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Wang Z, Wang YW, Kasuga T, Lopez-Giraldez F, Zhang Y, Zhang Z, Wang Y, Dong C, Sil A, Trail F, Yarden O, Townsend JP. Lineage-specific genes are clustered with HET-domain genes and respond to environmental and genetic manipulations regulating reproduction in Neurospora. PLoS Genet 2023; 19:e1011019. [PMID: 37934795 PMCID: PMC10684091 DOI: 10.1371/journal.pgen.1011019] [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: 05/23/2023] [Revised: 11/28/2023] [Accepted: 10/16/2023] [Indexed: 11/09/2023] Open
Abstract
Lineage-specific genes (LSGs) have long been postulated to play roles in the establishment of genetic barriers to intercrossing and speciation. In the genome of Neurospora crassa, most of the 670 Neurospora LSGs that are aggregated adjacent to the telomeres are clustered with 61% of the HET-domain genes, some of which regulate self-recognition and define vegetative incompatibility groups. In contrast, the LSG-encoding proteins possess few to no domains that would help to identify potential functional roles. Possible functional roles of LSGs were further assessed by performing transcriptomic profiling in genetic mutants and in response to environmental alterations, as well as examining gene knockouts for phenotypes. Among the 342 LSGs that are dynamically expressed during both asexual and sexual phases, 64% were detectable on unusual carbon sources such as furfural, a wildfire-produced chemical that is a strong inducer of sexual development, and the structurally-related furan 5-hydroxymethyl furfural (HMF). Expression of a significant portion of the LSGs was sensitive to light and temperature, factors that also regulate the switch from asexual to sexual reproduction. Furthermore, expression of the LSGs was significantly affected in the knockouts of adv-1 and pp-1 that regulate hyphal communication, and expression of more than one quarter of the LSGs was affected by perturbation of the mating locus. These observations encouraged further investigation of the roles of clustered lineage-specific and HET-domain genes in ecology and reproduction regulation in Neurospora, especially the regulation of the switch from the asexual growth to sexual reproduction, in response to dramatic environmental conditions changes.
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Affiliation(s)
- Zheng Wang
- Department of Biostatistics, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Yen-Wen Wang
- Department of Biostatistics, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Takao Kasuga
- College of Biological Sciences, University of California, Davis, California, United States of America
| | | | - Yang Zhang
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Zhang Zhang
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Yaning Wang
- Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Caihong Dong
- Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Anita Sil
- Department of Microbiology and Immunology, University of California, San Francisco, California, United States of America
| | - Frances Trail
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, Michigan, United States of America
| | - 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
| | - Jeffrey P. Townsend
- Department of Biostatistics, Yale School of Public Health, New Haven, Connecticut, United States of America
- Department of Ecology and Evolutionary Biology, Program in Microbiology, and Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, United States of America
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Montenegro-Montero A, Goity A, Canessa PF, Larrondo LF. Identification of a common secondary mutation in the Neurospora crassa knockout collection conferring a cell fusion-defective phenotype. Microbiol Spectr 2023; 11:e0208723. [PMID: 37623742 PMCID: PMC10580951 DOI: 10.1128/spectrum.02087-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 07/12/2023] [Indexed: 08/26/2023] Open
Abstract
Gene-deletion mutants represent a powerful tool to study gene function. The filamentous fungus Neurospora crassa is a well-established model organism, and features a comprehensive gene knockout strain collection. While these mutant strains have been used in numerous studies, resulting in the functional annotation of many Neurospora genes, direct confirmation of gene-phenotype relationships is often lacking, which is particularly relevant given the possibility of background mutations, sample contamination, and/or strain mislabeling. Indeed, spontaneous mutations resulting in phenotypes resembling many cell fusion mutants have long been known to occur at relatively high frequency in N. crassa, and these secondary mutations are common in the Neurospora deletion collection. The identity of these mutations, however, is largely unknown. Here, we report that the Δada-3 strain from the N. crassa knockout collection, which exhibits a cell fusion defect, harbors a secondary mutation responsible for this phenotype. Through whole-genome sequencing and genetic analyses, we found a ~30-Kb deletion in this strain affecting a known cell fusion-related gene, so/ham-1, and show that it is the absence of this gene-and not of ada-3-that underlies its cell fusion defect. We additionally found three other knockout strains harboring the same deletion, suggesting that this mutation may be common in the collection and could have impacted previous studies. Our findings provide a cautionary note and highlight the importance of proper functional validation of strains from mutant collections. We discuss our results in the context of the spread of cell fusion-defective cheater variants in N. crassa cultures. IMPORTANCE This study emphasizes the need for careful and detailed characterization of strains from mutant collections. Specifically, we found a common deletion in various strains from the Neurospora crassa gene knockout collection that results in a cell fusion-defective phenotype. This is noteworthy because this collection is known to contain background mutations-of a largely unclear nature-that produce cell fusion-defective phenotypes. Our results describe an example of such mutations, and highlight how this common genetic defect could have impacted previous studies that have used the affected strains. Furthermore, they provide a cautionary note about the use of Neurospora strains with similar phenotypes. Lastly, these findings offer additional details relevant to our understanding of the origin and spread of cell fusion-defective cheater variants in N. crassa cultures.
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Affiliation(s)
- Alejandro Montenegro-Montero
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
- Agencia Nacional de Investigación y Desarrollo-Millennium Science Initiative Program, Millennium Institute for Integrative Biology, Santiago, Chile
| | - Alejandra Goity
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
- Agencia Nacional de Investigación y Desarrollo-Millennium Science Initiative Program, Millennium Institute for Integrative Biology, Santiago, Chile
| | - Paulo F. Canessa
- Agencia Nacional de Investigación y Desarrollo-Millennium Science Initiative Program, Millennium Institute for Integrative Biology, Santiago, Chile
- Centro de Biotecnología Vegetal, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
| | - Luis F. Larrondo
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
- Agencia Nacional de Investigación y Desarrollo-Millennium Science Initiative Program, Millennium Institute for Integrative Biology, Santiago, Chile
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RFID Data Analysis and Evaluation Based on Big Data and Data Clustering. COMPUTATIONAL INTELLIGENCE AND NEUROSCIENCE 2022; 2022:3432688. [PMID: 35378806 PMCID: PMC8976611 DOI: 10.1155/2022/3432688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Accepted: 03/02/2022] [Indexed: 11/17/2022]
Abstract
The era people live in is the era of big data, and massive data carry a large amount of information. This study aims to analyze RFID data based on big data and clustering algorithms. In this study, a RFID data extraction technology based on joint Kalman filter fusion is proposed. In the system, the proposed data extraction technology can effectively read RFID tags. The data are recorded, and the KM-KL clustering algorithm is proposed for RFID data, which combines the advantages of the K-means algorithm. The improved KM-KL clustering algorithm can effectively analyze and evaluate RFID data. The experimental results of this study prove that the recognition error rate of the RFID data extraction technology based on the joint Kalman filter fusion is only 2.7%. The improved KM-KL clustering algorithm also has better performance than the traditional algorithm.
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Lütkenhaus R, Breuer J, Nowrousian M. Functional characterization of the developmental genes asm2, asm3, and spt3 required for fruiting body formation in the filamentous ascomycete Sordaria macrospora. Genetics 2021; 219:iyab103. [PMID: 34849873 PMCID: PMC8633134 DOI: 10.1093/genetics/iyab103] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 06/30/2021] [Indexed: 01/10/2023] Open
Abstract
The formation of fruiting bodies is one of the most complex developmental processes in filamentous ascomycetes. It requires the development of sexual structures that give rise to meiosporangia (asci) and meiotic spores (ascospores) as well as surrounding structures for protection and dispersal of the spores. Previous studies have shown that these developmental processes are accompanied by significant changes of the transcriptome, and comparative transcriptomics of different fungi as well as the analysis of transcriptome changes in developmental mutants have aided in the identification of differentially regulated genes that are themselves involved in regulating fruiting body development. In previous analyses, we used transcriptomics to identify the genes asm2 and spt3, which result in developmental phenotypes when deleted in Sordaria macrospora. In this study, we identified another gene, asm3, required for fruiting body formation, and performed transcriptomics analyses of Δasm2, Δasm3, and Δspt3. Deletion of spt3, which encodes a subunit of the SAGA complex, results in a block at an early stage of development and drastic changes in the transcriptome. Deletion mutants of asm2 and asm3 are able to form fruiting bodies, but have defects in ascospore maturation. Transcriptomics analysis of fruiting bodies revealed a large overlap in differentially regulated genes in Δasm2 and Δasm3 compared to the wild type. Analysis of nuclear distribution during ascus development showed that both mutants undergo meiosis and postmeiotic divisions, suggesting that the transcriptomic and morphological changes might be related to defects in the morphogenesis of structural features of the developing asci and ascospores.
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Affiliation(s)
- Ramona Lütkenhaus
- Lehrstuhl für Molekulare und Zelluläre Botanik, Ruhr-Universität Bochum, Bochum 44801, Germany
| | - Jan Breuer
- Lehrstuhl für Molekulare und Zelluläre Botanik, Ruhr-Universität Bochum, Bochum 44801, Germany
| | - Minou Nowrousian
- Lehrstuhl für Molekulare und Zelluläre Botanik, Ruhr-Universität Bochum, Bochum 44801, Germany
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