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Maiden NA, Syd Ali N, Ahmad K, Atan S, Wong MY. Growth and physiological responses of Hevea brasiliensis to Rigidoporus microporus infection. J RUBBER RES 2022. [DOI: 10.1007/s42464-022-00156-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Sahu N, Merényi Z, Bálint B, Kiss B, Sipos G, Owens RA, Nagy LG. Hallmarks of Basidiomycete Soft- and White-Rot in Wood-Decay -Omics Data of Two Armillaria Species. Microorganisms 2021; 9:149. [PMID: 33440901 PMCID: PMC7827401 DOI: 10.3390/microorganisms9010149] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 01/01/2021] [Accepted: 01/08/2021] [Indexed: 12/13/2022] Open
Abstract
Wood-decaying Basidiomycetes are among the most efficient degraders of plant cell walls, making them key players in forest ecosystems, global carbon cycle, and in bio-based industries. Recent insights from -omics data revealed a high functional diversity of wood-decay strategies, especially among the traditional white-rot and brown-rot dichotomy. We examined the mechanistic bases of wood-decay in the conifer-specialists Armillaria ostoyae and Armillaria cepistipes using transcriptomic and proteomic approaches. Armillaria spp. (Fungi, Basidiomycota) include devastating pathogens of temperate forests and saprotrophs that decay wood. They have been discussed as white-rot species, though their response to wood deviates from typical white-rotters. While we observed an upregulation of a diverse suite of plant cell wall degrading enzymes, unlike white-rotters, they possess and express an atypical wood-decay repertoire in which pectinases and expansins are enriched, whereas lignin-decaying enzymes (LDEs) are generally downregulated. This combination of wood decay genes resembles the soft-rot of Ascomycota and appears widespread among Basidiomycota that produce a superficial white rot-like decay. These observations are consistent with ancestral soft-rot decay machinery conserved across asco- and Basidiomycota, a gain of efficient lignin-degrading ability in white-rot fungi and repeated, complete, or partial losses of LDE encoding gene repertoires in brown- and secondarily soft-rot fungi.
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Affiliation(s)
- Neha Sahu
- Biological Research Center, Synthetic and Systems Biology Unit, 6726 Szeged, Hungary; (N.S.); (Z.M.); (B.B.); (B.K.)
- Doctoral School of Biology, Faculty of Science and Informatics, University of Szeged, 6726 Szeged, Hungary
| | - Zsolt Merényi
- Biological Research Center, Synthetic and Systems Biology Unit, 6726 Szeged, Hungary; (N.S.); (Z.M.); (B.B.); (B.K.)
| | - Balázs Bálint
- Biological Research Center, Synthetic and Systems Biology Unit, 6726 Szeged, Hungary; (N.S.); (Z.M.); (B.B.); (B.K.)
| | - Brigitta Kiss
- Biological Research Center, Synthetic and Systems Biology Unit, 6726 Szeged, Hungary; (N.S.); (Z.M.); (B.B.); (B.K.)
| | - György Sipos
- Research Center for Forestry and Wood Industry, Functional Genomics and Bioinformatics Group, University of Sopron, 9400 Sopron, Hungary;
- Swiss Federal Research Institute WSL, Zürcherstrasse 111, CH-8903 Birmensdorf, Switzerland
| | - Rebecca A. Owens
- Department of Biology, Maynooth University, W23 F2H6 Kildare, Ireland;
| | - László G. Nagy
- Biological Research Center, Synthetic and Systems Biology Unit, 6726 Szeged, Hungary; (N.S.); (Z.M.); (B.B.); (B.K.)
- Department of Plant Anatomy, Institute of Biology, Eötvös Loránd University, 1117 Budapest, Hungary
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Oghenekaro AO, Kovalchuk A, Raffaello T, Camarero S, Gressler M, Henrissat B, Lee J, Liu M, Martínez AT, Miettinen O, Mihaltcheva S, Pangilinan J, Ren F, Riley R, Ruiz-Dueñas FJ, Serrano A, Thon MR, Wen Z, Zeng Z, Barry K, Grigoriev IV, Martin F, Asiegbu FO. Genome sequencing of Rigidoporus microporus provides insights on genes important for wood decay, latex tolerance and interspecific fungal interactions. Sci Rep 2020; 10:5250. [PMID: 32251355 PMCID: PMC7089950 DOI: 10.1038/s41598-020-62150-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 03/10/2020] [Indexed: 11/27/2022] Open
Abstract
Fungal plant pathogens remain a serious threat to the sustainable agriculture and forestry, despite the extensive efforts undertaken to control their spread. White root rot disease is threatening rubber tree (Hevea brasiliensis) plantations throughout South and Southeast Asia and Western Africa, causing tree mortality and severe yield losses. Here, we report the complete genome sequence of the basidiomycete fungus Rigidoporus microporus, a causative agent of the disease. Our phylogenetic analysis confirmed the position of R. microporus among the members of Hymenochaetales, an understudied group of basidiomycetes. Our analysis further identified pathogen's genes with a predicted role in the decay of plant cell wall polymers, in the utilization of latex components and in interspecific interactions between the pathogen and other fungi. We also detected putative horizontal gene transfer events in the genome of R. microporus. The reported first genome sequence of a tropical rubber tree pathogen R. microporus should contribute to the better understanding of how the fungus is able to facilitate wood decay and nutrient cycling as well as tolerate latex and utilize resinous extractives.
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Affiliation(s)
- Abbot O Oghenekaro
- Faculty of Life Sciences, Department of Plant Biology and Biotechnology, University of Benin, P.M.B 1154, Benin City, Nigeria
- Faculty of Agriculture and Forestry, Department of Forest Sciences, University of Helsinki, P.O. Box 27, FIN-00014, Helsinki, Finland
- Department of Plant Science, University of Manitoba, MB R3T 2N2, Winnipeg, Canada
| | - Andriy Kovalchuk
- Faculty of Agriculture and Forestry, Department of Forest Sciences, University of Helsinki, P.O. Box 27, FIN-00014, Helsinki, Finland
| | - Tommaso Raffaello
- Faculty of Agriculture and Forestry, Department of Forest Sciences, University of Helsinki, P.O. Box 27, FIN-00014, Helsinki, Finland
| | - Susana Camarero
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu 9, E28040, Madrid, Spain
| | - Markus Gressler
- Department of Pharmaceutical Microbiology at the Hans Knöll Institute, Friedrich Schiller University, Jena, Germany
| | - Bernard Henrissat
- Aix-Marseille Université, Architecture et Fonction des Macromolécules Biologiques, CNRS, UMR 7257, 13288, Marseille, cedex 9, France
- USC1408 Architecture et Fonction des Macromolécules Biologiques, Institut National de la Recherche Agronomique, F-13288, Marseille, France
- Department of Biological Sciences, King Abdulaziz University, 23218, Jeddah, Saudi Arabia
| | - Juna Lee
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Mengxia Liu
- Faculty of Agriculture and Forestry, Department of Forest Sciences, University of Helsinki, P.O. Box 27, FIN-00014, Helsinki, Finland
| | - Angel T Martínez
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu 9, E28040, Madrid, Spain
| | - Otto Miettinen
- Mycology Unit, Botanical Museum, Finnish Museum of Natural History, University of Helsinki, P.O. Box 7, Helsinki, Finland
| | - Sirma Mihaltcheva
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Jasmyn Pangilinan
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Fei Ren
- Faculty of Agriculture and Forestry, Department of Forest Sciences, University of Helsinki, P.O. Box 27, FIN-00014, Helsinki, Finland
- Forestry experiment center of north China, Chinese Academy of Forestry, 102300, Beijing, China
| | - Robert Riley
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Francisco Javier Ruiz-Dueñas
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu 9, E28040, Madrid, Spain
| | - Ana Serrano
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu 9, E28040, Madrid, Spain
| | - Michael R Thon
- Universidad de Salamanca, Instituto Hispano-Luso de Investigaciones Agrarias (CIALE), Villamayor, Spain
| | - Zilan Wen
- Faculty of Agriculture and Forestry, Department of Forest Sciences, University of Helsinki, P.O. Box 27, FIN-00014, Helsinki, Finland
| | - Zhen Zeng
- Faculty of Agriculture and Forestry, Department of Forest Sciences, University of Helsinki, P.O. Box 27, FIN-00014, Helsinki, Finland
| | - Kerrie Barry
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Igor V Grigoriev
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, 94720, USA
| | - Francis Martin
- Institut National de la Recherche Agronomique (INRA), Laboratory of Excellence Advanced Research on the Biology of Tree and Forest Ecosystems (ARBRE), UMR 1136, Champenoux, France
- University of Lorraine, Laboratory of Excellence ARBRE, UMR 1136, Champenoux, France
| | - Fred O Asiegbu
- Faculty of Agriculture and Forestry, Department of Forest Sciences, University of Helsinki, P.O. Box 27, FIN-00014, Helsinki, Finland.
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De novo transcriptomic profiling of the clonal Leymus chinensis response to long-term overgrazing-induced memory. Sci Rep 2018; 8:17912. [PMID: 30559460 PMCID: PMC6297159 DOI: 10.1038/s41598-018-35605-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 11/07/2018] [Indexed: 01/26/2023] Open
Abstract
Sheepgrass (Leymus chinensis) is one of the dominant grass species present on typical steppes of the Inner Mongolia Plateau. However, L. chinensis has developed a dwarfing phenotype in response to the stressful habitat in grasslands that are severely degraded due to heavy grazing. The lack of transcriptomic and genomic information has prohibited the understanding of the transgenerational effect on physiological alterations in clonal L. chinensis at the molecular level in response to livestock grazing. To solve this problem, transcriptomic information from the leaves of clonal L. chinensis obtained from overgrazed (GR) and non-grazed (NG) grasslands was studied using a paired-end Illumina HiSeq 2500 sequencing platform. First, despite the influence of grazing being absent during the growth of clonal offspring in our hydroponic experiment, compared with those from the NG group, clonal L. chinensis from the GR group exhibited significant dwarf-type morphological traits. A total of 116,356 unigenes were subsequently generated and assembled de novo, of which 55,541 could be annotated to homologous matches in the NCBI non-redundant (Nr), Swiss-Prot, Clusters of Orthologous Groups (COG), gene ontology (GO), or Kyoto Encyclopedia of Genes and Genomes (KEGG) databases. The expression of 3,341 unigenes significantly differed between the GR group and the NG group with an absolute value of Log2 ratio ≥ 1. The altered expression of genes involved in defence and immune responses, pathogenic resistance and cell development indicates that livestock grazing induces a transgenerational effect on the growth inhibition of clonal L. chinensis. The results of the present study will provide important large-scale transcriptomic information on L. chinensis. Furthermore, the results facilitated our investigation of grazing-induced transgenerational effects on both the morphological and physiological characteristics of L. chinensis at the molecular levels.
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Wang L, Luo H, Hu W, Yang Y, Hong N, Wang G, Wang A, Wang L. De novo transcriptomic assembly and mRNA expression patterns of Botryosphaeria dothidea infection with mycoviruses chrysovirus 1 (BdCV1) and partitivirus 1 (BdPV1). Virol J 2018; 15:126. [PMID: 30103770 PMCID: PMC6088430 DOI: 10.1186/s12985-018-1033-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Accepted: 07/27/2018] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND Pear ring rot, caused by Botryosphaeria species, is responsible for substantial economic losses by causing severe recession of pear tree growth in China. Mycovirus-mediated hypovirulence in plant pathogenic fungi is a crucial biological method to control fungal diseases. METHODS We conducted a large-scale and comprehensive transcriptome analysis to identify mRNA in B. dothidea in response to mycovirus. De novo sequencing technology from four constructed libraries of LW-C (Botryosphaeria dothidea chrysovirus 1, BdCV1), LW-P (Botryosphaeria dothidea partitivirus 1, BdPV1), LW-CP (LW-1 strain infection with BdCV1 and BdPV1), and Mock (free virus) was used to investigate and compare gene expression changes in B.dothidea strains infected with mycovirus. RESULTS In total, 30,058 Unigenes with an average length of 2128 bp were obtained from 4 libraries of B. dothidea strains. These were annotated to specify their classified function. We demonstrate that mRNAs of B. dothidea strains in response to mycovirus are differentially expressed. In total, 5598 genes were up-regulated and 3298 were down-regulated in the LW-CP group, 4468 were up-regulated and 4291 down-regulated in the LW-C group, and 2590 were up-regulated and 2325 down-regulated in the LW-P group. RT-qPCR was used to validate the expression of 9 selected genes. The B. dothidea transcriptome was more affected by BdCV1 infection than BdPV1. We conducted GO enrichment analysis to characterize gene functions regulated by B. dothidea with mycovirus infection. These involved metabolic process, cellular process, catalytic activity, transporter activity, signaling, and other biological pathways. KEGG function analysis demonstrated that the enriched differentially expressed genes are involved in metabolism, transcription, signal transduction, and ABC transport. mRNA is therefore involved in the interaction between fungi and mycovirus. In addition, changes in differential accumulation levels of cp and RdRp of BdCV1 and BdPV1 in B. dothidea strains were evaluated, revealing that the accumulation of BdCV1 and BdPV1 is related to the phenotype and virulence of B. dothidea strain LW-1. CONCLUSIONS The identification and analysis of mRNAs from B. dothidea was first reported at the transcriptome level. Our analysis provides further insight into the interaction of B. dothidea strains infection with chrysovirus 1 (BdCV1) and partitivirus 1 (BdPV1) at the transcriptome level.
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Affiliation(s)
- Lihua Wang
- State Key Laboratory of Agricultural Microbiology, Wuhan, Hubei 430070 People’s Republic of China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070 People’s Republic of China
- Key Lab of Plant Pathology of Hubei Province, Wuhan, Hubei 430070 People’s Republic of China
| | - Hui Luo
- State Key Laboratory of Agricultural Microbiology, Wuhan, Hubei 430070 People’s Republic of China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070 People’s Republic of China
- Key Lab of Plant Pathology of Hubei Province, Wuhan, Hubei 430070 People’s Republic of China
| | - Wangcheng Hu
- State Key Laboratory of Agricultural Microbiology, Wuhan, Hubei 430070 People’s Republic of China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070 People’s Republic of China
- Key Lab of Plant Pathology of Hubei Province, Wuhan, Hubei 430070 People’s Republic of China
| | - Yuekun Yang
- State Key Laboratory of Agricultural Microbiology, Wuhan, Hubei 430070 People’s Republic of China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070 People’s Republic of China
- Key Lab of Plant Pathology of Hubei Province, Wuhan, Hubei 430070 People’s Republic of China
| | - Ni Hong
- State Key Laboratory of Agricultural Microbiology, Wuhan, Hubei 430070 People’s Republic of China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070 People’s Republic of China
- Key Lab of Plant Pathology of Hubei Province, Wuhan, Hubei 430070 People’s Republic of China
| | - Guoping Wang
- State Key Laboratory of Agricultural Microbiology, Wuhan, Hubei 430070 People’s Republic of China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070 People’s Republic of China
- Key Lab of Plant Pathology of Hubei Province, Wuhan, Hubei 430070 People’s Republic of China
| | - Aiming Wang
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON N5V 4T3 Canada
| | - Liping Wang
- State Key Laboratory of Agricultural Microbiology, Wuhan, Hubei 430070 People’s Republic of China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070 People’s Republic of China
- Key Lab of Plant Pathology of Hubei Province, Wuhan, Hubei 430070 People’s Republic of China
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León-Ramírez CG, Cabrera-Ponce JL, Martínez-Soto D, Sánchez-Arreguin A, Aréchiga-Carvajal ET, Ruiz-Herrera J. Transcriptomic analysis of basidiocarp development in Ustilago maydis (DC) Cda. Fungal Genet Biol 2017; 101:34-45. [PMID: 28285895 DOI: 10.1016/j.fgb.2017.02.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Revised: 02/07/2017] [Accepted: 02/28/2017] [Indexed: 01/20/2023]
Abstract
Previously, we demonstrated that when Ustilago maydis (DC) Cda., a phytopathogenic basidiomycete and the causal agent of corn smut, is grown in the vicinity of maize embryogenic calli in a medium supplemented with the herbicide Dicamba, it developed gastroid-like basidiocarps. To elucidate the molecular mechanisms involved in the basidiocarp development by the fungus, we proceeded to analyze the transcriptome of the process, identifying a total of 2002 and 1064 differentially expressed genes at two developmental stages, young and mature basidiocarps, respectively. Function of these genes was analyzed with the use of different databases. MIPS analysis revealed that in the stage of young basidiocarp, among the ca. two thousand differentially expressed genes, there were some previously described for basidiocarp development in other fungal species. Additional elements that operated at this stage included, among others, genes encoding the transcription factors FOXO3, MIG3, PRO1, TEC1, copper and MFS transporters, and cytochromes P450. During mature basidiocarp development, important up-regulated genes included those encoding hydrophobins, laccases, and ferric reductase (FRE/NOX). The demonstration that a mapkk mutant was unable to form basidiocarps, indicated the importance of the MAPK signaling pathway in this developmental process.
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Affiliation(s)
- C G León-Ramírez
- Departamento de Ingeniería Genética, Unidad Irapuato, Centro de Investigación y de Estudios Avanzados del IPN, 36825 Irapuato, Guanajuato, Mexico
| | - J L Cabrera-Ponce
- Departamento de Ingeniería Genética, Unidad Irapuato, Centro de Investigación y de Estudios Avanzados del IPN, 36825 Irapuato, Guanajuato, Mexico.
| | - D Martínez-Soto
- Departamento de Ingeniería Genética, Unidad Irapuato, Centro de Investigación y de Estudios Avanzados del IPN, 36825 Irapuato, Guanajuato, Mexico
| | - A Sánchez-Arreguin
- Departamento de Ingeniería Genética, Unidad Irapuato, Centro de Investigación y de Estudios Avanzados del IPN, 36825 Irapuato, Guanajuato, Mexico; Facultad de Ciencias Biológicas, Universidad Autónoma de Nuevo León, San Nicolas de los Garza, Nuevo León, Mexico
| | - E T Aréchiga-Carvajal
- Facultad de Ciencias Biológicas, Universidad Autónoma de Nuevo León, San Nicolas de los Garza, Nuevo León, Mexico
| | - J Ruiz-Herrera
- Departamento de Ingeniería Genética, Unidad Irapuato, Centro de Investigación y de Estudios Avanzados del IPN, 36825 Irapuato, Guanajuato, Mexico.
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