherlands
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11
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Song X, Chen M, Zhao Y, Zhang M, Zhang L, Zhang D, Song C, Shang X, Tan Q. Multi-stage nuclear transcriptomic insights of morphogenesis and biparental role changes in Lentinula edodes. Appl Microbiol Biotechnol 2023:10.1007/s00253-023-12624-y. [PMID: 37439832 DOI: 10.1007/s00253-023-12624-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2023] [Revised: 05/24/2023] [Accepted: 05/26/2023] [Indexed: 07/14/2023]
Abstract
Based on six offspring with different mitochondrial (M) and parental nuclear (N) genotypes, the multi-stage morphological characteristics and nuclear transcriptomes of Lentinula edodes were compared to investigate morphogenesis mechanisms during cultivation, the key reason for cultivar resistance to genotype changes, and regulation related to biparental role changes. Six offspring had specific transcriptomic data and morphological characteristics that were mainly regulated by the two parental nuclei, followed by the cytoplasm, at different growth stages. Importing a wild N genotype easily leads to failure or instability of fruiting; however, importing wild M genotypes may improve cultivars. Major facilitator superfamily (MFS) transporter genes encoding specific metabolites in spawns may play crucial roles in fruiting body formation. Pellets from submerged cultivation and spawns from sawdust substrate cultivation showed different carbon metabolic pathways, especially in secondary metabolism, degradation of lignin, cellulose and hemicellulose, and plasma membrane transport (mainly MFS). When the stage of small young pileus (SYP) was formed on the surface of the bag, the spawns inside were mainly involved in nutrient accumulation. Just broken pileus (JBP) showed a different expression of plasma membrane transporter genes related to intracellular material transport compared to SYP and showed different ribosomal proteins and cytochrome P450 functioning in protein biosynthesis and metabolism than near spreading pileus (NSP). Biparental roles mainly regulate offspring metabolism, growth, and morphogenesis by differentially expressing specific genes during different vegetative growth stages. Additionally, some genes encoding glycine-rich RNA-binding proteins, F-box, and folliculin-interacting protein repeat-containing proteins may be related to multi-stage morphogenesis. KEY POINTS: • Replacement of nuclear genotype is not suitable for cultivar breeding of L. edodes. • Some genes show a biparental role-divergent expression at mycelial growth stage. • Transcriptomic changes of some sawdust substrate cultivation stages have been elucidated.
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Affiliation(s)
- Xiaoxia Song
- Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, 201403, People's Republic of China
| | - Mingjie Chen
- Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, 201403, People's Republic of China
| | - Yan Zhao
- Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, 201403, People's Republic of China
| | - Meiyan Zhang
- Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, 201403, People's Republic of China
| | - Lujun Zhang
- Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, 201403, People's Republic of China
| | - Dang Zhang
- Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, 201403, People's Republic of China
| | - Chunyan Song
- Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, 201403, People's Republic of China.
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China.
| | - Xiaodong Shang
- Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, 201403, People's Republic of China
| | - Qi Tan
- Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, 201403, People's Republic of China
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Wang Z, Kim W, Wang YW, Yakubovich E, Dong C, Trail F, Townsend JP, Yarden O. The Sordariomycetes: an expanding resource with Big Data for mining in evolutionary genomics and transcriptomics. FRONTIERS IN FUNGAL BIOLOGY 2023; 4:1214537. [PMID: 37746130 PMCID: PMC10512317 DOI: 10.3389/ffunb.2023.1214537] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Accepted: 06/06/2023] [Indexed: 09/26/2023]
Abstract
Advances in genomics and transcriptomics accompanying the rapid accumulation of omics data have provided new tools that have transformed and expanded the traditional concepts of model fungi. Evolutionary genomics and transcriptomics have flourished with the use of classical and newer fungal models that facilitate the study of diverse topics encompassing fungal biology and development. Technological advances have also created the opportunity to obtain and mine large datasets. One such continuously growing dataset is that of the Sordariomycetes, which exhibit a richness of species, ecological diversity, economic importance, and a profound research history on amenable models. Currently, 3,574 species of this class have been sequenced, comprising nearly one-third of the available ascomycete genomes. Among these genomes, multiple representatives of the model genera Fusarium, Neurospora, and Trichoderma are present. In this review, we examine recently published studies and data on the Sordariomycetes that have contributed novel insights to the field of fungal evolution via integrative analyses of the genetic, pathogenic, and other biological characteristics of the fungi. Some of these studies applied ancestral state analysis of gene expression among divergent lineages to infer regulatory network models, identify key genetic elements in fungal sexual development, and investigate the regulation of conidial germination and secondary metabolism. Such multispecies investigations address challenges in the study of fungal evolutionary genomics derived from studies that are often based on limited model genomes and that primarily focus on the aspects of biology driven by knowledge drawn from a few model species. Rapidly accumulating information and expanding capabilities for systems biological analysis of Big Data are setting the stage for the expansion of the concept of model systems from unitary taxonomic species/genera to inclusive clusters of well-studied models that can facilitate both the in-depth study of specific lineages and also investigation of trait diversity across lineages. The Sordariomycetes class, in particular, offers abundant omics data and a large and active global research community. As such, the Sordariomycetes can form a core omics clade, providing a blueprint for the expansion of our knowledge of evolution at the genomic scale in the exciting era of Big Data and artificial intelligence, and serving as a reference for the future analysis of different taxonomic levels within the fungal kingdom.
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Affiliation(s)
- Zheng Wang
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, United States
| | - Wonyong Kim
- Korean Lichen Research Institute, Sunchon National University, Suncheon, Republic of Korea
| | - Yen-Wen Wang
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, United States
| | - Elizabeta Yakubovich
- Department of Plant Pathology and Microbiology, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Caihong Dong
- Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Frances Trail
- Department of Plant Biology, Michigan State University, East Lansing, MI, United States
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, United States
| | - Jeffrey P. Townsend
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, United States
- Department of Ecology and Evolutionary Biology, Program in Microbiology, and Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, United States
| | - Oded Yarden
- Department of Plant Pathology and Microbiology, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
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13
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In silico environmental sampling of emerging fungal pathogens via big data analysis. FUNGAL ECOL 2023. [DOI: 10.1016/j.funeco.2022.101212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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14
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Hartmann P, Schnabl B. Fungal infections and the fungal microbiome in hepatobiliary disorders. J Hepatol 2023; 78:836-851. [PMID: 36565724 PMCID: PMC10033447 DOI: 10.1016/j.jhep.2022.12.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 12/05/2022] [Accepted: 12/07/2022] [Indexed: 12/24/2022]
Abstract
Liver and biliary diseases affect more than a billion people worldwide, with high associated morbidity and mortality. The impact of the intestinal bacterial microbiome on liver diseases has been well established. However, the fungal microbiome, or mycobiome, has been overlooked for a long time. Recently, several studies have shed light on the role of the mycobiome in the development and progression of hepatobiliary diseases. In particular, the fungal genus Candida has been found to be involved in the pathogenesis of multiple hepatobiliary conditions. Herein, we compare colonisation and infection, describe mycobiome findings in the healthy state and across the various hepatobiliary conditions, and point toward communalities. We detail how quantitation of immune responses to fungal antigens can be employed to predict disease severity, e.g. using antibodies to Saccharomyces cerevisiae or specific anti-Candida albicans antibodies. We also show how fungal products (e.g. beta-glucans, candidalysin) activate the host's immune system to exacerbate liver and biliary diseases. Finally, we describe how the gut mycobiome can be modulated to ameliorate hepatobiliary conditions.
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Affiliation(s)
- Phillipp Hartmann
- Department of Medicine, University of California San Diego, La Jolla, CA, USA; Department of Pediatrics, University of California San Diego, La Jolla, CA, USA; Division of Gastroenterology, Hepatology & Nutrition, Rady Children's Hospital San Diego, San Diego, CA, USA
| | - Bernd Schnabl
- Department of Medicine, University of California San Diego, La Jolla, CA, USA; Department of Medicine, VA San Diego Healthcare System, San Diego, CA, USA.
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15
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Bhunjun CS, Phukhamsakda C, Hyde KD, McKenzie EHC, Saxena RK, Li Q. Do all fungi have ancestors with endophytic lifestyles? FUNGAL DIVERS 2023. [DOI: 10.1007/s13225-023-00516-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2023]
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16
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Sierra-Patev S, Min B, Naranjo-Ortiz M, Looney B, Konkel Z, Slot JC, Sakamoto Y, Steenwyk JL, Rokas A, Carro J, Camarero S, Ferreira P, Molpeceres G, Ruiz-Dueñas FJ, Serrano A, Henrissat B, Drula E, Hughes KW, Mata JL, Ishikawa NK, Vargas-Isla R, Ushijima S, Smith CA, Donoghue J, Ahrendt S, Andreopoulos W, He G, LaButti K, Lipzen A, Ng V, Riley R, Sandor L, Barry K, Martínez AT, Xiao Y, Gibbons JG, Terashima K, Grigoriev IV, Hibbett D. A global phylogenomic analysis of the shiitake genus Lentinula. Proc Natl Acad Sci U S A 2023; 120:e2214076120. [PMID: 36848567 PMCID: PMC10013852 DOI: 10.1073/pnas.2214076120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Accepted: 12/22/2022] [Indexed: 03/01/2023] Open
Abstract
Lentinula is a broadly distributed group of fungi that contains the cultivated shiitake mushroom, L. edodes. We sequenced 24 genomes representing eight described species and several unnamed lineages of Lentinula from 15 countries on four continents. Lentinula comprises four major clades that arose in the Oligocene, three in the Americas and one in Asia-Australasia. To expand sampling of shiitake mushrooms, we assembled 60 genomes of L. edodes from China that were previously published as raw Illumina reads and added them to our dataset. Lentinula edodes sensu lato (s. lat.) contains three lineages that may warrant recognition as species, one including a single isolate from Nepal that is the sister group to the rest of L. edodes s. lat., a second with 20 cultivars and 12 wild isolates from China, Japan, Korea, and the Russian Far East, and a third with 28 wild isolates from China, Thailand, and Vietnam. Two additional lineages in China have arisen by hybridization among the second and third groups. Genes encoding cysteine sulfoxide lyase (lecsl) and γ-glutamyl transpeptidase (leggt), which are implicated in biosynthesis of the organosulfur flavor compound lenthionine, have diversified in Lentinula. Paralogs of both genes that are unique to Lentinula (lecsl 3 and leggt 5b) are coordinately up-regulated in fruiting bodies of L. edodes. The pangenome of L. edodes s. lat. contains 20,308 groups of orthologous genes, but only 6,438 orthogroups (32%) are shared among all strains, whereas 3,444 orthogroups (17%) are found only in wild populations, which should be targeted for conservation.
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Affiliation(s)
| | - Byoungnam Min
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA94720
| | | | - Brian Looney
- Biology Department, Clark University, Worcester, MA01610
| | - Zachary Konkel
- Department of Plant Pathology, Ohio State University, Columbus, OH43210
| | - Jason C. Slot
- Department of Plant Pathology, Ohio State University, Columbus, OH43210
| | - Yuichi Sakamoto
- Iwate Biotechnology Research Center, Kitakami, Iwate024-0003, Japan
| | - Jacob L. Steenwyk
- Department of Biological Sciences and Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN37235
| | - Antonis Rokas
- Department of Biological Sciences and Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN37235
| | - Juan Carro
- Centro de Investigaciones Biológicas “Margarita Salas,” Consejo Superior de Investigaciones Científicas, MadridE-28040, Spain
| | - Susana Camarero
- Centro de Investigaciones Biológicas “Margarita Salas,” Consejo Superior de Investigaciones Científicas, MadridE-28040, Spain
| | - Patricia Ferreira
- Department of Biochemistry and Molecular and Cellular Biology, University of Zaragoza, 50009Zaragoza, Spain
- Institute of Biocomputation and Physics of Complex Systems, University of Zaragoza,50018Zaragoza, Spain
| | - Gonzalo Molpeceres
- Centro de Investigaciones Biológicas “Margarita Salas,” Consejo Superior de Investigaciones Científicas, MadridE-28040, Spain
| | - Francisco J. Ruiz-Dueñas
- Centro de Investigaciones Biológicas “Margarita Salas,” Consejo Superior de Investigaciones Científicas, MadridE-28040, Spain
| | - Ana Serrano
- Centro de Investigaciones Biológicas “Margarita Salas,” Consejo Superior de Investigaciones Científicas, MadridE-28040, Spain
| | - Bernard Henrissat
- DTU Bioengineering, Technical University of Denmark2800, Kgs. Lyngby, Denmark
- Department of Biological Sciences, King Abdulaziz University, Jeddah21589, Saudi Arabia
| | - Elodie Drula
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Université13288, Marseille, France
- INRAE, UMR 1163, Biodiversité et Biotechnologie Fongiques13009, Marseille, France
| | - Karen W. Hughes
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN37996
| | - Juan L. Mata
- Department of Biology, University of South Alabama, Mobile, AL36688
| | - Noemia Kazue Ishikawa
- Coordenação de Biodiversidade, Instituto Nacional de Pesquisas da Amazônia, Petrópolis, ManausAM 69067-375, Brazil
| | - Ruby Vargas-Isla
- Coordenação de Biodiversidade, Instituto Nacional de Pesquisas da Amazônia, Petrópolis, ManausAM 69067-375, Brazil
| | - Shuji Ushijima
- The Tottori Mycological Institute, Japan Kinoko Research Center Foundation, Tottori689-1125, Japan
| | - Chris A. Smith
- Manaaki Whenua - Landcare Research, Auckland1072, New Zealand
| | - John Donoghue
- Northwest Mycological Consultants, Corvallis, OR97330
| | - Steven Ahrendt
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA94720
| | - William Andreopoulos
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA94720
| | - Guifen He
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA94720
| | - Kurt LaButti
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA94720
| | - Anna Lipzen
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA94720
| | - Vivian Ng
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA94720
| | - Robert Riley
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA94720
| | - Laura Sandor
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA94720
| | - Kerrie Barry
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA94720
| | - Angel T. Martínez
- Centro de Investigaciones Biológicas “Margarita Salas,” Consejo Superior de Investigaciones Científicas, MadridE-28040, Spain
| | - Yang Xiao
- Institute of Applied Mycology, Huazhong Agricultural University, Wuhan, Hubei430070, China
| | - John G. Gibbons
- Department of Food Science, University of Massachusetts, Amherst, MA01003
| | - Kazuhisa Terashima
- The Tottori Mycological Institute, Japan Kinoko Research Center Foundation, Tottori689-1125, Japan
| | - Igor V. Grigoriev
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA94720
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA94720
| | - David Hibbett
- Biology Department, Clark University, Worcester, MA01610
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17
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Llewellyn T, Nowell RW, Aptroot A, Temina M, Prescott TAK, Barraclough TG, Gaya E. Metagenomics Shines Light on the Evolution of "Sunscreen" Pigment Metabolism in the Teloschistales (Lichen-Forming Ascomycota). Genome Biol Evol 2023; 15:6986375. [PMID: 36634008 PMCID: PMC9907504 DOI: 10.1093/gbe/evad002] [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: 09/26/2022] [Revised: 11/25/2022] [Accepted: 01/09/2023] [Indexed: 01/13/2023] Open
Abstract
Fungi produce a vast number of secondary metabolites that shape their interactions with other organisms and the environment. Characterizing the genes underpinning metabolite synthesis is therefore key to understanding fungal evolution and adaptation. Lichenized fungi represent almost one-third of Ascomycota diversity and boast impressive secondary metabolites repertoires. However, most lichen biosynthetic genes have not been linked to their metabolite products. Here we used metagenomic sequencing to survey gene families associated with production of anthraquinones, UV-protectant secondary metabolites present in various fungi, but especially abundant in a diverse order of lichens, the Teloschistales (class Lecanoromycetes, phylum Ascomycota). We successfully assembled 24 new, high-quality lichenized-fungal genomes de novo and combined them with publicly available Lecanoromycetes genomes from taxa with diverse secondary chemistry to produce a whole-genome tree. Secondary metabolite biosynthetic gene cluster (BGC) analysis showed that whilst lichen BGCs are numerous and highly dissimilar, core enzyme genes are generally conserved across taxa. This suggests metabolite diversification occurs via re-shuffling existing enzyme genes with novel accessory genes rather than BGC gains/losses or de novo gene evolution. We identified putative anthraquinone BGCs in our lichen dataset that appear homologous to anthraquinone clusters from non-lichenized fungi, suggesting these genes were present in the common ancestor of the subphylum Pezizomycotina. Finally, we identified unique transporter genes in Teloschistales anthraquinone BGCs that may explain why these metabolites are so abundant and ubiquitous in these lichens. Our results support the importance of metagenomics for understanding the secondary metabolism of non-model fungi such as lichens.
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Affiliation(s)
| | - Reuben W Nowell
- Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot, Berkshire, SL5 7PY, UK,Department of Biology, University of Oxford, 11a Mansfield Road, Oxford, OX1 3SZ, UK
| | - Andre Aptroot
- Instituto de Biociências, Universidade Federal de Mato Grosso do Sul, Avenida Costa e Silva s/n Bairro Universitário, Campo Grande, Mato Grosso do Sul CEP 79070-900, Brazil
| | - Marina Temina
- Institute of Evolution, University of Haifa, 199 Aba Khoushy Ave, Mount Carmel, Haifa, 3498838, Israel
| | - Thomas A K Prescott
- Comparative Fungal Biology, Royal Botanic Gardens, Kew, Jodrell Laboratory, Richmond, TW9 3DS, UK
| | - Timothy G Barraclough
- Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot, Berkshire, SL5 7PY, UK,Department of Biology, University of Oxford, 11a Mansfield Road, Oxford, OX1 3SZ, UK
| | - Ester Gaya
- Comparative Fungal Biology, Royal Botanic Gardens, Kew, Jodrell Laboratory, Richmond, TW9 3DS, UK
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18
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Itani A, Shida Y, Ogasawara W. A microfluidic device for simultaneous detection of enzyme secretion and elongation of a single hypha. Front Microbiol 2023; 14:1125760. [PMID: 36937311 PMCID: PMC10020217 DOI: 10.3389/fmicb.2023.1125760] [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: 12/16/2022] [Accepted: 02/16/2023] [Indexed: 03/06/2023] Open
Abstract
Filamentous fungi grow through elongation of their apical region by exocytosis and secrete enzymes that can be of commercial or industrial importance. Their hyphae exhibit extensive branching, making it difficult to control hyphal growth for observation and analysis. Therefore, although hyphal morphology and productivity are closely related, the relationship between the two has not yet been clarified. Conventional morphology and productivity studies have only compared the results of macro imaging of fungal pellets cultured in bulk with the averaged products in the culture medium. Filamentous fungi are multicellular and their expression differs between different hyphae. To truly understand the relationship between morphology and productivity, it is necessary to compare the morphology and productivity of individual hyphae. To achieve this, we developed a microfluidic system that confines hyphae to individual channels for observation and investigated the relationship between their growth, morphology, and enzyme productivity. Furthermore, using Trichoderma reesei, a potent cellulase-producing fungus, as a model, we developed a cellulase detection assay with 4-MUC substrate to detect hyphal growth and enzyme secretion in a microfluidic device in real time. Using a strain that expresses cellobiohydrolase I (CBH I) fused with AcGFP1, we compared fluorescence from the detection assay with GFP fluorescence intensity, which showed a strong correlation between the two. These results indicate that extracellular enzymes can be easily detected in the microfluidic device in real time because the production of cellulase is synchronized in T. reesei. This microfluidic system enables real-time visualization of the dynamics of hypha and enzymes during carbon source exchange and the quantitative dynamics of gene expression. This technology can be applied to many biosystems from bioenergy production to human health.
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Affiliation(s)
- Ayaka Itani
- Department of Bioengineering, Nagaoka University of Technology, Nagaoka, Japan
| | - Yosuke Shida
- Department of Bioengineering, Nagaoka University of Technology, Nagaoka, Japan
- *Correspondence: Yosuke Shida,
| | - Wataru Ogasawara
- Department of Bioengineering, Nagaoka University of Technology, Nagaoka, Japan
- Department of Science of Technology Innovation, Nagaoka University of Technology, Nagaoka, Japan
- Wataru Ogasawara,
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19
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Description and Genome Characterization of Three Novel Fungal Strains Isolated from Mars 2020 Mission-Associated Spacecraft Assembly Facility Surfaces-Recommendations for Two New Genera and One Species. J Fungi (Basel) 2022; 9:jof9010031. [PMID: 36675851 PMCID: PMC9864340 DOI: 10.3390/jof9010031] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 12/17/2022] [Accepted: 12/18/2022] [Indexed: 12/29/2022] Open
Abstract
National Aeronautics and Space Administration’s (NASA) spacecraft assembly facilities are monitored for the presence of any bacteria or fungi that might conceivably survive a transfer to an extraterrestrial environment. Fungi present a broad and diverse range of phenotypic and functional traits to adapt to extreme conditions, hence the detection of fungi and subsequent eradication of them are needed to prevent forward contamination for future NASA missions. During the construction and assembly for the Mars 2020 mission, three fungal strains with unique morphological and phylogenetic properties were isolated from spacecraft assembly facilities. The reconstruction of phylogenetic trees based on several gene loci (ITS, LSU, SSU, RPB, TUB, TEF1) using multi-locus sequence typing (MLST) and whole genome sequencing (WGS) analyses supported the hypothesis that these were novel species. Here we report the genus or species-level classification of these three novel strains via a polyphasic approach using phylogenetic analysis, colony and cell morphology, and comparative analysis of WGS. The strain FJI-L9-BK-P1 isolated from the Jet Propulsion Laboratory Spacecraft Assembly Facility (JPL-SAF) exhibited a putative phylogenetic relationship with the strain Aaosphaeria arxii CBS175.79 but showed distinct morphology and microscopic features. Another JPL-SAF strain, FJII-L3-CM-DR1, was phylogenetically distinct from members of the family Trichomeriaceae and exhibited morphologically different features from the genera Lithohypha and Strelitziana. The strain FKI-L1-BK-DR1 isolated from the Kennedy Space Center facility was identified as a member of Dothideomycetes incertae sedis and is closely related to the family Kirschsteiniotheliaceae according to a phylogenetic analysis. The polyphasic taxonomic approach supported the recommendation for establishing two novel genera and one novel species. The names Aaosphaeria pasadenensis (FJI-L9-BK-P1 = NRRL 64424 = DSM 114621), Pasadenomyces melaninifex (FJII-L3-CM-DR1 = NRRL 64433 = DSM 114623), and Floridaphiala radiotolerans (FKI-L1-BK-DR1 = NRRL 64434 = DSM 114624) are proposed as type species. Furthermore, resistance to ultraviolet-C and presence of specific biosynthetic gene cluster(s) coding for metabolically active compounds are unique to these strains.
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20
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The pan-genome of Aspergillus fumigatus provides a high-resolution view of its population structure revealing high levels of lineage-specific diversity driven by recombination. PLoS Biol 2022; 20:e3001890. [PMID: 36395320 PMCID: PMC9714929 DOI: 10.1371/journal.pbio.3001890] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 12/01/2022] [Accepted: 10/26/2022] [Indexed: 11/18/2022] Open
Abstract
Aspergillus fumigatus is a deadly agent of human fungal disease where virulence heterogeneity is thought to be at least partially structured by genetic variation between strains. While population genomic analyses based on reference genome alignments offer valuable insights into how gene variants are distributed across populations, these approaches fail to capture intraspecific variation in genes absent from the reference genome. Pan-genomic analyses based on de novo assemblies offer a promising alternative to reference-based genomics with the potential to address the full genetic repertoire of a species. Here, we evaluate 260 genome sequences of A. fumigatus including 62 newly sequenced strains, using a combination of population genomics, phylogenomics, and pan-genomics. Our results offer a high-resolution assessment of population structure and recombination frequency, phylogenetically structured gene presence-absence variation, evidence for metabolic specificity, and the distribution of putative antifungal resistance genes. Although A. fumigatus disperses primarily via asexual conidia, we identified extraordinarily high levels of recombination with the lowest linkage disequilibrium decay value reported for any fungal species to date. We provide evidence for 3 primary populations of A. fumigatus, with recombination occurring only rarely between populations and often within them. These 3 populations are structured by both gene variation and distinct patterns of gene presence-absence with unique suites of accessory genes present exclusively in each clade. Accessory genes displayed functional enrichment for nitrogen and carbohydrate metabolism suggesting that populations may be stratified by environmental niche specialization. Similarly, the distribution of antifungal resistance genes and resistance alleles were often structured by phylogeny. Altogether, the pan-genome of A. fumigatus represents one of the largest fungal pan-genomes reported to date including many genes unrepresented in the Af293 reference genome. These results highlight the inadequacy of relying on a single-reference genome-based approach for evaluating intraspecific variation and the power of combined genomic approaches to elucidate population structure, genetic diversity, and putative ecological drivers of clinically relevant fungi.
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21
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Gabaldón T, Hittinger CT. Editorial: Genomic insights on fungal hybrids. FRONTIERS IN FUNGAL BIOLOGY 2022; 3:1063609. [PMID: 37746239 PMCID: PMC10512351 DOI: 10.3389/ffunb.2022.1063609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 10/24/2022] [Indexed: 09/26/2023]
Affiliation(s)
- Toni Gabaldón
- Barcelona Supercomputing Centre (BSC-CNS). Plaça Eusebi Güell, Barcelona, Spain
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, Barcelona, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain
- Centro de Investigación Biomédica En Red de Enfermedades Infecciosas (CIBERINFEC), Barcelona, Spain
| | - Chris Todd Hittinger
- Laboratory of Genetics, DOE Great Lakes Bioenergy Research Center, J. F. Crow Institute for the Study of Evolution, Center for Genomic Science Innovation, Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, WI, United States
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22
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Moo-Koh FA, Cristóbal-Alejo J, Tun-Suárez JM, Medina-Baizabal IL, Arjona-Cruz AA, Gamboa-Angulo M. Activity of Aqueous Extracts from Native Plants of the Yucatan Peninsula against Fungal Pathogens of Tomato In Vitro and from Croton chichenensis against Corynespora cassiicola on Tomato. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11212821. [PMID: 36365274 PMCID: PMC9654290 DOI: 10.3390/plants11212821] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 10/14/2022] [Accepted: 10/17/2022] [Indexed: 05/29/2023]
Abstract
Plant extracts are a valuable alternative to control pathogens of horticultural crops. In the present study, four species of pathogenic fungi were isolated from leaf spots on Solanum lycopersicum and identified by traditional and molecular techniques as Alternaria alternata ITC24, Corynespora cassiicola ITC23, Curvularia lunata ITC22, and Fusarium equiseti ITC32. When 11 aqueous extracts from eight native plants of the Yucatan Peninsula were tested against the four fungi in vitro, the extract from Croton chichenensis roots was most active, inhibiting mycelial growth (79-100%), sporulation (100%), and conidial germination (71-100%) at 3% (w/v). A logarithmic-diagrammatic scale of the pathosystem C. cassiicola-S. lycopersicum was established and used to assess disease severity on inoculated tomato plants in a greenhouse after treatment with the aqueous extract from C. chichenensis roots at 12% (w/v). After 21 days, the disease severity was 57% lower than on the control without extract applied. This dose of the extract was not phytotoxic to tomato leaves and was compatible with the beneficial organisms Bacillus subtilis CBCK47 and Trichodema asperellum Ta13-17. The antifungal efficacy of C. chichenensis is highly promising for incorporation into integrated disease management of tomato crops.
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Affiliation(s)
- Felicia Amalia Moo-Koh
- Centro de Investigación Científica de Yucatán, Calle 43 No. 130, Col. Chuburná de Hidalgo, Yucatán, Mérida 97205, Mexico
- Tecnológico Nacional de México, Campus Conkal, Avenida Tecnológico s/n, Yucatán, Conkal 97345, Mexico
| | - Jairo Cristóbal-Alejo
- Tecnológico Nacional de México, Campus Conkal, Avenida Tecnológico s/n, Yucatán, Conkal 97345, Mexico
| | - José María Tun-Suárez
- Tecnológico Nacional de México, Campus Conkal, Avenida Tecnológico s/n, Yucatán, Conkal 97345, Mexico
| | - Irma Leticia Medina-Baizabal
- Centro de Investigación Científica de Yucatán, Calle 43 No. 130, Col. Chuburná de Hidalgo, Yucatán, Mérida 97205, Mexico
| | | | - Marcela Gamboa-Angulo
- Centro de Investigación Científica de Yucatán, Calle 43 No. 130, Col. Chuburná de Hidalgo, Yucatán, Mérida 97205, Mexico
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23
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Naranjo-Ortiz MA, Molina M, Fuentes D, Mixão V, Gabaldón T. Karyon: a computational framework for the diagnosis of hybrids, aneuploids, and other nonstandard architectures in genome assemblies. Gigascience 2022; 11:6751106. [PMID: 36205401 PMCID: PMC9540331 DOI: 10.1093/gigascience/giac088] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Revised: 11/23/2021] [Accepted: 08/24/2022] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Recent technological developments have made genome sequencing and assembly highly accessible and widely used. However, the presence in sequenced organisms of certain genomic features such as high heterozygosity, polyploidy, aneuploidy, heterokaryosis, or extreme compositional biases can challenge current standard assembly procedures and result in highly fragmented assemblies. Hence, we hypothesized that genome databases must contain a nonnegligible fraction of low-quality assemblies that result from such type of intrinsic genomic factors. FINDINGS Here we present Karyon, a Python-based toolkit that uses raw sequencing data and de novo genome assembly to assess several parameters and generate informative plots to assist in the identification of nonchanonical genomic traits. Karyon includes automated de novo genome assembly and variant calling pipelines. We tested Karyon by diagnosing 35 highly fragmented publicly available assemblies from 19 different Mucorales (Fungi) species. CONCLUSIONS Our results show that 10 (28.57%) of the assemblies presented signs of unusual genomic configurations, suggesting that these are common, at least for some lineages within the Fungi.
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Affiliation(s)
- Miguel A Naranjo-Ortiz
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona 08003, Spain,Health and Life Sciences, Universitat Pompeu Fabra (UPF), Barcelona 08003, Spain,Biology Department, Clark University, Worcester, MA 01610, USA,Naturhistoriskmuseum, University of Oslo, Oslo 0562, Norway
| | - Manu Molina
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona 08003, Spain,Health and Life Sciences, Universitat Pompeu Fabra (UPF), Barcelona 08003, Spain,Life Sciences Department, Barcelona Supercomputing Centre (BSC-CNS), Barcelona 08034, Spain
| | - Diego Fuentes
- Life Sciences Department, Barcelona Supercomputing Centre (BSC-CNS), Barcelona 08034, Spain,Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona 08028, Spain
| | - Verónica Mixão
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona 08003, Spain,Health and Life Sciences, Universitat Pompeu Fabra (UPF), Barcelona 08003, Spain,Life Sciences Department, Barcelona Supercomputing Centre (BSC-CNS), Barcelona 08034, Spain,Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona 08028, Spain
| | - Toni Gabaldón
- Correspondence address. Toni Gabaldón, Plaça Eusebi Güell, 1-3, Barcelona 08034, Spain. E-mail:
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24
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Gostinčar C, Sun X, Černoša A, Fang C, Gunde-Cimerman N, Song Z. Clonality, inbreeding, and hybridization in two extremotolerant black yeasts. Gigascience 2022; 11:giac095. [PMID: 36200832 PMCID: PMC9535773 DOI: 10.1093/gigascience/giac095] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 07/29/2022] [Accepted: 09/12/2022] [Indexed: 11/04/2022] Open
Abstract
BACKGROUND The great diversity of lifestyles and survival strategies observed in fungi is reflected in the many ways in which they reproduce and recombine. Although a complete absence of recombination is rare, it has been reported for some species, among them 2 extremotolerant black yeasts from Dothideomycetes: Hortaea werneckii and Aureobasidium melanogenum. Therefore, the presence of diploid strains in these species cannot be explained as the product of conventional sexual reproduction. RESULTS Genome sequencing revealed that the ratio of diploid to haploid strains in both H. werneckii and A. melanogenum is about 2:1. Linkage disequilibrium between pairs of polymorphic loci and a high degree of concordance between the phylogenies of different genomic regions confirmed that both species are clonal. Heterozygosity of diploid strains is high, with several hybridizing genome pairs reaching the intergenomic distances typically seen between different fungal species. The origin of diploid strains collected worldwide can be traced to a handful of hybridization events that produced diploids, which were stable over long periods of time and distributed over large geographic areas. CONCLUSIONS Our results, based on the genomes of over 100 strains of 2 black yeasts, show that although they are clonal, they occasionally form stable and highly heterozygous diploid intraspecific hybrids. The mechanism of these apparently rare hybridization events, which are not followed by meiosis or haploidization, remains unknown. Both extremotolerant yeasts, H. werneckii and even more so A. melanogenum, a close relative of the intensely recombining and biotechnologically relevant Aureobasidium pullulans, provide an attractive model for studying the role of clonality and ploidy in extremotolerant fungi.
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Affiliation(s)
- Cene Gostinčar
- Department of Biology, Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia
- Lars Bolund Institute of Regenerative Medicine, BGI-Qingdao, Qingdao 266555, China
| | - Xiaohuan Sun
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen 518083, China
| | - Anja Černoša
- Department of Biology, Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Chao Fang
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen 518083, China
| | - Nina Gunde-Cimerman
- Department of Biology, Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Zewei Song
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen 518083, China
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25
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Smith TJ, Donoghue PCJ. Evolution of fungal phenotypic disparity. Nat Ecol Evol 2022; 6:1489-1500. [PMID: 35970862 DOI: 10.1038/s41559-022-01844-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 06/29/2022] [Indexed: 11/09/2022]
Abstract
Organismal-grade multicellularity has been achieved only in animals, plants and fungi. All three kingdoms manifest phenotypically disparate body plans but their evolution has only been considered in detail for animals. Here we tested the general relevance of hypotheses on the evolutionary assembly of animal body plans by characterizing the evolution of fungal phenotypic variety (disparity). The distribution of living fungal form is defined by four distinct morphotypes: flagellated; zygomycetous; sac-bearing; and club-bearing. The discontinuity between morphotypes is a consequence of extinction, indicating that a complete record of fungal disparity would present a more homogeneous distribution of form. Fungal disparity expands episodically through time, punctuated by a sharp increase associated with the emergence of multicellular body plans. Simulations show these temporal trends to be non-random and at least partially shaped by hierarchical contingency. These trends are decoupled from changes in gene number, genome size and taxonomic diversity. Only differences in organismal complexity, characterized as the number of traits that constitute an organism, exhibit a meaningful relationship with fungal disparity. Both animals and fungi exhibit episodic increases in disparity through time, resulting in distributions of form made discontinuous by extinction. These congruences suggest a common mode of multicellular body plan evolution.
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Affiliation(s)
- Thomas J Smith
- Bristol Palaeobiology Group, School of Earth Sciences, University of Bristol, Bristol, UK.
| | - Philip C J Donoghue
- Bristol Palaeobiology Group, School of Earth Sciences, University of Bristol, Bristol, UK.
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26
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Rosenberg E. Rapid acquisition of microorganisms and microbial genes can help explain punctuated evolution. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.957708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The punctuated mode of evolution posits that evolution occurs in rare bursts of rapid evolutionary change followed by long periods of genetic stability (stasis). The accepted cause for the rapid changes in punctuated evolution is special ecological circumstances – selection forces brought about by changes in the environment. This article presents a complementary explanation for punctuated evolution by the rapid formation of genetic variants in animals and plants by the acquisition of microorganisms from the environment into microbiomes and microbial genes into host genomes by horizontal gene transfer. Several examples of major evolutionary events driven by microorganisms are discussed, including the formation of the first eukaryotic cell, the ability of some animals to digest cellulose and other plant cell-wall complex polysaccharides, dynamics of root system architecture, and the formation of placental mammals. These changes by cooperation were quantum leaps in the evolutionary development of complex bilolgical systems and can contribute to an understanding of the mechanisms underlying punctuated evolution.
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27
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Emerging Trends in the Use of Topical Antifungal-Corticosteroid Combinations. J Fungi (Basel) 2022; 8:jof8080812. [PMID: 36012800 PMCID: PMC9409645 DOI: 10.3390/jof8080812] [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: 07/11/2022] [Revised: 07/29/2022] [Accepted: 07/29/2022] [Indexed: 12/10/2022] Open
Abstract
A broad range of topical antifungal formulations containing miconazole or terbinafine as actives are commonly used as efficacious choices for combating fungal skin infections. Their many benefits, owing to their specific mechanism of action, include their ability to target the site of infection, enhance treatment efficacy and reduce the risk of systemic side effects. Their proven efficacy, and positioning in the treatment of fungal skin infections, is enhanced by high patient compliance, especially when appropriate vehicles such as creams, ointments and gels are used. However, inflammation as a result of fungal infection can often impede treatment, especially when combined with pruritus (itch), an unpleasant sensation that elicits an urge to scratch. The scratching that occurs in response to pruritus frequently accelerates skin damage, ultimately aggravating and spreading the fungal infection. To help overcome this issue, a topical antifungal-corticosteroid combination consisting of miconazole or terbinafine and corticosteroids of varying potencies should be used. Due to their inherent benefits, these topical antifungal-corticosteroid combinations can concomitantly and competently attenuate inflammation, relieve pruritus and treat fungal infection.
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28
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Kulik T, Molcan T, Fiedorowicz G, van Diepeningen A, Stakheev A, Treder K, Olszewski J, Bilska K, Beyer M, Pasquali M, Stenglein S. Whole-genome single nucleotide polymorphism analysis for typing the pandemic pathogen Fusarium graminearum sensu stricto. Front Microbiol 2022; 13:885978. [PMID: 35923405 PMCID: PMC9339996 DOI: 10.3389/fmicb.2022.885978] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 06/30/2022] [Indexed: 11/13/2022] Open
Abstract
Recent improvements in microbiology and molecular epidemiology were largely stimulated by whole- genome sequencing (WGS), which provides an unprecedented resolution in discriminating highly related genetic backgrounds. WGS is becoming the method of choice in epidemiology of fungal diseases, but its application is still in a pioneer stage, mainly due to the limited number of available genomes. Fungal pathogens often belong to complexes composed of numerous cryptic species. Detecting cryptic diversity is fundamental to understand the dynamics and the evolutionary relationships underlying disease outbreaks. In this study, we explore the value of whole-genome SNP analyses in identification of the pandemic pathogen Fusarium graminearum sensu stricto (F.g.). This species is responsible for cereal diseases and negatively impacts grain production worldwide. The fungus belongs to the monophyletic fungal complex referred to as F. graminearum species complex including at least sixteen cryptic species, a few among them may be involved in cereal diseases in certain agricultural areas. We analyzed WGS data from a collection of 99 F.g. strains and 33 strains representing all known cryptic species belonging to the FGSC complex. As a first step, we performed a phylogenomic analysis to reveal species-specific clustering. A RAxML maximum likelihood tree grouped all analyzed strains of F.g. into a single clade, supporting the clustering-based identification approach. Although, phylogenetic reconstructions are essential in detecting cryptic species, a phylogenomic tree does not fulfill the criteria for rapid and cost-effective approach for identification of fungi, due to the time-consuming nature of the analysis. As an alternative, analysis of WGS information by mapping sequence data from individual strains against reference genomes may provide useful markers for the rapid identification of fungi. We provide a robust framework for typing F.g. through the web-based PhaME workflow available at EDGE bioinformatics. The method was validated through multiple comparisons of assembly genomes to F.g. reference strain PH-1. We showed that the difference between intra- and interspecies variability was at least two times higher than intraspecific variation facilitating successful typing of F.g. This is the first study which employs WGS data for typing plant pathogenic fusaria.
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Affiliation(s)
- Tomasz Kulik
- Department of Botany and Nature Protection, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
- *Correspondence: Tomasz Kulik,,
| | - Tomasz Molcan
- Department of Bioinformatics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences (PAN), Warsaw, Poland
| | - Grzegorz Fiedorowicz
- Department of Botany and Nature Protection, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| | - Anne van Diepeningen
- Biointeractions and Plant Health, Wageningen Plant Research, Wageningen, Netherlands
| | - Alexander Stakheev
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Kinga Treder
- Department of Agriculture Systems, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| | | | - Katarzyna Bilska
- Department of Botany and Nature Protection, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| | - Marco Beyer
- Agro-Environmental Systems, Environmental Monitoring and Sensing Unit, Department of Environmental Research and Innovation, Luxembourg Institute of Science and Technology, Esch-sur-Alzette, Luxembourg
| | - Matias Pasquali
- Department of Food, Environmental and Nutritional Sciences, University of Milan, Milan, Italy
| | - Sebastian Stenglein
- National Scientific and Technical Research Council, Godoy Cruz, Argentina
- Universidad Nacional del Centro de la Provincia de Buenos Aires, Tandil, Argentina
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29
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Haro-Reyes T, Díaz-Peralta L, Galván-Hernández A, Rodríguez-López A, Rodríguez-Fragoso L, Ortega-Blake I. Polyene Antibiotics Physical Chemistry and Their Effect on Lipid Membranes; Impacting Biological Processes and Medical Applications. MEMBRANES 2022; 12:membranes12070681. [PMID: 35877884 PMCID: PMC9316096 DOI: 10.3390/membranes12070681] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 06/21/2022] [Accepted: 06/23/2022] [Indexed: 01/27/2023]
Abstract
This review examined a collection of studies regarding the molecular properties of some polyene antibiotic molecules as well as their properties in solution and in particular environmental conditions. We also looked into the proposed mechanism of action of polyenes, where membrane properties play a crucial role. Given the interest in polyene antibiotics as therapeutic agents, we looked into alternative ways of reducing their collateral toxicity, including semi-synthesis of derivatives and new formulations. We follow with studies on the role of membrane structure and, finally, recent developments regarding the most important clinical applications of these compounds.
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Affiliation(s)
- Tammy Haro-Reyes
- Instituto de Ciencias Físicas, Universidad Nacional Autónoma de México, Av. Universidad s/n, Col. Chamilpa, Cuernavaca 62210, Morelos, Mexico; (T.H.-R.); (L.D.-P.); (A.G.-H.)
| | - Lucero Díaz-Peralta
- Instituto de Ciencias Físicas, Universidad Nacional Autónoma de México, Av. Universidad s/n, Col. Chamilpa, Cuernavaca 62210, Morelos, Mexico; (T.H.-R.); (L.D.-P.); (A.G.-H.)
| | - Arturo Galván-Hernández
- Instituto de Ciencias Físicas, Universidad Nacional Autónoma de México, Av. Universidad s/n, Col. Chamilpa, Cuernavaca 62210, Morelos, Mexico; (T.H.-R.); (L.D.-P.); (A.G.-H.)
| | - Anahi Rodríguez-López
- Facultad de Farmacia, Universidad Autónoma del Estado de Morelos, Cuernavaca 62210, Morelos, Mexico; (A.R.-L.); (L.R.-F.)
| | - Lourdes Rodríguez-Fragoso
- Facultad de Farmacia, Universidad Autónoma del Estado de Morelos, Cuernavaca 62210, Morelos, Mexico; (A.R.-L.); (L.R.-F.)
| | - Iván Ortega-Blake
- Instituto de Ciencias Físicas, Universidad Nacional Autónoma de México, Av. Universidad s/n, Col. Chamilpa, Cuernavaca 62210, Morelos, Mexico; (T.H.-R.); (L.D.-P.); (A.G.-H.)
- Correspondence: ; Tel.: +52-77-7329-1762
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30
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Cote-L’Heureux A, Maurer-Alcalá XX, Katz LA. Old genes in new places: A taxon-rich analysis of interdomain lateral gene transfer events. PLoS Genet 2022; 18:e1010239. [PMID: 35731825 PMCID: PMC9255765 DOI: 10.1371/journal.pgen.1010239] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 07/05/2022] [Accepted: 05/06/2022] [Indexed: 11/26/2022] Open
Abstract
Vertical inheritance is foundational to Darwinian evolution, but fails to explain major innovations such as the rapid spread of antibiotic resistance among bacteria and the origin of photosynthesis in eukaryotes. While lateral gene transfer (LGT) is recognized as an evolutionary force in prokaryotes, the role of LGT in eukaryotic evolution is less clear. With the exception of the transfer of genes from organelles to the nucleus, a process termed endosymbiotic gene transfer (EGT), the extent of interdomain transfer from prokaryotes to eukaryotes is highly debated. A common critique of studies of interdomain LGT is the reliance on the topology of single-gene trees that attempt to estimate more than one billion years of evolution. We take a more conservative approach by identifying cases in which a single clade of eukaryotes is found in an otherwise prokaryotic gene tree (i.e. exclusive presence). Starting with a taxon-rich dataset of over 13,600 gene families and passing data through several rounds of curation, we identify and categorize the function of 306 interdomain LGT events into diverse eukaryotes, including 189 putative EGTs, 52 LGTs into Opisthokonta (i.e. animals, fungi and their microbial relatives), and 42 LGTs nearly exclusive to anaerobic eukaryotes. To assess differential gene loss as an explanation for exclusive presence, we compare branch lengths within each LGT tree to a set of vertically-inherited genes subsampled to mimic gene loss (i.e. with the same taxonomic sampling) and consistently find shorter relative distance between eukaryotes and prokaryotes in LGT trees, a pattern inconsistent with gene loss. Our methods provide a framework for future studies of interdomain LGT and move the field closer to an understanding of how best to model the evolutionary history of eukaryotes.
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Affiliation(s)
- Auden Cote-L’Heureux
- Department of Biological Sciences, Smith College, Northampton, Massachusetts, United States of America
| | | | - Laura A. Katz
- Department of Biological Sciences, Smith College, Northampton, Massachusetts, United States of America
- Program in Organismic Biology and Evolution, University of Massachusetts Amherst, Amherst, Massachusetts, United States of America
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31
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Spribille T, Resl P, Stanton DE, Tagirdzhanova G. Evolutionary biology of lichen symbioses. THE NEW PHYTOLOGIST 2022; 234:1566-1582. [PMID: 35302240 DOI: 10.1111/nph.18048] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 12/21/2021] [Indexed: 05/28/2023]
Abstract
Lichens are the symbiotic outcomes of open, interspecies relationships, central to which are a fungus and a phototroph, typically an alga and/or cyanobacterium. The evolutionary processes that led to the global success of lichens are poorly understood. In this review, we explore the goods and services exchange between fungus and phototroph and how this propelled the success of both symbiont and symbiosis. Lichen fungal symbionts count among the only filamentous fungi that expose most of their mycelium to an aerial environment. Phototrophs export carbohydrates to the fungus, which converts them to specific polyols. Experimental evidence suggests that polyols are not only growth and respiratory substrates but also play a role in anhydrobiosis, the capacity to survive desiccation. We propose that this dual functionality is pivotal to the evolution of fungal symbionts, enabling persistence in environments otherwise hostile to fungi while simultaneously imposing costs on growth. Phototrophs, in turn, benefit from fungal protection from herbivory and light stress, while appearing to exert leverage over fungal sex and morphogenesis. Combined with the recently recognized habit of symbionts to occur in multiple symbioses, this creates the conditions for a multiplayer marketplace of rewards and penalties that could drive symbiont selection and lichen diversification.
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Affiliation(s)
- Toby Spribille
- Department of Biological Sciences CW405, University of Alberta, Edmonton, AB, T6G 2R3, Canada
| | - Philipp Resl
- Institute of Biology, University of Graz, Universitätsplatz 3, Graz, 8010, Austria
| | - Daniel E Stanton
- Department of Ecology, Evolution and Behavior, University of Minnesota, Saint Paul, MN, 55108, USA
| | - Gulnara Tagirdzhanova
- Department of Biological Sciences CW405, University of Alberta, Edmonton, AB, T6G 2R3, Canada
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Phukhamsakda C, Nilsson RH, Bhunjun CS, de Farias ARG, Sun YR, Wijesinghe SN, Raza M, Bao DF, Lu L, Tibpromma S, Dong W, Tennakoon DS, Tian XG, Xiong YR, Karunarathna SC, Cai L, Luo ZL, Wang Y, Manawasinghe IS, Camporesi E, Kirk PM, Promputtha I, Kuo CH, Su HY, Doilom M, Li Y, Fu YP, Hyde KD. The numbers of fungi: contributions from traditional taxonomic studies and challenges of metabarcoding. FUNGAL DIVERS 2022. [DOI: 10.1007/s13225-022-00502-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
AbstractThe global diversity of fungi has been estimated using several different approaches. There is somewhere between 2–11 million estimated species, but the number of formally described taxa is around 150,000, a tiny fraction of the total. In this paper, we examine 12 ascomycete genera as case studies to establish trends in fungal species descriptions, and introduce new species in each genus. To highlight the importance of traditional morpho-molecular methods in publishing new species, we introduce novel taxa in 12 genera that are considered to have low species discovery. We discuss whether the species are likely to be rare or due to a lack of extensive sampling and classification. The genera are Apiospora, Bambusicola, Beltrania, Capronia, Distoseptispora, Endocalyx, Neocatenulostroma, Neodeightonia, Paraconiothyrium, Peroneutypa, Phaeoacremonium and Vanakripa. We discuss host-specificity in selected genera and compare the number of species epithets in each genus with the number of ITS (barcode) sequences deposited in GenBank and UNITE. We furthermore discuss the relationship between the divergence times of these genera with those of their hosts. We hypothesize whether there might be more species in these genera and discuss hosts and habitats that should be investigated for novel species discovery.
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Theelen B, Mixão V, Ianiri G, Goh JPZ, Dijksterhuis J, Heitman J, Dawson TL, Gabaldón T, Boekhout T. Multiple Hybridization Events Punctuate the Evolutionary Trajectory of Malassezia furfur. mBio 2022; 13:e0385321. [PMID: 35404119 PMCID: PMC9040865 DOI: 10.1128/mbio.03853-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 03/03/2022] [Indexed: 12/18/2022] Open
Abstract
Malassezia species are important fungal skin commensals and are part of the normal microbiota of humans and other animals. However, under certain circumstances these fungi can also display a pathogenic behavior. For example, Malassezia furfur is a common commensal of human skin and yet is often responsible for skin disorders but also systemic infections. Comparative genomics analysis of M. furfur revealed that some isolates have a hybrid origin, similar to several other recently described hybrid fungal pathogens. Because hybrid species exhibit genomic plasticity that can impact phenotypes, we sought to elucidate the genomic evolution and phenotypic characteristics of M. furfur hybrids in comparison to their parental lineages. To this end, we performed a comparative genomics analysis between hybrid strains and their presumptive parental lineages and assessed phenotypic characteristics. Our results provide evidence that at least two distinct hybridization events occurred between the same parental lineages and that the parental strains may have originally been hybrids themselves. Analysis of the mating-type locus reveals that M. furfur has a pseudobipolar mating system and provides evidence that after sexual liaisons of mating compatible cells, hybridization involved cell-cell fusion leading to a diploid/aneuploid state. This study provides new insights into the evolutionary trajectory of M. furfur and contributes with valuable genomic resources for future pathogenicity studies. IMPORTANCEMalassezia furfur is a common commensal member of human/animal microbiota that is also associated with several pathogenic states. Recent studies report involvement of Malassezia species in Crohn's disease, a type of inflammatory bowel disease, pancreatic cancer progression, and exacerbation of cystic fibrosis. A recent genomics analysis of M. furfur revealed the existence of hybrid isolates and identified their putative parental lineages. In this study, we explored the genomic and phenotypic features of these hybrids in comparison to their putative parental lineages. Our results revealed the existence of a pseudobipolar mating system in this species and showed evidence for the occurrence of multiple hybridization events in the evolutionary trajectory of M. furfur. These findings significantly advance our understanding of the evolution of this commensal microbe and are relevant for future studies exploring the role of hybridization in the adaptation to new niches or environments, including the emergence of pathogenicity.
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Affiliation(s)
- Bart Theelen
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
| | - Verónica Mixão
- Life Sciences Department, Barcelona Supercomputing Center, Barcelona, Spain
- Mechanisms of Disease Programme, Institute for Research in Biomedicine, Barcelona, Spain
| | - Giuseppe Ianiri
- Department of Agricultural, Environmental and Food Sciences, University of Molise, Campobasso, Italy
| | - Joleen Pei Zhen Goh
- A*STAR Skin Research Labs (A*SRL), Agency for Science, Technology and Research, Singapore
| | - Jan Dijksterhuis
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
| | - Joseph Heitman
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, USA
| | - Thomas L. Dawson
- A*STAR Skin Research Labs (A*SRL), Agency for Science, Technology and Research, Singapore
- Center for Cell Death, Injury and Regeneration, Departments of Drug Discovery and Biomedical Sciences and Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, South Carolina, USA
| | - Toni Gabaldón
- Life Sciences Department, Barcelona Supercomputing Center, Barcelona, Spain
- Mechanisms of Disease Programme, Institute for Research in Biomedicine, Barcelona, Spain
- Catalan Institution for Research and Advanced Studies, Barcelona, Spain
| | - Teun Boekhout
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
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34
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Yeasts Inhabiting Extreme Environments and Their Biotechnological Applications. Microorganisms 2022; 10:microorganisms10040794. [PMID: 35456844 PMCID: PMC9028089 DOI: 10.3390/microorganisms10040794] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 04/06/2022] [Accepted: 04/06/2022] [Indexed: 11/17/2022] Open
Abstract
Yeasts are microscopic fungi inhabiting all Earth environments, including those inhospitable for most life forms, considered extreme environments. According to their habitats, yeasts could be extremotolerant or extremophiles. Some are polyextremophiles, depending on their growth capacity, tolerance, and survival in the face of their habitat’s physical and chemical constitution. The extreme yeasts are relevant for the industrial production of value-added compounds, such as biofuels, lipids, carotenoids, recombinant proteins, enzymes, among others. This review calls attention to the importance of yeasts inhabiting extreme environments, including metabolic and adaptive aspects to tolerate conditions of cold, heat, water availability, pH, salinity, osmolarity, UV radiation, and metal toxicity, which are relevant for biotechnological applications. We explore the habitats of extreme yeasts, highlighting key species, physiology, adaptations, and molecular identification. Finally, we summarize several findings related to the industrially-important extremophilic yeasts and describe current trends in biotechnological applications that will impact the bioeconomy.
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35
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Franco MEE, Wisecaver JH, Arnold AE, Ju YM, Slot JC, Ahrendt S, Moore LP, Eastman KE, Scott K, Konkel Z, Mondo SJ, Kuo A, Hayes RD, Haridas S, Andreopoulos B, Riley R, LaButti K, Pangilinan J, Lipzen A, Amirebrahimi M, Yan J, Adam C, Keymanesh K, Ng V, Louie K, Northen T, Drula E, Henrissat B, Hsieh HM, Youens-Clark K, Lutzoni F, Miadlikowska J, Eastwood DC, Hamelin RC, Grigoriev IV, U'Ren JM. Ecological generalism drives hyperdiversity of secondary metabolite gene clusters in xylarialean endophytes. THE NEW PHYTOLOGIST 2022; 233:1317-1330. [PMID: 34797921 DOI: 10.1111/nph.17873] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 11/07/2021] [Indexed: 06/13/2023]
Abstract
Although secondary metabolites are typically associated with competitive or pathogenic interactions, the high bioactivity of endophytic fungi in the Xylariales, coupled with their abundance and broad host ranges spanning all lineages of land plants and lichens, suggests that enhanced secondary metabolism might facilitate symbioses with phylogenetically diverse hosts. Here, we examined secondary metabolite gene clusters (SMGCs) across 96 Xylariales genomes in two clades (Xylariaceae s.l. and Hypoxylaceae), including 88 newly sequenced genomes of endophytes and closely related saprotrophs and pathogens. We paired genomic data with extensive metadata on endophyte hosts and substrates, enabling us to examine genomic factors related to the breadth of symbiotic interactions and ecological roles. All genomes contain hyperabundant SMGCs; however, Xylariaceae have increased numbers of gene duplications, horizontal gene transfers (HGTs) and SMGCs. Enhanced metabolic diversity of endophytes is associated with a greater diversity of hosts and increased capacity for lignocellulose decomposition. Our results suggest that, as host and substrate generalists, Xylariaceae endophytes experience greater selection to diversify SMGCs compared with more ecologically specialised Hypoxylaceae species. Overall, our results provide new evidence that SMGCs may facilitate symbiosis with phylogenetically diverse hosts, highlighting the importance of microbial symbioses to drive fungal metabolic diversity.
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Affiliation(s)
- Mario E E Franco
- BIO5 Institute and Department of Biosystems Engineering, The University of Arizona, Tucson, AZ, 85721, USA
| | - Jennifer H Wisecaver
- Center for Plant Biology and Department of Biochemistry, Purdue University, West Lafayette, IN, 47907, USA
| | - A Elizabeth Arnold
- School of Plant Sciences and Department of Ecology and Evolutionary Biology, The University of Arizona, Tucson, AZ, 85721, USA
| | - Yu-Ming Ju
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 11529, Taiwan
| | - Jason C Slot
- Department of Plant Pathology, The Ohio State University, Columbus, OH, 43210, USA
| | - Steven Ahrendt
- Department of Energy, The Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Lillian P Moore
- BIO5 Institute and Department of Biosystems Engineering, The University of Arizona, Tucson, AZ, 85721, USA
| | - Katharine E Eastman
- Center for Plant Biology and Department of Biochemistry, Purdue University, West Lafayette, IN, 47907, USA
| | - Kelsey Scott
- Department of Plant Pathology, The Ohio State University, Columbus, OH, 43210, USA
| | - Zachary Konkel
- Department of Plant Pathology, The Ohio State University, Columbus, OH, 43210, USA
| | - Stephen J Mondo
- Department of Energy, The Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Alan Kuo
- Department of Energy, The Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Richard D Hayes
- Department of Energy, The Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Sajeet Haridas
- Department of Energy, The Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Bill Andreopoulos
- Department of Energy, The Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Robert Riley
- Department of Energy, The Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Kurt LaButti
- Department of Energy, The Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Jasmyn Pangilinan
- Department of Energy, The Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Anna Lipzen
- Department of Energy, The Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Mojgan Amirebrahimi
- Department of Energy, The Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Juying Yan
- Department of Energy, The Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Catherine Adam
- Department of Energy, The Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Keykhosrow Keymanesh
- Department of Energy, The Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Vivian Ng
- Department of Energy, The Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Katherine Louie
- Department of Energy, The Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Trent Northen
- Department of Energy, The Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Elodie Drula
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille Université, Marseille, 13288, France
- INRAE, Marseille, 13288, France
| | - Bernard Henrissat
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, DK-2800, Denmark
- Department of Biological Sciences, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
| | - Huei-Mei Hsieh
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 11529, Taiwan
| | - Ken Youens-Clark
- BIO5 Institute and Department of Biosystems Engineering, The University of Arizona, Tucson, AZ, 85721, USA
| | | | | | | | - Richard C Hamelin
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Igor V Grigoriev
- Department of Energy, The Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
| | - Jana M U'Ren
- BIO5 Institute and Department of Biosystems Engineering, The University of Arizona, Tucson, AZ, 85721, USA
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Evolutionary Morphogenesis of Sexual Fruiting Bodies in Basidiomycota: Toward a New Evo-Devo Synthesis. Microbiol Mol Biol Rev 2021; 86:e0001921. [PMID: 34817241 DOI: 10.1128/mmbr.00019-21] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The development of sexual fruiting bodies is one of the most complex morphogenetic processes in fungi. Mycologists have long been fascinated by the morphological and developmental diversity of fruiting bodies; however, evolutionary developmental biology of fungi still lags significantly behind that of animals or plants. Here, we summarize the current state of knowledge on fruiting bodies of mushroom-forming Basidiomycota, focusing on phylogenetic and developmental biology. Phylogenetic approaches have revealed a complex history of morphological transformations and convergence in fruiting body morphologies. Frequent transformations and convergence is characteristic of fruiting bodies in contrast to animals or plants, where main body plans are highly conserved. At the same time, insights into the genetic bases of fruiting body development have been achieved using forward and reverse genetic approaches in selected model systems. Phylogenetic and developmental studies of fruiting bodies have each yielded major advances, but they have produced largely disjunct bodies of knowledge. An integrative approach, combining phylogenetic, developmental, and functional biology, is needed to achieve a true fungal evolutionary developmental biology (evo-devo) synthesis for fungal fruiting bodies.
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37
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Seven Years at High Salinity-Experimental Evolution of the Extremely Halotolerant Black Yeast Hortaea werneckii. J Fungi (Basel) 2021; 7:jof7090723. [PMID: 34575761 PMCID: PMC8468603 DOI: 10.3390/jof7090723] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 08/30/2021] [Accepted: 09/02/2021] [Indexed: 01/26/2023] Open
Abstract
The experimental evolution of microorganisms exposed to extreme conditions can provide insight into cellular adaptation to stress. Typically, stress-sensitive species are exposed to stress over many generations and then examined for improvements in their stress tolerance. In contrast, when starting with an already stress-tolerant progenitor there may be less room for further improvement, it may still be able to tweak its cellular machinery to increase extremotolerance, perhaps at the cost of poorer performance under non-extreme conditions. To investigate these possibilities, a strain of extremely halotolerant black yeast Hortaea werneckii was grown for over seven years through at least 800 generations in a medium containing 4.3 M NaCl. Although this salinity is well above the optimum (0.8–1.7 M) for the species, the growth rate of the evolved H. werneckii did not change in the absence of salt or at high concentrations of NaCl, KCl, sorbitol, or glycerol. Other phenotypic traits did change during the course of the experimental evolution, including fewer multicellular chains in the evolved strains, significantly narrower cells, increased resistance to caspofungin, and altered melanisation. Whole-genome sequencing revealed the occurrence of multiple aneuploidies during the experimental evolution of the otherwise diploid H. werneckii. A significant overrepresentation of several gene groups was observed in aneuploid regions. Taken together, these changes suggest that long-term growth at extreme salinity led to alterations in cell wall and morphology, signalling pathways, and the pentose phosphate cycle. Although there is currently limited evidence for the adaptive value of these changes, they offer promising starting points for future studies of fungal halotolerance.
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Laundon D, Cunliffe M. A Call for a Better Understanding of Aquatic Chytrid Biology. FRONTIERS IN FUNGAL BIOLOGY 2021; 2:708813. [PMID: 37744140 PMCID: PMC10512372 DOI: 10.3389/ffunb.2021.708813] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 07/09/2021] [Indexed: 09/26/2023]
Abstract
The phylum Chytridiomycota (the "chytrids") is an early-diverging, mostly unicellular, lineage of fungi that consists of significant aquatic saprotrophs, parasites, and pathogens, and is of evolutionary interest because its members retain biological traits considered ancestral in the fungal kingdom. While the existence of aquatic chytrids has long been known, their fundamental biology has received relatively little attention. We are beginning to establish a detailed understanding of aquatic chytrid diversity and insights into their ecological functions and prominence. However, the underpinning biology governing their aquatic ecological activities and associated core processes remain largely understudied and therefore unresolved. Many biological questions are outstanding for aquatic chytrids. What are the mechanisms that control their development and life cycle? Which core processes underpin their aquatic influence? What can their biology tell us about the evolution of fungi and the wider eukaryotic tree of life? We propose that the field of aquatic chytrid ecology could be further advanced through the improved understanding of chytrid biology, including the development of model aquatic chytrids and targeted studies using culture-independent approaches.
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Affiliation(s)
- Davis Laundon
- Marine Biological Association, The Laboratory, Citadel Hill, Plymouth, United Kingdom
- School of Environmental Sciences, University of East Anglia, Norwich, United Kingdom
| | - Michael Cunliffe
- Marine Biological Association, The Laboratory, Citadel Hill, Plymouth, United Kingdom
- School of Biological and Marine Sciences, University of Plymouth, Plymouth, United Kingdom
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Gallo A, Perrone G. Current Approaches for Advancement in Understanding the Molecular Mechanisms of Mycotoxin Biosynthesis. Int J Mol Sci 2021; 22:ijms22157878. [PMID: 34360643 PMCID: PMC8346063 DOI: 10.3390/ijms22157878] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 07/20/2021] [Accepted: 07/21/2021] [Indexed: 12/17/2022] Open
Abstract
Filamentous fungi are able to synthesise a remarkable range of secondary metabolites, which play various key roles in the interaction between fungi and the rest of the biosphere, determining their ecological fitness. Many of them can have a beneficial activity to be exploited, as well as negative impact on human and animal health, as in the case of mycotoxins contaminating large quantities of food, feed, and agricultural products worldwide and posing serious health and economic risks. The elucidation of the molecular aspects of mycotoxin biosynthesis has been greatly sped up over the past decade due to the advent of next-generation sequencing technologies, which greatly reduced the cost of genome sequencing and related omic analyses. Here, we briefly highlight the recent progress in the use and integration of omic approaches for the study of mycotoxins biosynthesis. Particular attention has been paid to genomics and transcriptomic approaches for the identification and characterisation of biosynthetic gene clusters of mycotoxins and the understanding of the regulatory pathways activated in response to physiological and environmental factors leading to their production. The latest innovations in genome-editing technology have also provided a more powerful tool for the complete explanation of regulatory and biosynthesis pathways. Finally, we address the crucial issue of the interpretation of the combined omics data on the biology of the mycotoxigenic fungi. They are rapidly expanding and require the development of resources for more efficient integration, as well as the completeness and the availability of intertwined data for the research community.
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Affiliation(s)
- Antonia Gallo
- Institute of Sciences of Food Production (ISPA) National Research Council (CNR), 73100 Lecce, Italy
- Correspondence: (A.G.); (G.P.)
| | - Giancarlo Perrone
- Institute of Sciences of Food Production (ISPA) National Research Council (CNR), 70126 Bari, Italy
- Correspondence: (A.G.); (G.P.)
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40
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Kwak Y. An Update on Trichoderma Mitogenomes: Complete De Novo Mitochondrial Genome of the Fungal Biocontrol Agent Trichoderma harzianum (Hypocreales, Sordariomycetes), an Ex-Neotype Strain CBS 226.95, and Tracing the Evolutionary Divergences of Mitogenomes in Trichoderma. Microorganisms 2021; 9:1564. [PMID: 34442643 PMCID: PMC8401334 DOI: 10.3390/microorganisms9081564] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2021] [Revised: 07/08/2021] [Accepted: 07/19/2021] [Indexed: 12/13/2022] Open
Abstract
Members of the genus Trichoderma (Hypocreales), widely used as biofungicides, biofertilizers, and as model fungi for the industrial production of CAZymes, have actively been studied for the applications of their biological functions. Recently, the study of the nuclear genomes of Trichoderma has expanded in the directions of adaptation and evolution to gain a better understanding of their ecological traits. However, Trichoderma's mitochondria have received much less attention despite mitochondria being the most necessary element for sustaining cell life. In this study, a mitogenome of the fungus Trichoderma harzianum CBS 226.95 was assembled de novo. A 27,632 bp circular DNA molecule was revealed with specific features, such as the intronless of all core PCGs, one homing endonuclease, and a putative overlapping tRNA, on a closer phylogenetic relationship with T. reesei among hypocrealean fungi. Interestingly, the mitogenome of T. harzianum CBS 226.95 was predicted to have evolved earlier than those of other Trichoderma species and also assumed with a selection pressure in the cox3. Considering the bioavailability, both for the ex-neotype strain of the T. harzianum species complex and the most globally representative commercial fungal biocontrol agent, our results on the T. harzianum CBS 226.95 mitogenome provide crucial information which will be helpful criteria in future studies on Trichoderma.
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Affiliation(s)
- Yunyoung Kwak
- Écologie, Systématique et Évolution, CNRS, Université Paris Sud (Paris XI), Université Paris Saclay, AgroParisTech, 91400 Orsay, France;
- School of Applied Biosciences, Kyungpook National University, Daegu 41566, Korea
- Institute for Quality and Safety Assessment of Agricultural Products, Kyungpook National University, Daegu 41566, Korea
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Boekhout T, Aime MC, Begerow D, Gabaldón T, Heitman J, Kemler M, Khayhan K, Lachance MA, Louis EJ, Sun S, Vu D, Yurkov A. The evolving species concepts used for yeasts: from phenotypes and genomes to speciation networks. FUNGAL DIVERS 2021; 109:27-55. [PMID: 34720775 PMCID: PMC8550739 DOI: 10.1007/s13225-021-00475-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 05/31/2021] [Indexed: 12/12/2022]
Abstract
Here we review how evolving species concepts have been applied to understand yeast diversity. Initially, a phenotypic species concept was utilized taking into consideration morphological aspects of colonies and cells, and growth profiles. Later the biological species concept was added, which applied data from mating experiments. Biophysical measurements of DNA similarity between isolates were an early measure that became more broadly applied with the advent of sequencing technology, leading to a sequence-based species concept using comparisons of parts of the ribosomal DNA. At present phylogenetic species concepts that employ sequence data of rDNA and other genes are universally applied in fungal taxonomy, including yeasts, because various studies revealed a relatively good correlation between the biological species concept and sequence divergence. The application of genome information is becoming increasingly common, and we strongly recommend the use of complete, rather than draft genomes to improve our understanding of species and their genome and genetic dynamics. Complete genomes allow in-depth comparisons on the evolvability of genomes and, consequently, of the species to which they belong. Hybridization seems a relatively common phenomenon and has been observed in all major fungal lineages that contain yeasts. Note that hybrids may greatly differ in their post-hybridization development. Future in-depth studies, initially using some model species or complexes may shift the traditional species concept as isolated clusters of genetically compatible isolates to a cohesive speciation network in which such clusters are interconnected by genetic processes, such as hybridization.
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Affiliation(s)
- Teun Boekhout
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
- Institute of Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam, The Netherlands
| | - M. Catherine Aime
- Dept Botany and Plant Pathology, College of Agriculture, Purdue University, West Lafayette, IN 47907 USA
| | - Dominik Begerow
- Evolution of Plants and Fungi, Ruhr-University Bochum, 44801 Bochum, Germany
| | - Toni Gabaldón
- Barcelona Supercomputing Centre (BSC–CNS), Jordi Girona, 29, 08034 Barcelona, Spain
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028 Barcelona, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain
| | - Joseph Heitman
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710 USA
| | - Martin Kemler
- Evolution of Plants and Fungi, Ruhr-University Bochum, 44801 Bochum, Germany
| | - Kantarawee Khayhan
- Department of Microbiology and Parasitology, Faculty of Medical Sciences, University of Phayao, Phayao, 56000 Thailand
| | - Marc-André Lachance
- Department of Biology, University of Western Ontario, London, ON N6A 5B7 Canada
| | - Edward J. Louis
- Department of Genetics and Genome Biology, Genetic Architecture of Complex Traits, University of Leicester, Leicester, LE1 7RH UK
| | - Sheng Sun
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710 USA
| | - Duong Vu
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
| | - Andrey Yurkov
- German Collection of Microorganisms and Cell Cultures, Leibniz Institute DSMZ, Brunswick, Germany
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42
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Raihan T, Azad AK, Ahmed J, Shepon MR, Dey P, Chowdhury N, Aunkor TH, Ali H, Suhani S. Extracellular metabolites of endophytic fungi from Azadirachta indica inhibit multidrug-resistant bacteria and phytopathogens. Future Microbiol 2021; 16:557-576. [PMID: 33998269 DOI: 10.2217/fmb-2020-0259] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Aim: To evaluate antimicrobial activity of extracellular metabolites (EMs) of endophytic fungal isolates (EFIs) from Azadirachta indica. Materials & methods: EFIs were identified by internal transcribed spacer (ITS) sequencing. Antimicrobial activity, and minimum inhibitor concentration (MIC) and minimum bactericidal concentration (MBC) were determined using agar diffusion and microdilution method, respectively. Results: Seventeen EFIs were isolated from different organs of A. indica. Eight of them were identified based on ITS sequencing. The EMs of EFIs inhibited the growth of six multidrug-resistant (MDR) bacterial superbugs and three phytopathogenic fungi. The MDR bacterial superbugs are resistant to six commercial antibiotics of different generations but susceptible to EMs of EFIs. The MIC (0.125-1.0 μg/μl), MBC (0.5-4.0 μg/μl) and minimum fungicidal concentration (1.0-4.0 μg/μl) of the EMs from EFIs are lower enough. Conclusion: The EMs of the EFIs have promising antimicrobial activity against MDR bacteria and phytopathogenic fungi.
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Affiliation(s)
- Topu Raihan
- Department of Genetic Engineering & Biotechnology, Shahjalal University of Science & Technology, Sylhet, 3114, Bangladesh
| | - Abul K Azad
- Department of Genetic Engineering & Biotechnology, Shahjalal University of Science & Technology, Sylhet, 3114, Bangladesh
| | - Jahed Ahmed
- Department of Genetic Engineering & Biotechnology, Shahjalal University of Science & Technology, Sylhet, 3114, Bangladesh.,Louvain Institute of Biomolecular Science & Technology, Universite Catholique de Louvain, Louvain-la-Neuve, 1348, Belgium
| | - Mukhlesur R Shepon
- Department of Genetic Engineering & Biotechnology, Shahjalal University of Science & Technology, Sylhet, 3114, Bangladesh
| | - Prattay Dey
- Department of Genetic Engineering & Biotechnology, Shahjalal University of Science & Technology, Sylhet, 3114, Bangladesh
| | - Nandan Chowdhury
- Department of Genetic Engineering & Biotechnology, Shahjalal University of Science & Technology, Sylhet, 3114, Bangladesh
| | - Toasin H Aunkor
- Department of Genetic Engineering & Biotechnology, Shahjalal University of Science & Technology, Sylhet, 3114, Bangladesh
| | - Hazrat Ali
- Department of Genetic Engineering & Biotechnology, Shahjalal University of Science & Technology, Sylhet, 3114, Bangladesh
| | - Sabrina Suhani
- Department of Genetic Engineering & Biotechnology, Shahjalal University of Science & Technology, Sylhet, 3114, Bangladesh
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Zilber-Rosenberg I, Rosenberg E. Microbial driven genetic variation in holobionts. FEMS Microbiol Rev 2021; 45:6261188. [PMID: 33930136 DOI: 10.1093/femsre/fuab022] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 04/11/2021] [Indexed: 12/11/2022] Open
Abstract
Genetic variation in holobionts, (host and microbiome), occurring by changes in both host and microbiome genomes, can be observed from two perspectives: observable variations and the processes that bring about the variation. The observable includes the enormous genetic diversity of prokaryotes, which gave rise to eukaryotic organisms. Holobionts then evolved a rich microbiome with a stable core containing essential genes, less so common taxa, and a more diverse non-core enabling considerable genetic variation. The result being that, the human gut microbiome, for example, contains 1,000 times more unique genes than are present in the human genome. Microbial driven genetic variation processes in holobionts include: (1) Acquisition of novel microbes from the environment, which bring in multiple genes in one step, (2) amplification/reduction of certain microbes in the microbiome, that contribute to holobiont` s adaptation to changing conditions, (3) horizontal gene transfer between microbes and between microbes and host, (4) mutation, which plays an important role in optimizing interactions between different microbiota and between microbiota and host. We suggest that invertebrates and plants, where microbes can live intracellularly, have a greater chance of genetic exchange between microbiota and host, thus a greater chance of vertical transmission and a greater effect of microbiome on evolution of host than vertebrates. However, even in vertebrates the microbiome can aid in environmental fluctuations by amplification/reduction and by acquisition of novel microorganisms.
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Affiliation(s)
- Ilana Zilber-Rosenberg
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Ramat Aviv Israel
| | - Eugene Rosenberg
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Ramat Aviv Israel
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44
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Heineike BM, El-Samad H. Paralogs in the PKA Regulon Traveled Different Evolutionary Routes to Divergent Expression in Budding Yeast. FRONTIERS IN FUNGAL BIOLOGY 2021; 2:642336. [PMID: 37744115 PMCID: PMC10512328 DOI: 10.3389/ffunb.2021.642336] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 03/24/2021] [Indexed: 09/26/2023]
Abstract
Functional divergence of duplicate genes, or paralogs, is an important driver of novelty in evolution. In the model yeast Saccharomyces cerevisiae, there are 547 paralog gene pairs that survive from an interspecies Whole Genome Hybridization (WGH) that occurred ~100MYA. In this work, we report that ~1/6th (110) of these WGH paralogs pairs (or ohnologs) are differentially expressed with a striking pattern upon Protein Kinase A (PKA) inhibition. One member of each pair in this group has low basal expression that increases upon PKA inhibition, while the other has moderate and unchanging expression. For these genes, expression of orthologs upon PKA inhibition in the non-WGH species Kluyveromyces lactis and for PKA-related stresses in other budding yeasts shows unchanging expression, suggesting that lack of responsiveness to PKA was likely the typical ancestral phenotype prior to duplication. Promoter sequence analysis across related budding yeast species further revealed that the subsequent emergence of PKA-dependence took different evolutionary routes. In some examples, regulation by PKA and differential expression appears to have arisen following the WGH, while in others, regulation by PKA appears to have arisen in one of the two parental lineages prior to the WGH. More broadly, our results illustrate the unique opportunities presented by a WGH event for generating functional divergence by bringing together two parental lineages with separately evolved regulation into one species. We propose that functional divergence of two ohnologs can be facilitated through such regulatory divergence.
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Affiliation(s)
- Benjamin M. Heineike
- Bioinformatics Graduate Program, University of California, San Francisco, San Francisco, CA, United States
| | - Hana El-Samad
- Department of Biochemistry and Biophysics, California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, CA, United States
- Chan Zuckerberg Biohub, San Francisco, CA, United States
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45
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Ahumada-Rudolph R, Novoa V, Becerra J, Cespedes C, Cabrera-Pardo JR. Mycoremediation of oxytetracycline by marine fungi mycelium isolated from salmon farming areas in the south of Chile. Food Chem Toxicol 2021; 152:112198. [PMID: 33857548 DOI: 10.1016/j.fct.2021.112198] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 03/10/2021] [Accepted: 04/06/2021] [Indexed: 11/18/2022]
Abstract
Antibiotics are extensively used for growth promotion purposes in intensive aquaculture. In Chile, the use of antibiotics in salmon farming is excessive, approximately 62 times more than is used in Norway. In the salmon industry, antibiotics such as oxytetracycline (OTC) are administered in the diet, both in the juvenile stage in freshwater and in the fattening process of salmon in marine sectors. We have investigated the fjords of Chile, where many salmon farms are located, searching for fungi able to degrade this tetracycline antibiotic. We have evaluated the OTC degradation ability of the following; Penicillium commune, Epicoccum nigrum, Trichoderma harzianum, Aspergillus terreus and Beauveria bassiana, isolated from sediments in salmon farms from southern Chile. In all these fungal strains, the amount of OTC decreased in the culture medium, as adsorbed in the mycelia, after the third day of exposure. These strains were capable of degrading OTC at remarkable rates up to 78%, by the 15th day. This is the first study showing that the mycelium of these fungal strains has the ability to degrade OTC. We believe the knowledge produced by these results has the potential to serve as a basis for implementing a bioremediation process in the near future.
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Affiliation(s)
- Ramón Ahumada-Rudolph
- Laboratorio de Química Aplicada y Sustentable, Departamento de Química, Facultad de Ciencias, Universidad del Bío-Bío, Avenida Collao, 1202, PO Box 5-C, Concepción, Chile
| | - Vanessa Novoa
- Department of Spatial Planning, School of Environmental Sciences, EULA Center, Universidad de Concepción, Víctor Lamas, 1290, PO Box 160-C., Concepción, Chile; Centro de recursos hídricos para la agricultura y la minería, Fondap CRHIAM, Universidad de Concepción, Concepción, PC, 4070411, Chile
| | - Julio Becerra
- Laboratorio de Química Aplicada y Sustentable, Departamento de Química, Facultad de Ciencias, Universidad del Bío-Bío, Avenida Collao, 1202, PO Box 5-C, Concepción, Chile
| | - Carlos Cespedes
- Departamento de Ciencias Básicas, Facultad de Ciencias, Universidad del Bío-Bío, Avenida Collao, 1202, PO Box 5-C, Concepción, Chile
| | - Jaime R Cabrera-Pardo
- Laboratorio de Química Aplicada y Sustentable, Departamento de Química, Facultad de Ciencias, Universidad del Bío-Bío, Avenida Collao, 1202, PO Box 5-C, Concepción, Chile; Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, UT, 84112, USA.
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46
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Pozo MJ, Zabalgogeazcoa I, Vazquez de Aldana BR, Martinez-Medina A. Untapping the potential of plant mycobiomes for applications in agriculture. CURRENT OPINION IN PLANT BIOLOGY 2021; 60:102034. [PMID: 33827007 DOI: 10.1016/j.pbi.2021.102034] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 02/11/2021] [Accepted: 02/21/2021] [Indexed: 05/20/2023]
Abstract
Plant-fungal interactions are widespread in nature, and their multiple benefits for plant growth and health have been amply demonstrated. Endophytic and epiphytic fungi can significantly increase plant resilience, improving plant nutrition, stress tolerance and defence. Although some of these interactions have been known for decades, the relevance of the plant mycobiome within the plant microbiome has been largely underestimated. Our limited knowledge of fungal biology and their interactions with plants in the broader phytobiome context has hampered the development of optimal biotechnological applications in agrosystems and natural ecosystems. Exciting recent technical and knowledge advances in the context of molecular and systems biology open a plethora of opportunities for developing this field of research.
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Affiliation(s)
- Maria J Pozo
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, CSIC, Granada, Spain.
| | - Iñigo Zabalgogeazcoa
- Plant-Microbe Interactions, Institute of Natural Resources and Agrobiology of Salamanca, IRNASA-CSIC, Salamanca, Spain
| | - Beatriz R Vazquez de Aldana
- Plant-Microbe Interactions, Institute of Natural Resources and Agrobiology of Salamanca, IRNASA-CSIC, Salamanca, Spain
| | - Ainhoa Martinez-Medina
- Plant-Microbe Interactions, Institute of Natural Resources and Agrobiology of Salamanca, IRNASA-CSIC, Salamanca, Spain
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Uncovering Prospective Role and Applications of Existing and New Nutraceuticals from Bacterial, Fungal, Algal and Cyanobacterial, and Plant Sources. SUSTAINABILITY 2021. [DOI: 10.3390/su13073671] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Nutraceuticals are a category of products more often associated with food but having pharmaceuticals property and characteristics. However, there is still no internationally accepted concept of these food-pharmaceutical properties, and their interpretation can differ from country to country. Nutraceuticals are used as part of dietary supplements in most countries. They can be phytochemicals which are biologically active and have health benefits. These can be supplied as a supplement and/or as a functional food to the customer. For human health and longevity, these materials are likely to play a vital role. Consumption of these items is typical without a therapeutic prescription and/or supervision by the vast majority of the public. The development of nutraceuticals can be achieved through many bioresources and organisms. This review article will discuss the current research on nutraceuticals from different biological sources and their potential use as an agent for improving human health and well-being, as well as the gaps and future perspective of research related to nutraceutical development.
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48
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Romero-Zambrano GL, Bermúdez-Puga SA, Sánchez-Yumbo AF, Yánez-Galarza JK, Ortega-Andrade HM, Naranjo-Briceño L. Amphibian chytridiomycosis, a lethal pandemic disease caused by the killer fungus Batrachochytrium dendrobatidis: New approaches to host defense mechanisms and techniques for detection and monitoring. BIONATURA 2021. [DOI: 10.21931/rb/2021.06.01.28] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Chytridiomycosis is a catastrophic disease currently decimating worldwide amphibian populations, caused by the panzootic chytrid fungus Batrachochytrium dendrobatidis. Massive species decline to extinction catalyzes radical changes in ecosystems globally, including the largest continuous rainforest ecosystem on Earth, the Amazon rainforest. Innovative research that aims to propose feasible mechanisms of mitigation and the origins of the disease is vital, including studies addressing climatic effects on the expansion of chytridiomycosis. Thus, this publication aims to provide a comprehensive review of: i) the current technologies used for B. dendrobatidis detection and monitoring, and ii) the known Neotropical amphibian's skin microbiota with anti-fungal properties against B. dendrobatidis. Several immunologic and DNA-based methods are discussed to understand the emerging fungal pathogens and their effects on the biosphere, which can help to mitigate the devastating ecological impacts of mass amphibian morbidity. The establishment of rapid and highly accurate B. dendrobatidis detection techniques and methods for monitoring amphibian's cutaneous microbiome is crucial in the fight against chytridiomycosis.
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Affiliation(s)
- Génesis L. Romero-Zambrano
- Biotechnology Engineering Career. Faculty of Life Sciences. Universidad Regional Amazónica Ikiam, Tena, Ecuador 150150
| | - Stalin A. Bermúdez-Puga
- Biotechnology Engineering Career. Faculty of Life Sciences. Universidad Regional Amazónica Ikiam, Tena, Ecuador 150150
| | - Alex F. Sánchez-Yumbo
- Biotechnology Engineering Career. Faculty of Life Sciences. Universidad Regional Amazónica Ikiam, Tena, Ecuador 150150
| | - Jomira K. Yánez-Galarza
- Biotechnology Engineering Career. Faculty of Life Sciences. Universidad Regional Amazónica Ikiam, Tena, Ecuador 150150
| | - H. Mauricio Ortega-Andrade
- 2Biogeography and Spatial Ecology Research Group, Universidad Regional Amazónica Ikiam, Tena, Ecuador 150150 3Herpetology Division, Instituto Nacional de Biodiversidad (INABIO), calle Rumipamba 341 y Av. de los Shyris, Quito, Ecuador
| | - Leopoldo Naranjo-Briceño
- Biotechnology Engineering Career. Faculty of Life Sciences. Universidad Regional Amazónica Ikiam, Tena, Ecuador 150150
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Kulik T, Van Diepeningen AD, Hausner G. Editorial: The Significance of Mitogenomics in Mycology. Front Microbiol 2021; 11:628579. [PMID: 33488569 PMCID: PMC7817700 DOI: 10.3389/fmicb.2020.628579] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 12/10/2020] [Indexed: 01/30/2023] Open
Affiliation(s)
- Tomasz Kulik
- Department of Botany and Nature Protection, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| | - Anne D Van Diepeningen
- B.U. Biointeractions and Plant Health, Wageningen Plant Research, Wageningen University & Research, Wageningen, Netherlands
| | - Georg Hausner
- Department of Microbiology, University of Manitoba, Winnipeg, MB, Canada
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50
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Gabaldón T. Grand Challenges in Fungal Genomics and Evolution. FRONTIERS IN FUNGAL BIOLOGY 2020; 1:594855. [PMID: 37743874 PMCID: PMC10512400 DOI: 10.3389/ffunb.2020.594855] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 08/28/2020] [Indexed: 09/26/2023]
Affiliation(s)
- Toni Gabaldón
- Barcelona Supercomputing Center (BCS-CNS), Barcelona, Spain
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
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