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Baranda P, Islam S, Modi A, Mistry H, Al Obaid S, Ansari MJ, Yadav VK, Patel A, Joshi M, Sahoo DK, Bariya H. Whole-genome sequencing of marine water-derived Curvularia verruculosa KHW-7: a pioneering study. Front Microbiol 2024; 15:1363879. [PMID: 38846574 PMCID: PMC11155457 DOI: 10.3389/fmicb.2024.1363879] [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: 12/31/2023] [Accepted: 05/06/2024] [Indexed: 06/09/2024] Open
Abstract
Marine microorganisms are renowned for being a rich source of new secondary metabolites that are significant to humans. The fungi strain KHW-7 was isolated from the seawater collected from the Gulf of Khambhat, India, and identified as Curvularia verruculosa KHW-7. On a next-generation sequencing platform, C. verruculosa KHW-7's whole-genome sequencing (WGS) and gene annotation were carried out using several bioinformatic methods. The 31.59 MB genome size, 52.3% GC, and 158 bp mean read length were discovered using WGS. This genome also contained 9,745 protein-coding genes, including 852 secreted proteins and 2048 transmembrane proteins. The antiSMASH algorithm used to analyze genomes found 25 secondary metabolite biosynthetic gene clusters (BGCs) that are abundant in terpene, non-ribosomal peptide synthetase (NRPS), and polyketides type 1 (T1PKS). To our knowledge, this is the first whole-genome sequence report of C. verruculosa. The WGS analysis of C. verruculosa KHW-7 indicated that this marine-derived fungus could be an efficient generator of bioactive secondary metabolites and an important industrial enzyme, both of which demand further investigation and development.
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Affiliation(s)
- Payal Baranda
- Department of Life Sciences, Hemchandracharya North Gujarat University, Patan, India
| | - Shaikhul Islam
- Plant Pathology Division, Bangladesh Wheat and Maize Research Institute, Nashipur, Bangladesh
| | - Ashish Modi
- Department of Life Sciences, Hemchandracharya North Gujarat University, Patan, India
| | - Harsh Mistry
- Department of Life Sciences, Hemchandracharya North Gujarat University, Patan, India
| | - Sami Al Obaid
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Mohammad Javed Ansari
- Department of Botany, Hindu College Moradabad (Mahatma Jyotiba Phule Rohilkhand University Bareilly), Uttar Pradesh, India
| | - Virendra Kumar Yadav
- Department of Life Sciences, Hemchandracharya North Gujarat University, Patan, India
| | - Ashish Patel
- Department of Life Sciences, Hemchandracharya North Gujarat University, Patan, India
| | - Madhvi Joshi
- Gujarat Biotechnology Research Centre (GBRC), Gandhinagar, India
| | - Dipak Kumar Sahoo
- Department of Veterinary Clinical Sciences, College of Veterinary Medicine, Iowa State University, Ames, IA, United States
| | - Himanshu Bariya
- Department of Life Sciences, Hemchandracharya North Gujarat University, Patan, India
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Lin L, Sun T, Guo J, Lin L, Chen M, Wang Z, Bao J, Norvienyeku J, Zhang D, Han Y, Lu G, Rensing C, Zheng H, Zhong Z, Wang Z. Transposable elements impact the population divergence of rice blast fungus Magnaporthe oryzae. mBio 2024; 15:e0008624. [PMID: 38534157 PMCID: PMC11077969 DOI: 10.1128/mbio.00086-24] [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: 01/13/2024] [Accepted: 03/06/2024] [Indexed: 03/28/2024] Open
Abstract
Dynamic transposition of transposable elements (TEs) in fungal pathogens has significant impact on genome stability, gene expression, and virulence to the host. In Magnaporthe oryzae, genome plasticity resulting from TE insertion is a major driving force leading to the rapid evolution and diversification of this fungus. Despite their importance in M. oryzae population evolution and divergence, our understanding of TEs in this context remains limited. Here, we conducted a genome-wide analysis of TE transposition dynamics in the 11 most abundant TE families in M. oryzae populations. Our results show that these TEs have specifically expanded in recently isolated M. oryzae rice populations, with the presence/absence polymorphism of TE insertions highly concordant with population divergence on Geng/Japonica and Xian/Indica rice cultivars. Notably, the genes targeted by clade-specific TEs showed clade-specific expression patterns and are involved in the pathogenic process, suggesting a transcriptional regulation of TEs on targeted genes. Our study provides a comprehensive analysis of TEs in M. oryzae populations and demonstrates a crucial role of recent TE bursts in adaptive evolution and diversification of the M. oryzae rice-infecting lineage. IMPORTANCE Magnaporthe oryzae is the causal agent of the destructive blast disease, which caused massive loss of yield annually worldwide. The fungus diverged into distinct clades during adaptation toward the two rice subspecies, Xian/Indica and Geng/Japonica. Although the role of TEs in the adaptive evolution was well established, mechanisms underlying how TEs promote the population divergence of M. oryzae remain largely unknown. In this study, we reported that TEs shape the population divergence of M. oryzae by differentially regulating gene expression between Xian/Indica-infecting and Geng/Japonica-infecting populations. Our results revealed a TE insertion-mediated gene expression adaption that led to the divergence of M. oryzae population infecting different rice subspecies.
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Affiliation(s)
- Lianyu Lin
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Ting Sun
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jiayuan Guo
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, China
- Fuzhou Institute of Oceanography, Minjiang University, Fuzhou, China
| | - Lili Lin
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Meilian Chen
- Fuzhou Institute of Oceanography, Minjiang University, Fuzhou, China
| | - Zhe Wang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jiandong Bao
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-Products, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Justice Norvienyeku
- Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests, Ministry of Education, College of Plant Protection, Hainan University, Haikou, China
| | - Dongmei Zhang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yijuan Han
- Fuzhou Institute of Oceanography, Minjiang University, Fuzhou, China
| | - Guodong Lu
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Christopher Rensing
- Institute of Environmental Microbiology, College of Resource and Environment, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Huakun Zheng
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zhenhui Zhong
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, China
- Ministry of Education Key Laboratory for Bio-Resource and Eco-Environment, College of Life Sciences, Sichuan University, Chengdu, China
| | - Zonghua Wang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, China
- Fuzhou Institute of Oceanography, Minjiang University, Fuzhou, China
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Nallathambi P, Umamaheswari C, Reddy B, Aarthy B, Javed M, Ravikumar P, Watpade S, Kashyap PL, Boopalakrishnan G, Kumar S, Sharma A, Kumar A. Deciphering the Genomic Landscape and Virulence Mechanisms of the Wheat Powdery Mildew Pathogen Blumeria graminis f. sp. tritici Wtn1: Insights from Integrated Genome Assembly and Conidial Transcriptomics. J Fungi (Basel) 2024; 10:267. [PMID: 38667938 PMCID: PMC11051031 DOI: 10.3390/jof10040267] [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: 12/19/2023] [Revised: 03/16/2024] [Accepted: 03/19/2024] [Indexed: 04/28/2024] Open
Abstract
A high-quality genome sequence from an Indian isolate of Blumeria graminis f. sp. tritici Wtn1, a persistent threat in wheat farming, was obtained using a hybrid method. The assembly of over 9.24 million DNA-sequence reads resulted in 93 contigs, totaling a 140.61 Mb genome size, potentially encoding 8480 genes. Notably, more than 73.80% of the genome, spanning approximately 102.14 Mb, comprises retro-elements, LTR elements, and P elements, influencing evolution and adaptation significantly. The phylogenomic analysis placed B. graminis f. sp. tritici Wtn1 in a distinct monocot-infecting clade. A total of 583 tRNA anticodon sequences were identified from the whole genome of the native virulent strain B. graminis f. sp. tritici, which comprises distinct genome features with high counts of tRNA anticodons for leucine (70), cysteine (61), alanine (58), and arginine (45), with only two stop codons (Opal and Ochre) present and the absence of the Amber stop codon. Comparative InterProScan analysis unveiled "shared and unique" proteins in B. graminis f. sp. tritici Wtn1. Identified were 7707 protein-encoding genes, annotated to different categories such as 805 effectors, 156 CAZymes, 6102 orthologous proteins, and 3180 distinct protein families (PFAMs). Among the effectors, genes like Avra10, Avrk1, Bcg-7, BEC1005, CSEP0105, CSEP0162, BEC1016, BEC1040, and HopI1 closely linked to pathogenesis and virulence were recognized. Transcriptome analysis highlighted abundant proteins associated with RNA processing and modification, post-translational modification, protein turnover, chaperones, and signal transduction. Examining the Environmental Information Processing Pathways in B. graminis f. sp. tritici Wtn1 revealed 393 genes across 33 signal transduction pathways. The key pathways included yeast MAPK signaling (53 genes), mTOR signaling (38 genes), PI3K-Akt signaling (23 genes), and AMPK signaling (21 genes). Additionally, pathways like FoxO, Phosphatidylinositol, the two-component system, and Ras signaling showed significant gene representation, each with 15-16 genes, key SNPs, and Indels in specific chromosomes highlighting their relevance to environmental responses and pathotype evolution. The SNP and InDel analysis resulted in about 3.56 million variants, including 3.45 million SNPs, 5050 insertions, and 5651 deletions within the whole genome of B. graminis f. sp. tritici Wtn1. These comprehensive genome and transcriptome datasets serve as crucial resources for understanding the pathogenicity, virulence effectors, retro-elements, and evolutionary origins of B. graminis f. sp. tritici Wtn1, aiding in developing robust strategies for the effective management of wheat powdery mildew.
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Affiliation(s)
- Perumal Nallathambi
- ICAR-Indian Agricultural Research Institute, Regional Station, Wellington 643231, Tamil Nadu, India; (P.N.); (C.U.); (B.A.); (P.R.)
| | - Chandrasekaran Umamaheswari
- ICAR-Indian Agricultural Research Institute, Regional Station, Wellington 643231, Tamil Nadu, India; (P.N.); (C.U.); (B.A.); (P.R.)
| | - Bhaskar Reddy
- ICAR-Indian Agricultural Research Institute, Pusa Campus, New Delhi 110012, Delhi, India; (M.J.); (G.B.)
| | - Balakrishnan Aarthy
- ICAR-Indian Agricultural Research Institute, Regional Station, Wellington 643231, Tamil Nadu, India; (P.N.); (C.U.); (B.A.); (P.R.)
| | - Mohammed Javed
- ICAR-Indian Agricultural Research Institute, Pusa Campus, New Delhi 110012, Delhi, India; (M.J.); (G.B.)
| | - Priya Ravikumar
- ICAR-Indian Agricultural Research Institute, Regional Station, Wellington 643231, Tamil Nadu, India; (P.N.); (C.U.); (B.A.); (P.R.)
| | - Santosh Watpade
- ICAR-Indian Agricultural Research Institute, Regional Station, Shimla 171004, Himachal Pradesh, India;
| | - Prem Lal Kashyap
- ICAR-Indian Institute of Wheat and Barley Research, Karnal 132001, Haryana, India; (P.L.K.); (S.K.); (A.S.)
| | | | - Sudheer Kumar
- ICAR-Indian Institute of Wheat and Barley Research, Karnal 132001, Haryana, India; (P.L.K.); (S.K.); (A.S.)
| | - Anju Sharma
- ICAR-Indian Institute of Wheat and Barley Research, Karnal 132001, Haryana, India; (P.L.K.); (S.K.); (A.S.)
| | - Aundy Kumar
- ICAR-Indian Agricultural Research Institute, Pusa Campus, New Delhi 110012, Delhi, India; (M.J.); (G.B.)
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Liu X, Zhao L, Majid M, Huang Y. Orthoptera-TElib: a library of Orthoptera transposable elements for TE annotation. Mob DNA 2024; 15:5. [PMID: 38486291 PMCID: PMC10941475 DOI: 10.1186/s13100-024-00316-x] [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: 10/08/2023] [Accepted: 03/08/2024] [Indexed: 03/17/2024] Open
Abstract
Transposable elements (TEs) are a major component of eukaryotic genomes and are present in almost all eukaryotic organisms. TEs are highly dynamic between and within species, which significantly affects the general applicability of the TE databases. Orthoptera is the only known group in the class Insecta with a significantly enlarged genome (0.93-21.48 Gb). When analyzing the large genome using the existing TE public database, the efficiency of TE annotation is not satisfactory. To address this limitation, it becomes imperative to continually update the available TE resource library and the need for an Orthoptera-specific library as more insect genomes are publicly available. Here, we used the complete genome data of 12 Orthoptera species to de novo annotate TEs, then manually re-annotate the unclassified TEs to construct a non-redundant Orthoptera-specific TE library: Orthoptera-TElib. Orthoptera-TElib contains 24,021 TE entries including the re-annotated results of 13,964 unknown TEs. The naming of TE entries in Orthoptera-TElib adopts the same naming as RepeatMasker and Dfam and is encoded as the three-level form of "level1/level2-level3". Orthoptera-TElib can be directly used as an input reference database and is compatible with mainstream repetitive sequence analysis software such as RepeatMasker and dnaPipeTE. When analyzing TEs of Orthoptera species, Orthoptera-TElib performs better TE annotation as compared to Dfam and Repbase regardless of using low-coverage sequencing or genome assembly data. The most improved TE annotation result is Angaracris rhodopa, which has increased from 7.89% of the genome to 53.28%. Finally, Orthoptera-TElib is stored in Sqlite3 for the convenience of data updates and user access.
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Affiliation(s)
- Xuanzeng Liu
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Lina Zhao
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Muhammad Majid
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Yuan Huang
- College of Life Sciences, Shaanxi Normal University, Xi'an, China.
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5
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Guo M, Addy GA, Yang N, Asare E, Wu H, Saleh AA, Shi S, Gao B, Song C. PiggyBac Transposon Mining in the Small Genomes of Animals. BIOLOGY 2023; 13:24. [PMID: 38248455 PMCID: PMC10813416 DOI: 10.3390/biology13010024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 12/29/2023] [Indexed: 01/23/2024]
Abstract
TEs, including DNA transposons, are major contributors of genome expansions, and have played a very significant role in shaping the evolution of animal genomes, due to their capacity to jump from one genomic position to the other. In this study, we investigated the evolution landscapes of PB transposons, including their distribution, diversity, activity and structure organization in 79 species of small (compact) genomes of animals comprising both vertebrate and invertebrates. Overall, 212 PB transposon types were detected from almost half (37) of the total number of the small genome species (79) investigated. The detected PB transposon types, which were unevenly distributed in various genera and phyla, have been classified into seven distinct clades or families with good bootstrap support (>80%). The PB transposon types that were identified have a length ranging from 1.23 kb to 9.51 kb. They encode transposases of approximately ≥500 amino acids in length, and possess terminal inverted repeats (TIRs) ranging from 4 bp to 24 bp. Though some of the transposon types have long TIRs (528 bp), they still maintain the consistent and reliable 4 bp target site duplication (TSD) of TTAA. However, PiggyBac-2_Cvir transposon originating from the Crassostrea virginica species exhibits a unique TSD of TATG. The TIRs of the transposons in all the seven families display high divergence, with a highly conserved 5' end motif. The core transposase domains (DDD) were better conserved among the seven different families compared to the other protein domains, which were less prevalent in the vertebrate genome. The divergent evolution dynamics analysis also indicated that the majority of the PB transposon types identified in this study are either relatively young or old, with some being active. Additionally, numerous invasions of PB transposons were found in the genomes of both vertebrate and invertebrate animals. The data reveals that the PB superfamily is widely distributed in these species. PB transposons exhibit high diversity and activity in the small genomes of animals, and might play a crucial role in shaping the evolution of these small genomes of animals.
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Affiliation(s)
- Mengke Guo
- College of Animal Science & Technology, Yangzhou University, Yangzhou 225009, China; (M.G.); (G.A.A.); (N.Y.); (E.A.); (A.A.S.); (S.S.); (B.G.)
| | - George A. Addy
- College of Animal Science & Technology, Yangzhou University, Yangzhou 225009, China; (M.G.); (G.A.A.); (N.Y.); (E.A.); (A.A.S.); (S.S.); (B.G.)
| | - Naisu Yang
- College of Animal Science & Technology, Yangzhou University, Yangzhou 225009, China; (M.G.); (G.A.A.); (N.Y.); (E.A.); (A.A.S.); (S.S.); (B.G.)
| | - Emmanuel Asare
- College of Animal Science & Technology, Yangzhou University, Yangzhou 225009, China; (M.G.); (G.A.A.); (N.Y.); (E.A.); (A.A.S.); (S.S.); (B.G.)
| | - Han Wu
- Department of Immunology, School of Medicine, Shenzhen University, Shenzhen 518060, China;
| | - Ahmed A. Saleh
- College of Animal Science & Technology, Yangzhou University, Yangzhou 225009, China; (M.G.); (G.A.A.); (N.Y.); (E.A.); (A.A.S.); (S.S.); (B.G.)
- Animal and Fish Production Department, Faculty of Agriculture (Alshatby), Alexandria University, Alexandria City 11865, Egypt
| | - Shasha Shi
- College of Animal Science & Technology, Yangzhou University, Yangzhou 225009, China; (M.G.); (G.A.A.); (N.Y.); (E.A.); (A.A.S.); (S.S.); (B.G.)
| | - Bo Gao
- College of Animal Science & Technology, Yangzhou University, Yangzhou 225009, China; (M.G.); (G.A.A.); (N.Y.); (E.A.); (A.A.S.); (S.S.); (B.G.)
| | - Chengyi Song
- College of Animal Science & Technology, Yangzhou University, Yangzhou 225009, China; (M.G.); (G.A.A.); (N.Y.); (E.A.); (A.A.S.); (S.S.); (B.G.)
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Venice F, Spina F, Davolos D, Ghignone S, Varese GC. The genomes of Scedosporium between environmental challenges and opportunism. IMA Fungus 2023; 14:25. [PMID: 38049914 PMCID: PMC10694956 DOI: 10.1186/s43008-023-00128-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 11/05/2023] [Indexed: 12/06/2023] Open
Abstract
Emerging fungal pathogens are a global challenge for humankind. Many efforts have been made to understand the mechanisms underlying pathogenicity in bacteria, and OMICs techniques are largely responsible for those advancements. By contrast, our limited understanding of opportunism and antifungal resistance is preventing us from identifying, limiting and interpreting the emergence of fungal pathogens. The genus Scedosporium (Microascaceae) includes fungi with high tolerance to environmental pollution, whilst some species can be considered major human pathogens, such as Scedosporium apiospermum and Scedosporium boydii. However, unlike other fungal pathogens, little is known about the genome evolution of these organisms. We sequenced two novel genomes of Scedosporium aurantiacum and Scedosporium minutisporum isolated from extreme, strongly anthropized environments. We compared all the available Scedosporium and Microascaceae genomes, that we systematically annotated and characterized ex novo in most cases. The genomes in this family were integrated in a Phylum-level comparison to infer the presence of putative, shared genomic traits in filamentous ascomycetes with pathogenic potential. The analysis included the genomes of 100 environmental and clinical fungi, revealing poor evolutionary convergence of putative pathogenicity traits. By contrast, several features in Microascaceae and Scedosporium were detected that might have a dual role in responding to environmental challenges and allowing colonization of the human body, including chitin, melanin and other cell wall related genes, proteases, glutaredoxins and magnesium transporters. We found these gene families to be impacted by expansions, orthologous transposon insertions, and point mutations. With RNA-seq, we demonstrated that most of these anciently impacted genomic features responded to the stress imposed by an antifungal compound (voriconazole) in the two environmental strains S. aurantiacum MUT6114 and S. minutisporum MUT6113. Therefore, the present genomics and transcriptomics investigation stands on the edge between stress resistance and pathogenic potential, to elucidate whether fungi were pre-adapted to infect humans. We highlight the strengths and limitations of genomics applied to opportunistic human pathogens, the multifactoriality of pathogenicity and resistance to drugs, and suggest a scenario where pressures other than anthropic contributed to forge filamentous human pathogens.
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Affiliation(s)
- Francesco Venice
- Department of Life Sciences and System Biology, University of Turin, Viale Mattioli 25, 10125, Turin, Italy
| | - Federica Spina
- Department of Life Sciences and System Biology, University of Turin, Viale Mattioli 25, 10125, Turin, Italy
| | - Domenico Davolos
- Department of Technological Innovations and Safety of Plants, Products and Anthropic Settlements (DIT), INAIL, Research Area, Via R. Ferruzzi 38/40, 00143, Rome, Italy
| | - Stefano Ghignone
- Institute for Sustainable Plant Protection (IPSP), SS Turin-National Research Council (CNR), Viale Mattioli 25, 10125, Turin, Italy
| | - Giovanna Cristina Varese
- Department of Life Sciences and System Biology, University of Turin, Viale Mattioli 25, 10125, Turin, Italy.
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Nakamoto AA, Joubert PM, Krasileva KV. Intraspecific Variation of Transposable Elements Reveals Differences in the Evolutionary History of Fungal Phytopathogen Pathotypes. Genome Biol Evol 2023; 15:evad206. [PMID: 37975814 PMCID: PMC10691877 DOI: 10.1093/gbe/evad206] [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: 04/27/2023] [Revised: 11/01/2023] [Accepted: 11/09/2023] [Indexed: 11/19/2023] Open
Abstract
Transposable elements (TEs) contribute to intraspecific variation and play important roles in the evolution of fungal genomes. However, our understanding of the processes that shape TE landscapes is limited, as is our understanding of the relationship between TE content, population structure, and evolutionary history of fungal species. Fungal plant pathogens, which often have host-specific populations, are useful systems in which to study intraspecific TE content diversity. Here, we describe TE dynamics in five lineages of Magnaporthe oryzae, the fungus that causes blast disease of rice, wheat, and many other grasses. We identified differences in TE content across these lineages and showed that recent lineage-specific expansions of certain TEs have contributed to overall greater TE content in rice-infecting and Setaria-infecting lineages. We reconstructed the evolutionary histories of long terminal repeat-retrotransposon expansions and found that in some cases they were caused by complex proliferation dynamics of one element and in others by multiple elements from an older population of TEs multiplying in parallel. Additionally, we found evidence suggesting the recent transfer of a DNA transposon between rice- and wheat-infecting M. oryzae lineages and a region showing evidence of homologous recombination between those lineages, which could have facilitated such a transfer. By investigating intraspecific TE content variation, we uncovered key differences in the proliferation dynamics of TEs in various pathotypes of a fungal plant pathogen, giving us a better understanding of the evolutionary history of the pathogen itself.
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Affiliation(s)
- Anne A Nakamoto
- Department of Plant and Microbial Biology, University of California, Berkeley, California, USA
| | - Pierre M Joubert
- Department of Plant and Microbial Biology, University of California, Berkeley, California, USA
| | - Ksenia V Krasileva
- Department of Plant and Microbial Biology, University of California, Berkeley, California, USA
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8
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Gurjar MS, Kumar TPJ, Shakouka MA, Saharan MS, Rawat L, Aggarwal R. Draft genome sequencing of Tilletia caries inciting common bunt of wheat provides pathogenicity-related genes. Front Microbiol 2023; 14:1283613. [PMID: 38033590 PMCID: PMC10684912 DOI: 10.3389/fmicb.2023.1283613] [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: 08/26/2023] [Accepted: 10/05/2023] [Indexed: 12/02/2023] Open
Abstract
Common bunt of wheat caused by Tilletia caries is an important disease worldwide. The T. caries TC1_MSG genome was sequenced using the Illumina HiSeq 2500 and Nanopore ONT platforms. The Nanopore library was prepared using the ligation sequencing kit SQK-LSK110 to generate approximately 24 GB for sequencing. The assembly size of 38.18 Mb was generated with a GC content of 56.10%. The whole genome shotgun project was deposited at DDBJ/ENA/GenBank under the accession number JALUTQ000000000. Forty-six contigs were obtained with N50 of 1,798,756 bp. In total, 10,698 genes were predicted in the assembled genome. Out of 10,698 genes, 10,255 genes were predicted significantly in the genome. The repeat sequences made up approximately 1.57% of the genome. Molecular function, cellular components, and biological processes for predicted genes were mapped into the genome. In addition, repeat elements in the genome were assessed. In all, 0.89% of retroelements were observed, followed by long terminal repeat elements (0.86%) in the genome. In simple sequence repeat (SSR) analysis, 8,582 SSRs were found in the genome assembly. The trinucleotide SSR type (3,703) was the most abundant. Few putative secretory signal peptides and pathogenicity-related genes were predicted. The genomic information of T. caries will be valuable in understanding the pathogenesis mechanism as well as developing new methods for the management of the common bunt disease of wheat.
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Affiliation(s)
- Malkhan Singh Gurjar
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | | | - Mohamad Ayham Shakouka
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Mahender Singh Saharan
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Laxmi Rawat
- College of Hill Agriculture, VCSG Uttarakhand University of Horticulture and Forestry, Ranichauri, Uttarakhand, India
| | - Rashmi Aggarwal
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, India
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Khayi S, Armitage AD, Gaboun F, Meftah-kadmiri I, Lahlali R, Fokar M, Mentag R. Chromosome-scale assembly uncovers genomic compartmentation of Fusarium oxysporum f. sp. albedinis, the causal agent of Bayoud disease in date palm. Front Microbiol 2023; 14:1268051. [PMID: 37886058 PMCID: PMC10599148 DOI: 10.3389/fmicb.2023.1268051] [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: 07/27/2023] [Accepted: 09/25/2023] [Indexed: 10/28/2023] Open
Abstract
Date palm (Phoenixdactylifera) is the most significant crop across North Africa and the Middle East. However, the crop faces a severe threat from Bayoud disease caused by the fungal pathogen Fusarium oxysporum f. sp. albedinis (FOA). FOA is a soil-borne fungus that infects the roots and vascular system of date palms, leading to widespread destruction of date palm plantations in North Africa over the last century. This is considered the most devastating pathogen of oasis agriculture in North Africa and responsible for loss of 13 million trees in Algeria and Morocco alone. In this study, we present a chromosome-scale high-quality genome assembly of the virulent isolate Foa 44, which provides valuable insights into understanding the genetic basis of Bayoud disease. The genome assembly consists of 11 chromosomes and 40 unplaced contigs, totalling 65,971,825 base pairs in size. It exhibits a GC ratio of 47.77% and a TE (transposable element) content of 17.30%. Through prediction and annotation, we identified 20,416 protein-coding genes. By combining gene and repeat densities analysis with alignment to Fusarium oxysporum f. sp. lycopersici (FOL) 4287 isolate genome sequence, we determined the core and lineage-specific compartments in Foa 44, shedding light on the genome structure of this pathogen. Furthermore, a phylogenomic analysis based on the 3,292 BUSCOs core genome revealed a distinct clade of FOA isolates within the Fusarium oxysporum species complex (FOSC). Notably, the genealogies of the five identified Secreted In Xylem (SIX) genes (1, 6, 9, 11 and 14) in FOA displayed a polyphyletic pattern, suggesting a horizontal inheritance of these effectors. These findings provide a valuable genomics toolbox for further research aimed at combatting the serious biotic constraints posed by FOA to date palm. This will pave the way for a deeper understanding of Bayoud disease and facilitate the development of effective diagnostic tools and control measures.
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Affiliation(s)
- Slimane Khayi
- Biotechnology Research Unit, Regional Center of Agricultural Research of Rabat, National Institute of Agricultural Research, Rabat, Morocco
| | - Andrew D. Armitage
- Natural Resources Institute, University of Greenwich, Chatham Maritime, Greenwich, United Kingdom
| | - Fatima Gaboun
- Biotechnology Research Unit, Regional Center of Agricultural Research of Rabat, National Institute of Agricultural Research, Rabat, Morocco
| | - Issam Meftah-kadmiri
- Plant and Microbial Biotechnology Center, Moroccan Foundation of Advanced Science Innovation and Research MAScIR, Ben Guerir, Morocco
- Plant and Soil Microbiome Sub-Program, AgroBioSciences, Mohammed VI Polytechnic University (UM6P), Ben Guerir, Morocco
| | - Rachid Lahlali
- Phytopathology Unit, Department of Plant Protection, Ecole Nationale D’Agriculture de Meknes, Meknès, Morocco
- Plant Pathology Laboratory, AgroBioSciences, College of Sustainable Agriculture and Environmental Sciences, Mohammed VI Polytechnic University, Ben Guerir, Morocco
| | - Mohamed Fokar
- Center for Biotechnology and Genomics, Texas Tech University, Lubbock, TX, United States
| | - Rachid Mentag
- Biotechnology Research Unit, Regional Center of Agricultural Research of Rabat, National Institute of Agricultural Research, Rabat, Morocco
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10
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Duhamel M, Hood ME, Rodríguez de la Vega RC, Giraud T. Dynamics of transposable element accumulation in the non-recombining regions of mating-type chromosomes in anther-smut fungi. Nat Commun 2023; 14:5692. [PMID: 37709766 PMCID: PMC10502011 DOI: 10.1038/s41467-023-41413-4] [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: 12/23/2022] [Accepted: 08/30/2023] [Indexed: 09/16/2023] Open
Abstract
In the absence of recombination, the number of transposable elements (TEs) increases due to less efficient selection, but the dynamics of such TE accumulations are not well characterized. Leveraging a dataset of 21 independent events of recombination cessation of different ages in mating-type chromosomes of Microbotryum fungi, we show that TEs rapidly accumulated in regions lacking recombination, but that TE content reached a plateau at ca. 50% of occupied base pairs by 1.5 million years following recombination suppression. The same TE superfamilies have expanded in independently evolved non-recombining regions, in particular rolling-circle replication elements (Helitrons). Long-terminal repeat (LTR) retrotransposons of the Copia and Ty3 superfamilies also expanded, through transposition bursts (distinguished from gene conversion based on LTR divergence), with both non-recombining regions and autosomes affected, suggesting that non-recombining regions constitute TE reservoirs. This study improves our knowledge of genome evolution by showing that TEs can accumulate through bursts, following non-linear decelerating dynamics.
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Affiliation(s)
- Marine Duhamel
- Ecologie Systématique Evolution, IDEEV, CNRS, Université Paris-Saclay, AgroParisTech, Bâtiment 680, 12 route RD128, 91190, Gif-sur-Yvette, France.
- Evolution der Pflanzen und Pilze, Ruhr-Universität Bochum, Universitätsstraße 150, 44780, Bochum, Germany.
| | - Michael E Hood
- Department of Biology, Amherst College, 01002-5000, Amherst, MA, USA
| | - Ricardo C Rodríguez de la Vega
- Ecologie Systématique Evolution, IDEEV, CNRS, Université Paris-Saclay, AgroParisTech, Bâtiment 680, 12 route RD128, 91190, Gif-sur-Yvette, France
| | - Tatiana Giraud
- Ecologie Systématique Evolution, IDEEV, CNRS, Université Paris-Saclay, AgroParisTech, Bâtiment 680, 12 route RD128, 91190, Gif-sur-Yvette, France
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11
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Zaccaron AZ, Neill T, Corcoran J, Mahaffee WF, Stergiopoulos I. A chromosome-scale genome assembly of the grape powdery mildew pathogen Erysiphe necator reveals its genomic architecture and previously unknown features of its biology. mBio 2023; 14:e0064523. [PMID: 37341476 PMCID: PMC10470754 DOI: 10.1128/mbio.00645-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 04/13/2023] [Indexed: 06/22/2023] Open
Abstract
Erysiphe necator is an obligate fungal pathogen that causes grape powdery mildew, globally the most important disease on grapevines. Previous attempts to obtain a quality genome assembly for this pathogen were hindered by its high repetitive DNA content. Here, chromatin conformation capture (Hi-C) with long-read PacBio sequencing was combined to obtain a chromosome-scale assembly and a high-quality annotation for E. necator isolate EnFRAME01. The resulting 81.1 Mb genome assembly is 98% complete and consists of 34 scaffolds, 11 of which represent complete chromosomes. All chromosomes contain large centromeric-like regions and lack synteny to the 11 chromosomes of the cereal PM pathogen Blumeria graminis. Further analysis of their composition showed that repeats and transposable elements (TEs) occupy 62.7% of their content. TEs were almost evenly interspersed outside centromeric and telomeric regions and massively overlapped with regions of annotated genes, suggesting that they could have a significant functional impact. Abundant gene duplicates were observed as well, particularly in genes encoding candidate secreted effector proteins. Moreover, younger in age gene duplicates exhibited more relaxed selection pressure and were more likely to be located physically close in the genome than older duplicates. A total of 122 genes with copy number variations among six isolates of E. necator were also identified and were enriched in genes that were duplicated in EnFRAME01, indicating they may reflect an adaptive variation. Taken together, our study illuminates higher-order genomic architectural features of E. necator and provides a valuable resource for studying genomic structural variations in this pathogen. IMPORTANCE Grape powdery mildew caused by the ascomycete fungus Erysiphe necator is economically the most important and recurrent disease in vineyards across the world. The obligate biotrophic nature of E. necator hinders the use of typical genetic methods to elucidate its pathogenicity and adaptation to adverse conditions, and thus comparative genomics has been a major method to study its genome biology. However, the current reference genome of E. necator isolate C-strain is highly fragmented with many non-coding regions left unassembled. This incompleteness prohibits in-depth comparative genomic analyses and the study of genomic structural variations (SVs) that are known to affect several aspects of microbial life, including fitness, virulence, and host adaptation. By obtaining a chromosome-scale genome assembly and a high-quality gene annotation for E. necator, we reveal the organization of its chromosomal content, unearth previously unknown features of its biology, and provide a reference for studying genomic SVs in this pathogen.
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Affiliation(s)
- Alex Z. Zaccaron
- Department of Plant Pathology, University of California Davis, Davis, California, USA
| | - Tara Neill
- USDA-ARS, Horticultural Crops Disease and Pest Management Research Unit, Corvallis, Oregon, USA
| | - Jacob Corcoran
- USDA-ARS, Horticultural Crops Disease and Pest Management Research Unit, Corvallis, Oregon, USA
| | - Walter F. Mahaffee
- USDA-ARS, Horticultural Crops Disease and Pest Management Research Unit, Corvallis, Oregon, USA
| | - Ioannis Stergiopoulos
- Department of Plant Pathology, University of California Davis, Davis, California, USA
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12
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Sobol MS, Hoshino T, Delgado V, Futagami T, Kadooka C, Inagaki F, Kiel Reese B. Genome characterization of two novel deep-sea sediment fungi, Penicillium pacificagyrus sp. nov. and Penicillium pacificasedimenti sp. nov., from South Pacific Gyre subseafloor sediments, highlights survivability. BMC Genomics 2023; 24:249. [PMID: 37165355 PMCID: PMC10173653 DOI: 10.1186/s12864-023-09320-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 04/18/2023] [Indexed: 05/12/2023] Open
Abstract
BACKGROUND Marine deep subsurface sediments were once thought to be devoid of eukaryotic life, but advances in molecular technology have unlocked the presence and activity of well-known closely related terrestrial and marine fungi. Commonly detected fungi in deep marine sediment environments includes Penicillium, Aspergillus, Cladosporium, Fusarium, and Schizophyllum, which could have important implications in carbon and nitrogen cycling in this isolated environment. In order to determine the diversity and unknown metabolic capabilities of fungi in deep-sea sediments, their genomes need to be fully analyzed. In this study, two Penicillium species were isolated from South Pacific Gyre sediment enrichments during Integrated Ocean Drilling Program Expedition 329. The inner gyre has very limited productivity, organic carbon, and nutrients. RESULTS Here, we present high-quality genomes of two proposed novel Penicillium species using Illumina HiSeq and PacBio sequencing technologies. Single-copy homologues within the genomes were compared to other closely related genomes using OrthoMCL and maximum-likelihood estimation, which showed that these genomes were novel species within the genus Penicillium. We propose to name isolate SPG-F1 as Penicillium pacificasedimenti sp. nov. and SPG-F15 as Penicillium pacificagyrus sp. nov. The resulting genome sizes were 32.6 Mbp and 36.4 Mbp, respectively, and both genomes were greater than 98% complete as determined by the presence of complete single-copy orthologs. The transposable elements for each genome were 4.87% for P. pacificasedimenti and 10.68% for P. pacificagyrus. A total of 12,271 genes were predicted in the P. pacificasedimenti genome and 12,568 genes in P. pacificagyrus. Both isolates contained genes known to be involved in the degradation of recalcitrant carbon, amino acids, and lignin-derived carbon. CONCLUSIONS Our results provide the first constructed genomes of novel Penicillium isolates from deep marine sediments, which will be useful for future studies of marine subsurface fungal diversity and function. Furthermore, these genomes shed light on the potential impact fungi in marine sediments and the subseafloor could have on global carbon and nitrogen biogeochemical cycles and how they may be persisting in the most energy-limited sedimentary biosphere.
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Affiliation(s)
- Morgan S Sobol
- Institute for Biological Interfaces 5, Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen, Baden-Württemberg, Germany
| | - Tatsuhiko Hoshino
- Kochi Institute for Core Sample Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Nankoku, Kochi, 783-8502, Japan
| | - Victor Delgado
- Department of Life Sciences, TX A&M University, Corpus Christi, Texas, USA
| | - Taiki Futagami
- Education and Research Center for Fermentation Studies, Faculty of Agriculture, Kagoshima University, Kagoshima, Japan
- United Graduate School of Agricultural Sciences, Kagoshima University, 1-21-24 Korimoto, Kagoshima, 890-0065, Japan
| | - Chihiro Kadooka
- Department of Biotechnology and Life Science, Faculty of Biotechnology and Life Science, Sojo University, Ikeda, Nishiku, Kumamoto, 860-0082, Japan
| | - Fumio Inagaki
- Mantle Drilling Promotion Office, Institute for Marine Earth Exploration and Engineering (MarE3), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokohama, 236- 0001, Japan
- Department of Earth Sciences, Graduate School of Science, Tohoku University, Sendai, 980-8574, Japan
| | - Brandi Kiel Reese
- Dauphin Island Sea Lab, Dauphin Island, Alabama, USA.
- Stokes School of Marine and Environmental Sciences, University of South Alabama, Mobile, AL, USA.
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13
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Gupta YK, Marcelino-Guimarães FC, Lorrain C, Farmer A, Haridas S, Ferreira EGC, Lopes-Caitar VS, Oliveira LS, Morin E, Widdison S, Cameron C, Inoue Y, Thor K, Robinson K, Drula E, Henrissat B, LaButti K, Bini AMR, Paget E, Singan V, Daum C, Dorme C, van Hoek M, Janssen A, Chandat L, Tarriotte Y, Richardson J, Melo BDVA, Wittenberg AHJ, Schneiders H, Peyrard S, Zanardo LG, Holtman VC, Coulombier-Chauvel F, Link TI, Balmer D, Müller AN, Kind S, Bohnert S, Wirtz L, Chen C, Yan M, Ng V, Gautier P, Meyer MC, Voegele RT, Liu Q, Grigoriev IV, Conrath U, Brommonschenkel SH, Loehrer M, Schaffrath U, Sirven C, Scalliet G, Duplessis S, van Esse HP. Major proliferation of transposable elements shaped the genome of the soybean rust pathogen Phakopsora pachyrhizi. Nat Commun 2023; 14:1835. [PMID: 37005409 PMCID: PMC10067951 DOI: 10.1038/s41467-023-37551-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 03/22/2023] [Indexed: 04/04/2023] Open
Abstract
With >7000 species the order of rust fungi has a disproportionately large impact on agriculture, horticulture, forestry and foreign ecosystems. The infectious spores are typically dikaryotic, a feature unique to fungi in which two haploid nuclei reside in the same cell. A key example is Phakopsora pachyrhizi, the causal agent of Asian soybean rust disease, one of the world's most economically damaging agricultural diseases. Despite P. pachyrhizi's impact, the exceptional size and complexity of its genome prevented generation of an accurate genome assembly. Here, we sequence three independent P. pachyrhizi genomes and uncover a genome up to 1.25 Gb comprising two haplotypes with a transposable element (TE) content of ~93%. We study the incursion and dominant impact of these TEs on the genome and show how they have a key impact on various processes such as host range adaptation, stress responses and genetic plasticity.
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Affiliation(s)
- Yogesh K Gupta
- 2Blades, Evanston, Illinois, USA
- The Sainsbury Laboratory, University of East Anglia, Norwich, UK
| | | | - Cécile Lorrain
- Pathogen Evolutionary Ecology, ETH Zürich, Zürich, Switzerland
| | - Andrew Farmer
- National Center for Genome Resources, Santa Fe, New Mexico, USA
| | - Sajeet Haridas
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Everton Geraldo Capote Ferreira
- 2Blades, Evanston, Illinois, USA
- The Sainsbury Laboratory, University of East Anglia, Norwich, UK
- Brazilian Agricultural Research Corporation - National Soybean Research Center (Embrapa Soja), Paraná, Brazil
| | - Valéria S Lopes-Caitar
- Brazilian Agricultural Research Corporation - National Soybean Research Center (Embrapa Soja), Paraná, Brazil
| | - Liliane Santana Oliveira
- Brazilian Agricultural Research Corporation - National Soybean Research Center (Embrapa Soja), Paraná, Brazil
- Department of Computer Science, Federal University of Technology of Paraná (UTFPR), Paraná, Brazil
| | | | | | - Connor Cameron
- National Center for Genome Resources, Santa Fe, New Mexico, USA
| | - Yoshihiro Inoue
- 2Blades, Evanston, Illinois, USA
- The Sainsbury Laboratory, University of East Anglia, Norwich, UK
| | - Kathrin Thor
- 2Blades, Evanston, Illinois, USA
- The Sainsbury Laboratory, University of East Anglia, Norwich, UK
| | - Kelly Robinson
- 2Blades, Evanston, Illinois, USA
- The Sainsbury Laboratory, University of East Anglia, Norwich, UK
| | - Elodie Drula
- AFMB, Aix-Marseille Univ., INRAE, Marseille, France
- Biodiversité et Biotechnologie Fongiques, INRAE, Marseille, France
| | - Bernard Henrissat
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
- DTU Bioengineering, Technical University of Denmark, Kgs, Lyngby, Denmark
| | - Kurt LaButti
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Aline Mara Rudsit Bini
- Brazilian Agricultural Research Corporation - National Soybean Research Center (Embrapa Soja), Paraná, Brazil
- Department of Computer Science, Federal University of Technology of Paraná (UTFPR), Paraná, Brazil
| | - Eric Paget
- Bayer SAS, Crop Science Division, Lyon, France
| | - Vasanth Singan
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Christopher Daum
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | - Tobias I Link
- Institute of Phytomedicine, University of Hohenheim, Stuttgart, Germany
| | - Dirk Balmer
- Syngenta Crop Protection AG, Stein, Switzerland
| | - André N Müller
- Department of Plant Physiology, RWTH Aachen University, Aachen, Germany
| | - Sabine Kind
- Department of Plant Physiology, RWTH Aachen University, Aachen, Germany
| | - Stefan Bohnert
- Department of Plant Physiology, RWTH Aachen University, Aachen, Germany
| | - Louisa Wirtz
- Department of Plant Physiology, RWTH Aachen University, Aachen, Germany
| | - Cindy Chen
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Mi Yan
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Vivian Ng
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | | | - Maurício Conrado Meyer
- Brazilian Agricultural Research Corporation - National Soybean Research Center (Embrapa Soja), Paraná, Brazil
| | | | - Qingli Liu
- Syngenta Crop Protection, LLC, Research Triangle Park, Durham, NC, USA
| | - Igor V Grigoriev
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, USA
| | - Uwe Conrath
- Department of Plant Physiology, RWTH Aachen University, Aachen, Germany
| | | | - Marco Loehrer
- Department of Plant Physiology, RWTH Aachen University, Aachen, Germany
| | - Ulrich Schaffrath
- Department of Plant Physiology, RWTH Aachen University, Aachen, Germany
| | | | | | | | - H Peter van Esse
- 2Blades, Evanston, Illinois, USA.
- The Sainsbury Laboratory, University of East Anglia, Norwich, UK.
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14
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Liang J, Li Y, Dodds PN, Figueroa M, Sperschneider J, Han S, Tsui CKM, Zhang K, Li L, Ma Z, Cai L. Haplotype-phased and chromosome-level genome assembly of Puccinia polysora, a giga-scale fungal pathogen causing southern corn rust. Mol Ecol Resour 2023; 23:601-620. [PMID: 36403246 DOI: 10.1111/1755-0998.13739] [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: 05/30/2022] [Revised: 11/16/2022] [Accepted: 11/17/2022] [Indexed: 11/21/2022]
Abstract
Rust fungi are characterized by large genomes with high repeat content and have two haploid nuclei in most life stages, which makes achieving high-quality genome assemblies challenging. Here, we described a pipeline using HiFi reads and Hi-C data to assemble a gigabase-sized fungal pathogen, Puccinia polysora f.sp. zeae, to haplotype-phased and chromosome-scale. The final assembled genome is 1.71 Gbp, with ~850 Mbp and 18 chromosomes in each haplotype, being currently one of the two giga-scale fungi assembled to chromosome level. Transcript-based annotation identified 47,512 genes for the dikaryotic genome with a similar number for each haplotype. A high level of interhaplotype variation was found with 10% haplotype-specific BUSCO genes, 5.8 SNPs/kbp, and structural variation accounting for 3% of the genome size. The P. polysora genome displayed over 85% repeat contents, with genome-size expansion and copy number increasing of species-specific orthogroups. Interestingly, these features did not affect overall synteny with other Puccinia species having smaller genomes. Fine-time-point transcriptomics revealed seven clusters of coexpressed secreted proteins that are conserved between two haplotypes. The fact that candidate effectors interspersed with all genes indicated the absence of a "two-speed genome" evolution in P. polysora. Genome resequencing of 79 additional isolates revealed a clonal population structure of P. polysora in China with low geographic differentiation. Nevertheless, a minor population differentiated from the major population by having mutations on secreted proteins including AvrRppC, indicating the ongoing virulence to evade recognition by RppC, a major resistance gene in Chinese corn cultivars. The high-quality assembly provides valuable genomic resources for future studies on disease management and the evolution of P. polysora.
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Affiliation(s)
- Junmin Liang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Yuanjie Li
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Peter N Dodds
- Commonwealth Scientific and Industrial Research Organization, Agriculture and Food, Canberra, Australian Capital Territory, Australia
| | - Melania Figueroa
- Commonwealth Scientific and Industrial Research Organization, Agriculture and Food, Canberra, Australian Capital Territory, Australia
| | - Jana Sperschneider
- Commonwealth Scientific and Industrial Research Organization, Agriculture and Food, Canberra, Australian Capital Territory, Australia
| | - Shiling Han
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Clement K M Tsui
- Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada.,National Centre for Infectious Diseases, Tan Tock Seng Hospital, Singapore City, Singapore.,LKC School of Medicine, Nanyang Technological University, Singapore City, Singapore
| | - Keyu Zhang
- Department of Plant Pathology, China Agricultural University, Beijing, China
| | - Leifu Li
- Department of Plant Pathology, China Agricultural University, Beijing, China
| | - Zhanhong Ma
- Department of Plant Pathology, China Agricultural University, Beijing, China
| | - Lei Cai
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
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15
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Pezenti LF, Dionisio JF, Sosa-Gómez DR, de Souza RF, da Rosa R. Transposable elements in the transcriptome of the velvetbean caterpillar Anticarsia gemmatalis Hübner, 1818 (Lepidoptera: Erebidae). Genome 2023. [DOI: 10.1139/gen-2022-0066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023]
Abstract
Transposable elements (TEs) are DNA sequences that possess the ability to move from one genomic location to another. These sequences contribute to a significant fraction of the genomes of most eukaryotes and can impact their architecture and regulation. In this paper, we present the first data related to the identification and characterization of TEs present in the transcriptome of Anticarsia gemmatalis. Approximately, 835 transcripts showed significant similarity to TEs and (or) characteristic domains. Retrotransposons accounted for 71.2% (595 sequences) of the identified elements, while DNA transposons were less abundant, with 240 annotations (28.8%). TEs were classified into 30 superfamilies, with SINE3/5S and Gypsy being the most abundant. Based on the sequences of TEs found in the transcriptome, we were able to locate conserved regions in the chromosomes of this species. The analysis of differential expression of TEs in susceptible and resistant strains, challenged and not challenged with Bacillus thuringiensis ( Bt) from in silico analysis, indicated that exposure to Bt can regulate the transcription of mobile genetic elements in the velvetbean caterpillar. Thus, these data contribute significantly to the knowledge of the structure and composition of these elements in the genome of this species, and suggest the role of stress on their expression.
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16
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Masunaga N, Kitaoka T, Ichinose H. Biocatalyst collection and heterologous expression of sesquiterpene synthases from basidiomycetous fungi: Discovery of a novel sesquiterpene hydrocarbon. Microb Biotechnol 2023; 16:632-644. [PMID: 36576879 PMCID: PMC9948225 DOI: 10.1111/1751-7915.14204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Revised: 12/07/2022] [Accepted: 12/11/2022] [Indexed: 12/29/2022] Open
Abstract
Basidiomycetes produce a wide variety of sesquiterpenoids, which attract significant interest in pharmaceutical and industrial applications. Structural diversification of sesquiterpenoids is performed by sesquiterpene synthases (STSs), which produce a wide array of backbone structures; therefore, functional characterization and increased biocatalyst collection of STSs are important for expanding scientific knowledge and meeting the needs of advanced biotechnology. Gene identification and functional annotation of STSs from the basidiomycetous fungi Agaricus bisporus, Auriscalpium vulgare, Lepista nuda, Pleurotus ostreatus and Trametes versicolor were conducted. Through these investigations, the catalytic functions of 30 STSs were revealed using recombinant enzymes heterologously expressed in Saccharomyces cerevisiae. Furthermore, the unique function of an STS from P. ostreatus, PoSTS-06, was revealed to be the production of a novel sesquiterpene hydrocarbon that we named pleostene. The absolute structure of pleostene was determined by NMR spectroscopy and X-ray crystallography using the crystalline sponge method.
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Affiliation(s)
| | - Takuya Kitaoka
- Faculty of Agriculture, Kyushu University, Fukuoka, Japan
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17
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Chen JJ, Zhang Z, Wang Y, Yuan XL, Wang J, Yang YM, Zheng Y. Transcriptome Analysis of Antrodia cinnamomea Mycelia from Different Wood Substrates. MYCOBIOLOGY 2023; 51:49-59. [PMID: 36846623 PMCID: PMC9946338 DOI: 10.1080/12298093.2023.2175434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 01/20/2023] [Accepted: 01/27/2023] [Indexed: 06/18/2023]
Abstract
Antrodia cinnamomea, an edible and medicinal fungus with significant economic value and application prospects, is rich in terpenoids, benzenoids, lignans, polysaccharides, and benzoquinone, succinic and maleic derivatives. In this study, the transcriptome of A. cinnamomea cultured on the wood substrates of Cinnamomum glanduliferum (YZM), C. camphora (XZM), and C. kanehirae (NZM) was sequenced using the high-throughput sequencing technology Illumina HiSeq 2000, and the data were assembled by de novo strategy to obtain 78,729 Unigenes with an N50 of 4,463 bp. Compared with public databases, about 11,435, 6,947, and 5,994 Unigenes were annotated to the Non-Redundant (NR), Gene Ontology (GO), and Kyoto Encyclopedia of Genes and Genome (KEGG), respectively. The comprehensive analysis of the mycelium terpene biosynthesis-related genes in A. cinnamomea revealed that the expression of acetyl-CoA acetyltransferase (AACT), acyl-CoA dehydrogenase (MCAD), 3-hydroxy-3-methylglutaryl-coenzyme A (HMG-CoA), mevalonate pyrophosphate decarboxylase (MVD), and isopentenyl diphosphate isomerase (IDI) was significantly higher on NZM compared to the other two wood substrates. Similarly, the expression of geranylgeranyltransferase (GGT) was significantly higher on YZM compared to NZM and XZM, and the expression of farnesyl transferase (FTase) was significantly higher on XZM. Furthermore, the expressions of 2,3-oxidized squalene cyclase (OCS), squalene synthase (SQS), and squalene epoxidase (SE) were significantly higher on NZM. Overall, this study provides a potential approach to explore the molecular regulation mechanism of terpenoid biosynthesis in A. cinnamomea.
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Affiliation(s)
- Jiao-Jiao Chen
- College of Forestry, Southwest Forestry University, Kunming, China
- Yunnan Key Laboratory of Forest Plant Cultivation, Development and Utilization, Yunnan Academy of Forestry and Grassland, Kunming, China
- Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming, China
| | - Zhang Zhang
- College of Forestry, Southwest Forestry University, Kunming, China
- Yunnan Key Laboratory of Forest Plant Cultivation, Development and Utilization, Yunnan Academy of Forestry and Grassland, Kunming, China
| | - Yi Wang
- Yunnan Key Laboratory of Forest Plant Cultivation, Development and Utilization, Yunnan Academy of Forestry and Grassland, Kunming, China
- Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming, China
| | - Xiao-Long Yuan
- Yunnan Key Laboratory of Forest Plant Cultivation, Development and Utilization, Yunnan Academy of Forestry and Grassland, Kunming, China
| | - Juan Wang
- Institute of Green Development, Southwest Forestry University, Kunming, China
| | - Yu-Ming Yang
- Institute of Green Development, Southwest Forestry University, Kunming, China
| | - Yuan Zheng
- College of Forestry, Southwest Forestry University, Kunming, China
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18
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Li C, Qiao L, Lu Y, Xing G, Wang X, Zhang G, Qian H, Shen Y, Zhang Y, Yao W, Cheng K, Ma Z, Liu N, Wang D, Zheng W. Gapless Genome Assembly of Puccinia triticina Provides Insights into Chromosome Evolution in Pucciniales. Microbiol Spectr 2023; 11:e0282822. [PMID: 36688678 PMCID: PMC9927501 DOI: 10.1128/spectrum.02828-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 12/02/2022] [Indexed: 01/24/2023] Open
Abstract
Chromosome evolution drives species evolution, speciation, and adaptive radiation. Accurate genome assembly is crucial to understanding chromosome evolution of species, such as dikaryotic fungi. Rust fungi (Pucciniales) in dikaryons represent the largest group of plant pathogens, but the evolutionary process of adaptive radiation in Pucciniales remains poorly understood. Here, we report a gapless genome for the wheat leaf rust fungus Puccinia triticina determined using PacBio high-fidelity (HiFi) sequencing. This gapless assembly contains two sets of chromosomes, showing that one contig represents one chromosome. Comparisons of homologous chromosomes between the phased haplotypes revealed that highly frequent small-scale sequence divergence shapes haplotypic variation. Genome analyses of Puccinia triticina along with other rusts revealed that recent transposable element bursts and extensive segmental gene duplications synergistically highlight the evolution of chromosome structures. Comparative analysis of chromosomes indicated that frequent chromosomal rearrangements may act as a major contributor to rapid radiation of Pucciniales. This study presents the first gapless, phased assembly for a dikaryotic rust fungus and provides insights into adaptive evolution and species radiation in Pucciniales. IMPORTANCE Rust fungi (Pucciniales) are the largest group of plant pathogens. Adaptive radiation is a predominant feature in Pucciniales evolution. Chromosome evolution plays an important role in adaptive evolution. Accurate chromosome-scale assembly is required to understand the role of chromosome evolution in Pucciniales. We took advantage of HiFi sequencing to construct a gapless, phased genome for Puccinia triticina. Further analyses revealed that the evolution of chromosome structures in rust lineage is shaped by the combination of transposable element bursts and segmental gene duplications. Chromosome comparisons of Puccinia triticina and other rusts suggested that frequent chromosomal arrangements may make remarkable contributions to high species diversity of rust fungi. Our results present the first gapless genome for Pucciniales and shed light on the feature of chromosome evolution in Pucciniales.
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Affiliation(s)
- Chuang Li
- State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, China
- State Key Laboratory of Wheat and Maize Crop Science, College of Agronomy and Center for Crop Genome Engineering, Henan Agricultural University, Zhengzhou, China
| | - Liuhui Qiao
- State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, China
- State Key Laboratory of Wheat and Maize Crop Science, College of Agronomy and Center for Crop Genome Engineering, Henan Agricultural University, Zhengzhou, China
| | - Yanan Lu
- State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - Guozhen Xing
- State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - Xiaodong Wang
- State Key Laboratory of North China Crop Improvement and Regulation, College of Plant Protection, Hebei Agricultural University, Baoding, China
| | | | - Huimin Qian
- State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - Yilin Shen
- State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - Yibo Zhang
- State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - Wen Yao
- State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - Kun Cheng
- State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - Zhenling Ma
- State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - Na Liu
- State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - Daowen Wang
- State Key Laboratory of Wheat and Maize Crop Science, College of Agronomy and Center for Crop Genome Engineering, Henan Agricultural University, Zhengzhou, China
| | - Wenming Zheng
- State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, China
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Heterochromatin and RNAi act independently to ensure genome stability in Mucorales human fungal pathogens. Proc Natl Acad Sci U S A 2023; 120:e2220475120. [PMID: 36745785 PMCID: PMC9963178 DOI: 10.1073/pnas.2220475120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Chromatin modifications play a fundamental role in controlling transcription and genome stability and yet despite their importance, are poorly understood in early-diverging fungi. We present a comprehensive study of histone lysine and DNA methyltransferases across the Mucoromycota, emphasizing heterochromatin formation pathways that rely on the Clr4 complex involved in H3K9-methylation, the Polycomb-repressive complex 2 driving H3K27-methylation, or DNMT1-like methyltransferases that catalyze 5mC DNA methylation. Our analysis uncovered H3K9-methylated heterochromatin as the major chromatin modification repressing transcription in these fungi, which lack both Polycomb silencing and cytosine methylation. Although small RNAs generated by RNA interference (RNAi) pathways facilitate the formation of heterochromatin in many eukaryotic organisms, we show that RNAi is not required to maintain either genomic or centromeric heterochromatin in Mucor. H3K9-methylation and RNAi act independently to control centromeric regions, suggesting a functional subspecialization. Whereas the H3K9 methyltransferase Clr4 and heterochromatin formation are essential for cell viability, RNAi is dispensable for viability yet acts as the main epigenetic, regulatory force repressing transposition of centromeric GremLINE1 elements. Mutations inactivating canonical RNAi lead to rampant transposition and insertional inactivation of targets resulting in antimicrobial drug resistance. This fine-tuned, Rdrp2-dependent RNAi activity is critical for genome stability, restricting GremLINE1 retroelements to the centromeres where they occupy long heterochromatic islands. Taken together, our results suggest that RNAi and heterochromatin formation are independent genome defense and regulatory mechanisms in the Mucorales, contributing to a paradigm shift from the cotranscriptional gene silencing observed in fission yeasts to models in which heterochromatin and RNAi operate independently in early-diverging fungi.
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20
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Nakagame S, Minagawa H, Motegi N. Purification and Characterization of Class III Lipase from a White-Rot Fungus Pleurotus ostreatus. Appl Biochem Biotechnol 2023; 195:1085-1095. [PMID: 36322285 DOI: 10.1007/s12010-022-04211-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/21/2022] [Indexed: 01/20/2023]
Abstract
Pleurotus ostreatus is an edible white-rot fungus with lignocellulosic biomass degrading enzymes that have been studied extensively. However, until now, lipolytic enzymes from P. ostreatus, which degrade extractives in lignocellulosic biomass, have not been purified and characterized. In this study, P. ostreatus was inoculated into the rapeseed oil containing culture to induce lipase. The lipase in the culture broth was successfully purified to homogeneity by chromatographic methods. The molecular weight of the purified lipase was 27 kDa, and its optimal pH and temperature were 5.0 and 30 °C, respectively. The purified lipase showed high activity with the substrates 4-methylumbelliferyl (4-MU) decanoate (C10:0) and 4-MU oleate (C18:1), and no activity with 4-MU acetate (C2:0) and 4-MU butyrate (C4:0). The amino acid sequences and substrate specificities of the purified lipase suggested that it belonged to class III. Kinetic parameters measurements (Km and Vmax) showed that 4-MU palmitate had a high affinity for the purified lipase, and it was the substrate most efficiently hydrolyzed by the purified lipase.
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Affiliation(s)
- Seiji Nakagame
- Department of Applied Bioscience, Kanagawa Institute of Technology, 1030 Shimo-Ogino, Atsugi, Kanagawa, 243-0292, Japan.
| | - Hu Minagawa
- Department of Applied Bioscience, Kanagawa Institute of Technology, 1030 Shimo-Ogino, Atsugi, Kanagawa, 243-0292, Japan
| | - Nagi Motegi
- Department of Applied Bioscience, Kanagawa Institute of Technology, 1030 Shimo-Ogino, Atsugi, Kanagawa, 243-0292, Japan
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21
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Wacker T, Helmstetter N, Wilson D, Fisher MC, Studholme DJ, Farrer RA. Two-speed genome evolution drives pathogenicity in fungal pathogens of animals. Proc Natl Acad Sci U S A 2023; 120:e2212633120. [PMID: 36595674 PMCID: PMC9926174 DOI: 10.1073/pnas.2212633120] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 11/14/2022] [Indexed: 01/05/2023] Open
Abstract
The origins and evolution of virulence in amphibian-infecting chytrids Batrachochytrium dendrobatidis (Bd) and Batrachochytrium salamandrivorans (Bsal) are largely unknown. Here, we use deep nanopore sequencing of Bsal and comparative genomics against 21 high-quality genome assemblies that span the fungal Chytridiomycota. We discover that Bsal has the most repeat-rich genome of the Chytridiomycota, comprising 40.9% repetitive elements; this genome has expanded to more than 3× the length of its conspecific Bd, with autonomous and fully functional LTR/Gypsy elements contributing significantly to the expansion. The M36 metalloprotease virulence factors are highly expanded (n = 177) in Bsal, most of which (53%) are flanked by transposable elements, suggesting they have a repeat-associated expansion. We find enrichment upstream of M36 metalloprotease genes of three novel repeat families belonging to the repeat superfamily of LINEs that are implicated with gene copy number variations. Additionally, Bsal has a highly compartmentalized genome architecture, with virulence factors enriched in gene-sparse/repeat-rich compartments, while core conserved genes are enriched in gene-rich/repeat-poor compartments. Genes upregulated during infection are primarily found in the gene-sparse/repeat-rich compartment in both Bd and Bsal. Furthermore, genes with signatures of positive selection in Bd are enriched in repeat-rich regions, suggesting these regions are a cradle for the evolution of chytrid pathogenicity. These are the hallmarks of two-speed genome evolution, and this study provides evidence of two-speed genomes in an animal pathogen, shedding light on the evolution of fungal pathogens of vertebrates driving global declines and extinctions.
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Affiliation(s)
- Theresa Wacker
- Medical Research Council Centre for Medical Mycology at the University of Exeter, ExeterEX4 4QD, United Kingdom
| | - Nicolas Helmstetter
- Medical Research Council Centre for Medical Mycology at the University of Exeter, ExeterEX4 4QD, United Kingdom
| | - Duncan Wilson
- Medical Research Council Centre for Medical Mycology at the University of Exeter, ExeterEX4 4QD, United Kingdom
| | - Matthew C. Fisher
- Medical Research Council (MRC) Centre for Global Infectious Disease Analysis, Imperial College London, LondonW12 0BZ, United Kingdom
| | - David J. Studholme
- Department of Biosciences, University of Exeter, ExeterEX4 4QD, United Kingdom
| | - Rhys A. Farrer
- Medical Research Council Centre for Medical Mycology at the University of Exeter, ExeterEX4 4QD, United Kingdom
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22
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Srivastava AK, Srivastava R, Yadav J, Singh AK, Tiwari PK, Srivastava AK, Sahu PK, Singh SM, Kashyap PL. Virulence and pathogenicity determinants in whole genome sequence of Fusarium udum causing wilt of pigeon pea. Front Microbiol 2023; 14:1066096. [PMID: 36876067 PMCID: PMC9981795 DOI: 10.3389/fmicb.2023.1066096] [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: 10/10/2022] [Accepted: 01/23/2023] [Indexed: 02/19/2023] Open
Abstract
The present study deals with whole genome analysis of Fusarium udum, a wilt causing pathogen of pigeon pea. The de novo assembly identified a total of 16,179 protein-coding genes, of which 11,892 genes (73.50%) were annotated using BlastP and 8,928 genes (55.18%) from KOG annotation. In addition, 5,134 unique InterPro domains were detected in the annotated genes. Apart from this, we also analyzed genome sequence for key pathogenic genes involved in virulence, and identified 1,060 genes (6.55%) as virulence genes as per the PHI-BASE database. The secretome profiling of these virulence genes indicated the presence of 1,439 secretory proteins. Of those, an annotation of 506 predicted secretory proteins through CAZyme database indicated maximum abundance of Glycosyl hydrolase (GH, 45%) family proteins followed by auxiliary activity (AA) family proteins. Interestingly, the presence of effectors for cell wall degradation, pectin degradation, and host cell death was found. The genome comprised approximately 895,132 bp of repetitive elements, which includes 128 long terminal repeats (LTRs), and 4,921 simple sequence repeats (SSRs) of 80,875 bp length. The comparative mining of effector genes among different Fusarium species revealed five common and two specific effectors in F. udum that are related to host cell death. Furthermore, wet lab experiment validated the presence of effector genes like SIX (for Secreted in Xylem). We conclude that deciphering the whole genome of F. udum would be instrumental in understanding evolution, virulence determinants, host-pathogen interaction, possible control strategies, ecological behavior, and many other complexities of the pathogen.
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Affiliation(s)
- Alok K Srivastava
- ICAR-National Bureau of Agriculturally Important Microorganisms (NBAIM), Maunath Bhanjan, Uttar Pradesh, India
| | - Ruchi Srivastava
- ICAR-National Bureau of Agriculturally Important Microorganisms (NBAIM), Maunath Bhanjan, Uttar Pradesh, India
| | - Jagriti Yadav
- ICAR-National Bureau of Agriculturally Important Microorganisms (NBAIM), Maunath Bhanjan, Uttar Pradesh, India
| | - Alok K Singh
- ICAR-National Bureau of Agriculturally Important Microorganisms (NBAIM), Maunath Bhanjan, Uttar Pradesh, India
| | - Praveen K Tiwari
- ICAR-National Bureau of Agriculturally Important Microorganisms (NBAIM), Maunath Bhanjan, Uttar Pradesh, India
| | - Anchal K Srivastava
- ICAR-National Bureau of Agriculturally Important Microorganisms (NBAIM), Maunath Bhanjan, Uttar Pradesh, India
| | - Pramod K Sahu
- ICAR-National Bureau of Agriculturally Important Microorganisms (NBAIM), Maunath Bhanjan, Uttar Pradesh, India
| | - Shiv M Singh
- Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi, Uttar Pradesh, India
| | - Prem Lal Kashyap
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, Haryana, India
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23
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Gupta NC, Yadav S, Arora S, Mishra DC, Budhlakoti N, Gaikwad K, Rao M, Prasad L, Rai PK, Sharma P. Draft genome sequencing and secretome profiling of Sclerotinia sclerotiorum revealed effector repertoire diversity and allied broad-host range necrotrophy. Sci Rep 2022; 12:21855. [PMID: 36528657 PMCID: PMC9759525 DOI: 10.1038/s41598-022-22028-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 10/07/2022] [Indexed: 12/23/2022] Open
Abstract
White mold commonly known as Sclerotinia sclerotiorum causes stem rot disease and has emerged as one of the major fungal pathogens of oilseed Brassica across the world. In the present study, consistently virulent S. sclerotiorum isolate "ESR-01" was sequenced and an assembly size of ~ 41 Mb with 328 scaffolds having N50 of 447,128 was obtained. Additionally, 27,450 single nucleotide polymorphisms (SNPs) were identified from 155 scaffolds against S. sclerotiorum 1980 isolate, with an average SNP density of ~ 1.5 per kb genome. 667 repetitive elements were identified and approximately comprised 7% of the total annotated genes. The DDE_1 with 454 in numbers was found to be the most abundant and accounts for 68% of the total predicted repetitive elements. In total, 3844 simple sequence repeats are identified in the 328 scaffolds. A total of 9469 protein-coding genes were predicted from the whole genome assembly with an average gene length of 1587 bp and their distribution as 230.95 genes per Mb in the genome. Out of 9469 predicted protein-coding genes, 529 genes were observed encoding the CAZymes (Carbohydrate-Active enzymes) capable of degradation of the complex polysaccharides. Glycosyltransferase (GT) families were most abundant (49.71%) among the predicted CAZymes and GT2 (23%), GT4 (20%), and glycoside hydrolase (GH) 23% with GH18 (11%) were the prominent cell wall degrading enzyme families in the ESR-01 secretome. Besides this, 156 genes essential for the pathogen-host interactions were also identified. The effector analysis in the whole genome proteomics dataset revealed a total of 57 effector candidates (ECs) and 27 of them were having their analogs whereas the remaining 30 were novel ones. Eleven selected ECs were validated experimentally by analyzing the expression profile of the ESR-01 isolate of S. sclerotiorum. Together, the present investigation offers a better understanding of the S. sclerotiorum genome, secretome, and its effector repertoire which will help in refining the present knowledge on S. sclerotiorum-Brassica interactions and necrotrophic lifestyle of the phytopathogen in general.
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Affiliation(s)
- Navin C. Gupta
- grid.418105.90000 0001 0643 7375ICAR-National Institute for Plant Biotechnology, New Delhi, India
| | - Sunita Yadav
- grid.463150.50000 0001 2218 1322Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Shaweta Arora
- grid.418105.90000 0001 0643 7375ICAR-National Institute for Plant Biotechnology, New Delhi, India
| | - Dwijesh C. Mishra
- grid.463150.50000 0001 2218 1322Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Neeraj Budhlakoti
- grid.463150.50000 0001 2218 1322Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Kishore Gaikwad
- grid.418105.90000 0001 0643 7375ICAR-National Institute for Plant Biotechnology, New Delhi, India
| | - Mahesh Rao
- grid.418105.90000 0001 0643 7375ICAR-National Institute for Plant Biotechnology, New Delhi, India
| | - Lakshman Prasad
- grid.418196.30000 0001 2172 0814ICAR-Indian Agricultural Research Institute, Pusa, New Delhi, India
| | - Pramod K. Rai
- grid.505951.d0000 0004 1768 6555ICAR-Directorate of Rapeseed-Mustard Research, Bharatpur, Rajasthan India
| | - Pankaj Sharma
- grid.505951.d0000 0004 1768 6555ICAR-Directorate of Rapeseed-Mustard Research, Bharatpur, Rajasthan India
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24
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Towards Understanding the Function of Aegerolysins. Toxins (Basel) 2022; 14:toxins14090629. [PMID: 36136567 PMCID: PMC9505663 DOI: 10.3390/toxins14090629] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Revised: 09/04/2022] [Accepted: 09/09/2022] [Indexed: 11/17/2022] Open
Abstract
Aegerolysins are remarkable proteins. They are distributed over the tree of life, being relatively widespread in bacteria and fungi, but also present in some insects, plants, protozoa, and viruses. Despite their abundance in cells of certain developmental stages and their presence in secretomes, only a few aegerolysins have been studied in detail. Their function, in particular, is intriguing. Here, we summarize previously published findings on the distribution, molecular interactions, and function of these versatile aegerolysins. They have very diverse protein sequences but a common fold. The machine learning approach of the AlphaFold2 algorithm, which incorporates physical and biological knowledge of protein structures and multisequence alignments, provides us new insights into the aegerolysins and their pore-forming partners, complemented by additional genomic support. We hypothesize that aegerolysins are involved in the mechanisms of competitive exclusion in the niche.
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25
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Ogaji YO, Lee RC, Sawbridge TI, Cocks BG, Daetwyler HD, Kaur S. De Novo Long-Read Whole-Genome Assemblies and the Comparative Pan-Genome Analysis of Ascochyta Blight Pathogens Affecting Field Pea. J Fungi (Basel) 2022; 8:jof8080884. [PMID: 36012871 PMCID: PMC9410150 DOI: 10.3390/jof8080884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 08/12/2022] [Accepted: 08/15/2022] [Indexed: 11/16/2022] Open
Abstract
Ascochyta Blight (AB) is a major disease of many cool-season legumes globally. In field pea, three fungal pathogens have been identified to be responsible for this disease in Australia, namely Peyronellaea pinodes, Peyronellaea pinodella and Phoma koolunga. Limited genomic resources for these pathogens have been generated, which has hampered the implementation of effective management strategies and breeding for resistant cultivars. Using Oxford Nanopore long-read sequencing, we report the first high-quality, fully annotated, near-chromosome-level nuclear and mitochondrial genome assemblies for 18 isolates from the Australian AB complex. Comparative genome analysis was performed to elucidate the differences and similarities between species and isolates using phylogenetic relationships and functional diversity. Our data indicated that P. pinodella and P. koolunga are heterothallic, while P. pinodes is homothallic. More homology and orthologous gene clusters are shared between P. pinodes and P. pinodella compared to P. koolunga. The analysis of the repetitive DNA content showed differences in the transposable repeat composition in the genomes and their expression in the transcriptomes. Significant repeat expansion in P. koolunga’s genome was seen, with strong repeat-induced point mutation (RIP) activity being evident. Phylogenetic analysis revealed that genetic diversity can be exploited for species marker development. This study provided the much-needed genetic resources and characterization of the AB species to further drive research in key areas such as disease epidemiology and host–pathogen interactions.
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Affiliation(s)
- Yvonne O. Ogaji
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, 5 Ring Road, Melbourne, VIC 3083, Australia
- School of Applied Systems Biology, La Trobe University, Melbourne, VIC 3086, Australia
| | - Robert C. Lee
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Perth, WA 6102, Australia
| | - Tim I. Sawbridge
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, 5 Ring Road, Melbourne, VIC 3083, Australia
- School of Applied Systems Biology, La Trobe University, Melbourne, VIC 3086, Australia
| | - Benjamin G. Cocks
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, 5 Ring Road, Melbourne, VIC 3083, Australia
- School of Applied Systems Biology, La Trobe University, Melbourne, VIC 3086, Australia
| | - Hans D. Daetwyler
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, 5 Ring Road, Melbourne, VIC 3083, Australia
- School of Applied Systems Biology, La Trobe University, Melbourne, VIC 3086, Australia
| | - Sukhjiwan Kaur
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, 5 Ring Road, Melbourne, VIC 3083, Australia
- Correspondence:
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Comparative Genome Analyses of Plant Rust Pathogen Genomes Reveal a Confluence of Pathogenicity Factors to Quell Host Plant Defense Responses. PLANTS 2022; 11:plants11151962. [PMID: 35956440 PMCID: PMC9370660 DOI: 10.3390/plants11151962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 07/18/2022] [Accepted: 07/20/2022] [Indexed: 12/05/2022]
Abstract
Switchgrass rust caused by Puccinia novopanici (P. novopanici) has the ability to significantly affect the biomass yield of switchgrass, an important biofuel crop in the United States. A comparative genome analysis of P. novopanici with rust pathogen genomes infecting monocot cereal crops wheat, barley, oats, maize and sorghum revealed the presence of larger structural variations contributing to their genome sizes. A comparative alignment of the rust pathogen genomes resulted in the identification of collinear and syntenic relationships between P. novopanici and P. sorghi; P. graminis tritici 21–0 (Pgt 21) and P. graminis tritici Ug99 (Pgt Ug99) and between Pgt 21 and P. triticina (Pt). Repeat element analysis indicated a strong presence of retro elements among different Puccinia genomes, contributing to the genome size variation between ~1 and 3%. A comparative look at the enriched protein families of Puccinia spp. revealed a predominant role of restriction of telomere capping proteins (RTC), disulfide isomerases, polysaccharide deacetylases, glycoside hydrolases, superoxide dismutases and multi-copper oxidases (MCOs). All the proteomes of Puccinia spp. share in common a repertoire of 75 secretory and 24 effector proteins, including glycoside hydrolases cellobiohydrolases, peptidyl-propyl isomerases, polysaccharide deacetylases and protein disulfide-isomerases, that remain central to their pathogenicity. Comparison of the predicted effector proteins from Puccinia spp. genomes to the validated proteins from the Pathogen–Host Interactions database (PHI-base) resulted in the identification of validated effector proteins PgtSR1 (PGTG_09586) from P. graminis and Mlp124478 from Melampsora laricis across all the rust pathogen genomes.
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Genome-wide comparison deciphers lifestyle adaptation and glass biodeterioration property of Curvularia eragrostidis C52. Sci Rep 2022; 12:11411. [PMID: 35794131 PMCID: PMC9259613 DOI: 10.1038/s41598-022-15334-z] [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: 11/08/2021] [Accepted: 06/22/2022] [Indexed: 11/24/2022] Open
Abstract
Glass biodeterioration by fungi has caused irreversible damage to valuable glass materials such as cultural heritages and optical devices. To date, knowledge about metabolic potential and genomic profile of biodeteriorative fungi is still scarce. Here, we report for the first time the whole genome sequence of Curvularia eragrostidis C52 that strongly degraded silica-based glasses coated with fluorine and hafnium, as expressed by the hyphal surface coverage of 46.16 ± 3.3% and reduced light transmission of 50.93 ± 1.45%. The genome of C. eragrostidis C52 is 36.9 Mb long with a GC content of 52.1% and contains 14,913 protein-coding genes, which is the largest genome ever recorded in the genus Curvularia. Phylogenomic analysis revealed C. eragrostidis C52 formed a distinct cluster with Curvularia sp. IFB-Z10 and was not evolved from compared genomes. Genome-wide comparison showed that strain C52 harbored significantly higher proportion of proteins involved in carbohydrate-active enzymes, peptidases, secreted proteins, and transcriptional factors, which may be potentially attributed to a lifestyle adaptation. Furthermore, 72 genes involved in the biosynthesis of 6 different organic acids were identified and expected to be crucial for the fungal survival in the glass environment. To form biofilm against stress, the fungal strain utilized 32 genes responsible for exopolysaccharide production. These findings will foster a better understanding of the biology of C. eragrostidis and the mechanisms behind fungal biodeterioration in the future.
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Maia T, Rody HVS, Bombardelli RGH, Souto TG, Camargo LEA, Monteiro-Vitorello CB. A Bacterial Type Three Secretion-Based Delivery System for Functional Characterization of Sporisorium scitamineum Plant Immune Suppressing Effector Proteins. PHYTOPATHOLOGY 2022; 112:1513-1523. [PMID: 35050679 DOI: 10.1094/phyto-08-21-0326-r] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The facultative biotrophic basidiomycete Sporisorium scitamineum causes smut disease in sugarcane. This study applied an assay to identify S. scitamineum candidate effectors (CEs) with plant immunity suppression activities by delivering them into Nicotiana benthamiana cells via the type-three secretion system of Pseudomonas fluorescens EtHAn. Six CEs were individually cloned into the pEDV6 vector and expressed by P. fluorescens EtHAn for translocation into the plant cells. Three CEs (g1052, g3890, and g5159) could suppress pattern-triggered immunity (PTI) responses with high reproducibility in different coinfiltration experiments with P. syringae pv. tomato DC3000. In addition, three CEs (g1052, g4549, and g5159) were also found to be AvrB-induced suppressors of effector-triggered immunity (ETI), demonstrating for the first time that S. scitamineum can defeat both PTI and ETI responses. A transcriptomic analysis at different stages of infection by the smut fungus of three sugarcane cultivars with contrasting responses to the pathogen revealed that suppressors g1052, g3890, g4549, and g5159 were induced at the early stage of infection. By contrast, the two CEs (g2666 and g6610) that did not exhibit suppression activities expressed only at the late stage of infection. Moreover, genomic structures of the CEs and searches for orthologs in other smut species suggested duplication events and further divergence in CEs evolution of S. scitamineum. Thus, the transient assay applied here demonstrated the potential of pEDV6 and P. fluorescens EtHAn as biological tools for identifying plant immune suppressors from S. scitamineum.
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Affiliation(s)
- Thiago Maia
- Departamento de Fitopatologia e Nematologia, Universidade de São Paulo (USP), Escola Superior de Agricultura Luiz de Queiroz (ESALQ), Piracicaba, SP, Brazil
- Departamento de Genética, USP, ESALQ, Piracicaba, SP, Brazil
| | - Hugo V S Rody
- Departamento de Genética, USP, ESALQ, Piracicaba, SP, Brazil
| | | | - Tiarla Graciane Souto
- Departamento de Fitopatologia e Nematologia, Universidade de São Paulo (USP), Escola Superior de Agricultura Luiz de Queiroz (ESALQ), Piracicaba, SP, Brazil
- Departamento de Genética, USP, ESALQ, Piracicaba, SP, Brazil
| | - Luis Eduardo Aranha Camargo
- Departamento de Fitopatologia e Nematologia, Universidade de São Paulo (USP), Escola Superior de Agricultura Luiz de Queiroz (ESALQ), Piracicaba, SP, Brazil
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Exploring a novel genomic safe-haven site in the human pathogenic mould Aspergillus fumigatus. Fungal Genet Biol 2022; 161:103702. [PMID: 35569804 DOI: 10.1016/j.fgb.2022.103702] [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: 04/04/2022] [Revised: 05/04/2022] [Accepted: 05/07/2022] [Indexed: 11/24/2022]
Abstract
Aspergillus fumigatus is the most important airborne fungal pathogen and allergen of humans causing high morbidity and mortality worldwide. The factors that govern pathogenicity of this organism are multi-factorial and are poorly understood. Molecular tools to dissect the mechanisms of pathogenicity in A. fumigatus have improved significantly over the last 20 years however many procedures have not been standardised for A. fumigatus. Here, we present a new genomic safe-haven locus at the site of an inactivated transposon, named SH-aft4, which can be used to insert DNA sequences in the genome of this fungus without impacting its phenotype. We show that we are able to effectively express a transgene construct from the SH-aft4 and that natural regulation of promoter function is conserved at this site. Furthermore, the SH-aft4 locus is highly conserved in the genome of a wide range of clinical and environmental isolates including the isolates commonly used by many laboratories CEA10, Af293 and ATCC46645, allowing a wide range of isolates to be manipulated. Our results show that the aft4 locus can serve as a site for integration of a wide range of genetic constructs to aid functional genomics studies of this important human fungal pathogen.
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Lebreton A, Tang N, Kuo A, LaButti K, Andreopoulos W, Drula E, Miyauchi S, Barry K, Clum A, Lipzen A, Mousain D, Ng V, Wang R, Dai Y, Henrissat B, Grigoriev IV, Guerin-Laguette A, Yu F, Martin FM. Comparative genomics reveals a dynamic genome evolution in the ectomycorrhizal milk-cap (Lactarius) mushrooms. THE NEW PHYTOLOGIST 2022; 235:306-319. [PMID: 35383395 DOI: 10.1111/nph.18143] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 03/16/2022] [Indexed: 06/14/2023]
Abstract
Ectomycorrhizal fungi play a key role in forests by establishing mutualistic symbioses with woody plants. Genome analyses have identified conserved symbiosis-related traits among ectomycorrhizal fungal species, but the molecular mechanisms underlying host specificity remain poorly known. We sequenced and compared the genomes of seven species of milk-cap fungi (Lactarius, Russulales) with contrasting host specificity. We also compared these genomes with those of symbiotic and saprotrophic Russulales species, aiming to identify genes involved in their ecology and host specificity. The size of Lactarius genomes is significantly larger than other Russulales species, owing to a massive accumulation of transposable elements and duplication of dispensable genes. As expected, their repertoire of genes coding for plant cell wall-degrading enzymes is restricted, but they retained a substantial set of genes involved in microbial cell wall degradation. Notably, Lactarius species showed a striking expansion of genes encoding proteases, such as secreted ectomycorrhiza-induced sedolisins. A high copy number of genes coding for small secreted LysM proteins and Lactarius-specific lectins were detected, which may be linked to host specificity. This study revealed a large diversity in the genome landscapes and gene repertoires within Russulaceae. The known host specificity of Lactarius symbionts may be related to mycorrhiza-induced species-specific genes, including secreted sedolisins.
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Affiliation(s)
- Annie Lebreton
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, 100083, China
- Université de Lorraine, INRAE, Unité mixte de recherche Interactions Arbres/Microorganismes, Centre INRAE, Grand Est-Nancy, 54280, Champenoux, France
| | - Nianwu Tang
- Université de Lorraine, INRAE, Unité mixte de recherche Interactions Arbres/Microorganismes, Centre INRAE, Grand Est-Nancy, 54280, Champenoux, France
- Germplasm Bank of Wild Species, Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Alan Kuo
- Lawrence Berkeley National Laboratory, US Department of Energy Joint Genome Institute, Berkeley, CA, 94720, USA
| | - Kurt LaButti
- Lawrence Berkeley National Laboratory, US Department of Energy Joint Genome Institute, Berkeley, CA, 94720, USA
| | - William Andreopoulos
- US Department of Energy Joint Genome Institute, University of California Berkeley, Berkeley, CA, 94720, USA
| | - Elodie Drula
- CNRS, Aix-Marseille Université, Marseille, 13288, France
- USC1408 AFMB, INRAE, Marseille, 13288, France
| | - Shingo Miyauchi
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, 50829, Germany
| | - Kerrie Barry
- Lawrence Berkeley National Laboratory, US Department of Energy Joint Genome Institute, Berkeley, CA, 94720, USA
| | - Alicia Clum
- Lawrence Berkeley National Laboratory, US Department of Energy Joint Genome Institute, Berkeley, CA, 94720, USA
| | - Anna Lipzen
- Lawrence Berkeley National Laboratory, US Department of Energy Joint Genome Institute, Berkeley, CA, 94720, USA
| | | | - Vivian Ng
- Lawrence Berkeley National Laboratory, US Department of Energy Joint Genome Institute, Berkeley, CA, 94720, USA
| | - Ran Wang
- Germplasm Bank of Wild Species, Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Yucheng Dai
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, 100083, China
| | - Bernard Henrissat
- Department of Biotechnology and Biomedicine (DTU Bioengineering), Technical University of Denmark, Kgs. Lyngby, 2800, Denmark
- Department of Biological Sciences, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
| | - Igor V Grigoriev
- Lawrence Berkeley National Laboratory, US Department of Energy Joint Genome Institute, Berkeley, CA, 94720, USA
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, 94720, USA
| | - Alexis Guerin-Laguette
- Mycotree C/- Southern Woods Nursery, 1002 Robinsons Road, RD8, Christchurch, 7678, New Zealand
| | - Fuqiang Yu
- Germplasm Bank of Wild Species, Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Francis M Martin
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, 100083, China
- Université de Lorraine, INRAE, Unité mixte de recherche Interactions Arbres/Microorganismes, Centre INRAE, Grand Est-Nancy, 54280, Champenoux, France
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de Melo Teixeira M, Stajich JE, Sahl JW, Thompson GR, Brem RB, Dubin CA, Blackmon AV, Mead HL, Keim P, Barker BM. A chromosomal-level reference genome of the widely utilized Coccidioides posadasii laboratory strain "Silveira". G3 (BETHESDA, MD.) 2022; 12:jkac031. [PMID: 35137016 PMCID: PMC8982387 DOI: 10.1093/g3journal/jkac031] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 12/29/2021] [Indexed: 12/14/2022]
Abstract
Coccidioidomycosis is a common fungal disease that is endemic to arid and semi-arid regions of both American continents. Coccidioides immitis and Coccidioides posadasii are the etiological agents of the disease, also known as Valley Fever. For several decades, the C. posadasii strain Silveira has been used widely in vaccine studies, is the source strain for production of diagnostic antigens, and is a widely used experimental strain for functional studies. In 2009, the genome was sequenced using Sanger sequencing technology, and a draft assembly and annotation were made available. In this study, the genome of the Silveira strain was sequenced using single molecule real-time sequencing PacBio technology, assembled into chromosomal-level contigs, genotyped, and the genome was reannotated using sophisticated and curated in silico tools. This high-quality genome sequencing effort has improved our understanding of chromosomal structure, gene set annotation, and lays the groundwork for identification of structural variants (e.g. transversions, translocations, and copy number variants), assessment of gene gain and loss, and comparison of transposable elements in future phylogenetic and population genomics studies.
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Affiliation(s)
- Marcus de Melo Teixeira
- Faculty of Medicine, University of Brasília, Brasília 70910-900, Brazil
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ 86011, USA
| | - Jason E Stajich
- Institute for Integrative Genome Biology, University of California Riverside, Riverside, CA 92521, USA
- Department of Microbiology and Plant Pathology, University of California Riverside, Riverside, CA 92521, USA
| | - Jason W Sahl
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ 86011, USA
| | - George R Thompson
- Department of Medical Microbiology and Immunology, University of California Davis, Davis, CA 95616, USA
| | - Rachel B Brem
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | - Claire A Dubin
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | - Austin V Blackmon
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ 86011, USA
| | - Heather L Mead
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ 86011, USA
| | - Paul Keim
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ 86011, USA
| | - Bridget M Barker
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ 86011, USA
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Zaccaron AZ, Chen LH, Samaras A, Stergiopoulos I. A chromosome-scale genome assembly of the tomato pathogen Cladosporium fulvum reveals a compartmentalized genome architecture and the presence of a dispensable chromosome. Microb Genom 2022; 8:000819. [PMID: 35471194 PMCID: PMC9453070 DOI: 10.1099/mgen.0.000819] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Accepted: 03/29/2022] [Indexed: 01/25/2023] Open
Abstract
Cladosporium fulvum is a fungal pathogen that causes leaf mould of tomato. The reference genome of this pathogen was released in 2012 but its high repetitive DNA content prevented a contiguous assembly and further prohibited the analysis of its genome architecture. In this study, we combined third generation sequencing technology with the Hi-C chromatin conformation capture technique, to produce a high-quality and near complete genome assembly and gene annotation of a Race 5 isolate of C. fulvum. The resulting genome assembly contained 67.17 Mb organized into 14 chromosomes (Chr1-to-Chr14), all of which were assembled telomere-to-telomere. The smallest of the chromosomes, Chr14, is only 460 kb in size and contains 25 genes that all encode hypothetical proteins. Notably, PCR assays revealed that Chr14 was absent in 19 out of 24 isolates of a world-wide collection of C. fulvum, indicating that Chr14 is dispensable. Thus, C. fulvum is currently the second species of Capnodiales shown to harbour dispensable chromosomes. The genome of C. fulvum Race 5 is 49.7 % repetitive and contains 14 690 predicted genes with an estimated completeness of 98.9%, currently one of the highest among the Capnodiales. Genome structure analysis revealed a compartmentalized architecture composed of gene-dense and repeat-poor regions interspersed with gene-sparse and repeat-rich regions. Nearly 39.2 % of the C. fulvum Race 5 genome is affected by Repeat-Induced Point (RIP) mutations and evidence of RIP leakage toward non-repetitive regions was observed in all chromosomes, indicating the RIP plays an important role in the evolution of this pathogen. Finally, 345 genes encoding candidate effectors were identified in C. fulvum Race 5, with a significant enrichment of their location in gene-sparse regions, in accordance with the 'two-speed genome' model of evolution. Overall, the new reference genome of C. fulvum presents several notable features and is a valuable resource for studies in plant pathogens.
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Affiliation(s)
- Alex Z. Zaccaron
- Department of Plant Pathology, University of California Davis, Davis, USA
| | - Li-Hung Chen
- Department of Plant Pathology, University of California Davis, Davis, USA
- Present address: Department of Plant Pathology, National Chung Hsing University, Taichung, Taiwan, ROC
| | - Anastasios Samaras
- Department of Plant Pathology, University of California Davis, Davis, USA
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De Miccolis Angelini RM, Landi L, Raguseo C, Pollastro S, Faretra F, Romanazzi G. Tracking of Diversity and Evolution in the Brown Rot Fungi Monilinia fructicola, Monilinia fructigena, and Monilinia laxa. Front Microbiol 2022; 13:854852. [PMID: 35356516 PMCID: PMC8959702 DOI: 10.3389/fmicb.2022.854852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 02/15/2022] [Indexed: 11/13/2022] Open
Abstract
Monilinia species are among the most devastating fungi worldwide as they cause brown rot and blossom blight on fruit trees. To understand the molecular bases of their pathogenic lifestyles, we compared the newly assembled genomes of single strains of Monilinia fructicola, M. fructigena and M. laxa, with those of Botrytis cinerea and Sclerotinia sclerotiorum, as the closest species within Sclerotiniaceae. Phylogenomic analysis of orthologous proteins and syntenic investigation suggest that M. laxa is closer to M. fructigena than M. fructicola, and is closest to the other investigated Sclerotiniaceae species. This indicates that M. laxa was the earliest result of the speciation process. Distinct evolutionary profiles were observed for transposable elements (TEs). M. fructicola and M. laxa showed older bursts of TE insertions, which were affected (mainly in M. fructicola) by repeat-induced point (RIP) mutation gene silencing mechanisms. These suggested frequent occurrence of the sexual process in M. fructicola. More recent TE expansion linked with low RIP action was observed in M. fructigena, with very little in S. sclerotiorum and B. cinerea. The detection of active non-syntenic TEs is indicative of horizontal gene transfer and has resulted in alterations in specific gene functions. Analysis of candidate effectors, biosynthetic gene clusters for secondary metabolites and carbohydrate-active enzymes, indicated that Monilinia genus has multiple virulence mechanisms to infect host plants, including toxins, cell-death elicitor, putative virulence factors and cell-wall-degrading enzymes. Some species-specific pathogenic factors might explain differences in terms of host plant and organ preferences between M. fructigena and the other two Monilinia species.
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Affiliation(s)
| | - Lucia Landi
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University, Ancona, Italy
| | - Celeste Raguseo
- Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, Bari, Italy
| | - Stefania Pollastro
- Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, Bari, Italy
| | - Francesco Faretra
- Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, Bari, Italy
| | - Gianfranco Romanazzi
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University, Ancona, Italy
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Ličytė J, Kvederavičiūtė K, Rukšėnaitė A, Godliauskaitė E, Gibas P, Tomkutė V, Petraitytė G, Masevičius V, Klimašauskas S, Kriukienė E. Distribution and regulatory roles of oxidized 5-methylcytosines in DNA and RNA of the basidiomycete fungi Laccaria bicolor and Coprinopsis cinerea. Open Biol 2022; 12:210302. [PMID: 35232254 PMCID: PMC8889193 DOI: 10.1098/rsob.210302] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
The formation of three oxidative DNA 5-methylcytosine (5mC) modifications (oxi-mCs)-5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC)-by the TET/JBP family of dioxygenases prompted intensive studies of their functional roles in mammalian cells. However, the functional interplay of these less abundant modified nucleotides in other eukaryotic lineages remains poorly understood. We carried out a systematic study of the content and distribution of oxi-mCs in the DNA and RNA of the basidiomycetes Laccaria bicolor and Coprinopsis cinerea, which are established models to study DNA methylation and developmental and symbiotic processes. Quantitative liquid chromatography-tandem mass spectrometry revealed persistent but uneven occurrences of 5hmC, 5fC and 5caC in the DNA and RNA of the two organisms, which could be upregulated by vitamin C. 5caC in RNA (5carC) was predominantly found in non-ribosomal RNA, which potentially includes non-coding, messenger and small RNA species. Genome-wide mapping of 5hmC and 5fC using the single CG analysis techniques hmTOP-seq and foTOP-seq pointed at involvement of oxi-mCs in the regulation of gene expression and silencing of transposable elements. The implicated diverse roles of 5mC and oxi-mCs in the two fungi highlight the epigenetic importance of the latter modifications, which are often neglected in standard whole-genome bisulfite analyses.
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Affiliation(s)
- Janina Ličytė
- Department of Biological DNA Modification, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio av. 7, Vilnius 10257, Lithuania
| | - Kotryna Kvederavičiūtė
- Department of Biological DNA Modification, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio av. 7, Vilnius 10257, Lithuania
| | - Audronė Rukšėnaitė
- Department of Biological DNA Modification, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio av. 7, Vilnius 10257, Lithuania
| | - Eglė Godliauskaitė
- Department of Biological DNA Modification, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio av. 7, Vilnius 10257, Lithuania
| | - Povilas Gibas
- Department of Biological DNA Modification, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio av. 7, Vilnius 10257, Lithuania
| | - Vita Tomkutė
- Department of Biological DNA Modification, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio av. 7, Vilnius 10257, Lithuania
| | - Gražina Petraitytė
- Department of Biological DNA Modification, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio av. 7, Vilnius 10257, Lithuania
| | - Viktoras Masevičius
- Department of Biological DNA Modification, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio av. 7, Vilnius 10257, Lithuania
| | - Saulius Klimašauskas
- Department of Biological DNA Modification, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio av. 7, Vilnius 10257, Lithuania
| | - Edita Kriukienė
- Department of Biological DNA Modification, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio av. 7, Vilnius 10257, Lithuania
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Severn-Ellis AA, Schoeman MH, Bayer PE, Hane JK, Rees DJG, Edwards D, Batley J. Genome Analysis of the Broad Host Range Necrotroph Nalanthamala psidii Highlights Genes Associated With Virulence. FRONTIERS IN PLANT SCIENCE 2022; 13:811152. [PMID: 35283890 PMCID: PMC8914235 DOI: 10.3389/fpls.2022.811152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 01/18/2022] [Indexed: 06/14/2023]
Abstract
Guava wilt disease is caused by the fungus Nalanthamala psidii. The wilt disease results in large-scale destruction of orchards in South Africa, Taiwan, and several Southeast Asian countries. De novo assembly, annotation, and in-depth analysis of the N. psidii genome were carried out to facilitate the identification of characteristics associated with pathogenicity and pathogen evolution. The predicted secretome revealed a range of CAZymes, proteases, lipases and peroxidases associated with plant cell wall degradation, nutrient acquisition, and disease development. Further analysis of the N. psidii carbohydrate-active enzyme profile exposed the broad-spectrum necrotrophic lifestyle of the pathogen, which was corroborated by the identification of putative effectors and secondary metabolites with the potential to induce tissue necrosis and cell surface-dependent immune responses. Putative regulatory proteins including transcription factors and kinases were identified in addition to transporters potentially involved in the secretion of secondary metabolites. Transporters identified included important ABC and MFS transporters involved in the efflux of fungicides. Analysis of the repetitive landscape and the detection of mechanisms linked to reproduction such as het and mating genes rendered insights into the biological complexity and evolutionary potential of N. psidii as guava pathogen. Hence, the assembly and annotation of the N. psidii genome provided a valuable platform to explore the pathogenic potential and necrotrophic lifestyle of the guava wilt pathogen.
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Affiliation(s)
- Anita A. Severn-Ellis
- School of Biological Sciences, Institute of Agriculture, The University of Western Australia, Crawley, WA, Australia
- Aquaculture Research and Development, Department of Primary Industries and Regional Development, Indian Ocean Marine Research Centre, Watermans Bay, WA, Australia
| | - Maritha H. Schoeman
- Institute for Tropical and Subtropical Crops, Agricultural Research Council, Nelspruit, South Africa
| | - Philipp E. Bayer
- School of Biological Sciences, Institute of Agriculture, The University of Western Australia, Crawley, WA, Australia
| | - James K. Hane
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia
| | - D. Jasper G. Rees
- Agricultural Research Council, Biotechnology Platform, Pretoria, South Africa
- Botswana University of Agriculture and Natural Resources, Gaborone, Botswana
| | - David Edwards
- School of Biological Sciences, Institute of Agriculture, The University of Western Australia, Crawley, WA, Australia
| | - Jacqueline Batley
- School of Biological Sciences, Institute of Agriculture, The University of Western Australia, Crawley, WA, Australia
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36
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Chen CL, Li WC, Chuang YC, Liu HC, Huang CH, Lo KY, Chen CY, Chang FM, Chang GA, Lin YL, Yang WD, Su CH, Yeh TM, Wang TF. Sexual Crossing, Chromosome-Level Genome Sequences, and Comparative Genomic Analyses for the Medicinal Mushroom Taiwanofungus Camphoratus (Syn. Antrodia Cinnamomea, Antrodia Camphorata). Microbiol Spectr 2022; 10:e0203221. [PMID: 35196809 PMCID: PMC8865532 DOI: 10.1128/spectrum.02032-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 01/27/2022] [Indexed: 12/24/2022] Open
Abstract
Taiwanofungus camphoratus mushrooms are a complementary and alternative medicine for hangovers, cancer, hypertension, obesity, diabetes, and inflammation. Though Taiwanofungus camphoratus has attracted considerable biotechnological and pharmacological attention, neither classical genetic nor genomic approaches have been properly established for it. We isolated four sexually competent monokaryons from two T. camphoratus dikaryons used for the commercial cultivation of orange-red (HC1) and milky-white (SN1) mushrooms, respectively. We also sequenced, annotated, and comparatively analyzed high-quality and chromosome-level genome sequences of these four monokaryons. These genomic resources represent a valuable basis for understanding the biology, evolution, and secondary metabolite biosynthesis of this economically important mushrooms. We demonstrate that T. camphoratus has a tetrapolar mating system and that HC1 and SN1 represent two intraspecies isolates displaying karyotypic variation. Compared with several edible mushroom model organisms, T. camphoratus underwent a significant contraction in the gene family and individual gene numbers, most notably for plant, fungal, and bacterial cell-wall-degrading enzymes, explaining why T. camphoratus mushrooms are rare in natural environments, are difficult and time-consuming to artificially cultivate, and are susceptible to fungal and bacterial infections. Our results lay the foundation for an in-depth T. camphoratus study, including precise genetic manipulation, improvements to mushroom fruiting, and synthetic biology applications for producing natural medicinal products. IMPORTANCETaiwanofungus camphoratus (Tc) is a basidiomycete fungus that causes brown heart rot of the aromatic tree Cinnamomum kanehirae. The Tc fruiting bodies have been used to treat hangovers, abdominal pain, diarrhea, hypertension, and other diseases first by aboriginal Taiwanese and later by people in many countries. To establish classical genetic and genomic approaches for this economically important medicinal mushroom, we first isolated and characterized four sexually competent monokaryons from two dikaryons wildly used for commercial production of Tc mushrooms. We applied PacBio single molecule, real-time sequencing technology to determine the near-completed genome sequences of four monokaryons. These telomere-to-telomere and gapless haploid genome sequences reveal all genomic variants needed to be studied and discovered, including centromeres, telomeres, retrotransposons, mating type loci, biosynthetic, and metabolic gene clusters. Substantial interspecies diversities are also discovered between Tc and several other mushroom model organisms, including Agrocybe aegerita, Coprinopsis cinerea, and Schizophyllum commune, and Ganoderma lucidum.
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Affiliation(s)
- Chia-Ling Chen
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
| | - Wan-Chen Li
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
| | - Yu-Chien Chuang
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
| | - Hou-Cheng Liu
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
| | - Chien-Hao Huang
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
| | - Ko-Yun Lo
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
| | - Chung-Yu Chen
- Shen Nong Fungal Biotechnology Co. Ltd., Taoyuan City, Taiwan
| | - Fang-Mo Chang
- School of Dentistry, College of Oral Medicine, Taipei Medical University, Taipei, Taiwan
| | | | | | | | - Ching-Hua Su
- Department of Microbiology and Immunology, Taipei Medical University, Taipei, Taiwan
| | - Tsung-Ming Yeh
- Shen Nong Fungal Biotechnology Co. Ltd., Taoyuan City, Taiwan
| | - Ting-Fang Wang
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
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37
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Ying H, Hayward DC, Klimovich A, Bosch TCG, Baldassarre L, Neeman T, Forêt S, Huttley G, Reitzel AM, Fraune S, Ball EE, Miller DJ. The role of DNA methylation in genome defense in Cnidaria and other invertebrates. Mol Biol Evol 2022; 39:6516040. [PMID: 35084499 PMCID: PMC8857917 DOI: 10.1093/molbev/msac018] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Considerable attention has recently been focused on the potential involvement of DNA methylation in regulating gene expression in cnidarians. Much of this work has been centered on corals, in the context of changes in methylation perhaps facilitating adaptation to higher seawater temperatures and other stressful conditions. Although first proposed more than 30 years ago, the possibility that DNA methylation systems function in protecting animal genomes against the harmful effects of transposon activity has largely been ignored since that time. Here, we show that transposons are specifically targeted by the DNA methylation system in cnidarians, and that the youngest transposons (i.e., those most likely to be active) are most highly methylated. Transposons in longer and highly active genes were preferentially methylated and, as transposons aged, methylation levels declined, reducing the potentially harmful side effects of CpG methylation. In Cnidaria and a range of other invertebrates, correlation between the overall extent of methylation and transposon content was strongly supported. Present transposon burden is the dominant factor in determining overall level of genomic methylation in a range of animals that diverged in or before the early Cambrian, suggesting that genome defense represents the ancestral role of CpG methylation.
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Affiliation(s)
- Hua Ying
- Research School of Biology, Australian National University, Canberra, ACT, Australia
| | - David C Hayward
- Research School of Biology, Australian National University, Canberra, ACT, Australia
| | | | - Thomas C G Bosch
- Zoological Institute, Christian Albrechts University, Kiel, Germany.,Collaborative Research Center for the Origin and Function of Metaorganisms, Christian Albrechts University, Kiel, Germany
| | - Laura Baldassarre
- Department of Zoology and Organismal Interactions, Heinrich-Heine-University Düsseldorf, Germany
| | - Teresa Neeman
- Biological Data Institute, Australian National University, Canberra, ACT, Australia
| | - Sylvain Forêt
- Research School of Biology, Australian National University, Canberra, ACT, Australia.,ARC Centre of Excellence for Coral Reef Studies, Australian National University, Canberra, ACT, Australia
| | - Gavin Huttley
- Research School of Biology, Australian National University, Canberra, ACT, Australia
| | - Adam M Reitzel
- Department of Biological Sciences, University of North Carolina, Charlotte, USA
| | - Sebastian Fraune
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Queensland, Australia
| | - Eldon E Ball
- Research School of Biology, Australian National University, Canberra, ACT, Australia.,ARC Centre of Excellence for Coral Reef Studies, Australian National University, Canberra, ACT, Australia
| | - David J Miller
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Queensland, Australia.,College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, Queensland, Australia.,Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Townsville, Queensland, Australia.,Marine Climate Change Unit, Okinawa Institute of Science and Technology, Japan
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38
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Dal Grande F, Jamilloux V, Choisne N, Calchera A, Rolshausen G, Petersen M, Schulz M, Nilsson MA, Schmitt I. Transposable Elements in the Genome of the Lichen-Forming Fungus Umbilicaria pustulata and Their Distribution in Different Climate Zones along Elevation. BIOLOGY 2021; 11:biology11010024. [PMID: 35053022 PMCID: PMC8773270 DOI: 10.3390/biology11010024] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Revised: 12/07/2021] [Accepted: 12/20/2021] [Indexed: 11/16/2022]
Abstract
Transposable elements (TEs) are an important source of genome plasticity across the tree of life. Drift and natural selection are important forces shaping TE distribution and accumulation. Fungi, with their multifaceted phenotypic diversity and relatively small genome size, are ideal models to study the role of TEs in genome evolution and their impact on the host's ecological and life history traits. Here we present an account of all TEs found in a high-quality reference genome of the lichen-forming fungus Umbilicaria pustulata, a macrolichen species comprising two climatic ecotypes: Mediterranean and cold temperate. We trace the occurrence of the newly identified TEs in populations along three elevation gradients using a Pool-Seq approach to identify TE insertions of potential adaptive significance. We found that TEs cover 21.26% of the 32.9 Mbp genome, with LTR Gypsy and Copia clades being the most common TEs. We identified 28 insertions displaying consistent insertion frequency differences between the two host ecotypes across the elevation gradients. Most of the highly differentiated insertions were located near genes, indicating a putative function. This pioneering study of the content and climate niche-specific distribution of TEs in a lichen-forming fungus contributes to understanding the roles of TEs in fungal evolution.
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Affiliation(s)
- Francesco Dal Grande
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Senckenberganlage 25, 60325 Frankfurt am Main, Germany; (A.C.); (M.S.); (M.A.N.); (I.S.)
- LOEWE Centre for Translational Biodiversity Genomics (TBG), Senckenberganlage 25, 60325 Frankfurt am Main, Germany
- Correspondence: ; Tel.: +49-(0)69-7542-1856
| | - Véronique Jamilloux
- INRAE URGI, Centre de Versailles, Bâtiment 18, Route de Saint Cyr, 78026 Versailles, France; (V.J.); (N.C.)
| | - Nathalie Choisne
- INRAE URGI, Centre de Versailles, Bâtiment 18, Route de Saint Cyr, 78026 Versailles, France; (V.J.); (N.C.)
| | - Anjuli Calchera
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Senckenberganlage 25, 60325 Frankfurt am Main, Germany; (A.C.); (M.S.); (M.A.N.); (I.S.)
| | - Gregor Rolshausen
- Senckenberg Center for Wildlife Genetics, Clamecystrasse 12, 63571 Gelnhausen, Germany;
| | - Malte Petersen
- Max Planck Institute of Immunobiology and Epigenetics, Stübeweg 51, 79108 Freiburg, Germany;
| | - Meike Schulz
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Senckenberganlage 25, 60325 Frankfurt am Main, Germany; (A.C.); (M.S.); (M.A.N.); (I.S.)
| | - Maria A. Nilsson
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Senckenberganlage 25, 60325 Frankfurt am Main, Germany; (A.C.); (M.S.); (M.A.N.); (I.S.)
- LOEWE Centre for Translational Biodiversity Genomics (TBG), Senckenberganlage 25, 60325 Frankfurt am Main, Germany
| | - Imke Schmitt
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Senckenberganlage 25, 60325 Frankfurt am Main, Germany; (A.C.); (M.S.); (M.A.N.); (I.S.)
- LOEWE Centre for Translational Biodiversity Genomics (TBG), Senckenberganlage 25, 60325 Frankfurt am Main, Germany
- Institut für Ökologie, Evolution und Diversität, Goethe-Universität Frankfurt, Max-von-Laue-Strasse. 9, 60438 Frankfurt am Main, Germany
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39
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Bahram M, Netherway T. Fungi as mediators linking organisms and ecosystems. FEMS Microbiol Rev 2021; 46:6468741. [PMID: 34919672 PMCID: PMC8892540 DOI: 10.1093/femsre/fuab058] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 12/15/2021] [Indexed: 12/03/2022] Open
Abstract
Fungi form a major and diverse component of most ecosystems on Earth. They are both micro and macroorganisms with high and varying functional diversity as well as great variation in dispersal modes. With our growing knowledge of microbial biogeography, it has become increasingly clear that fungal assembly patterns and processes differ from other microorganisms such as bacteria, but also from macroorganisms such as plants. The success of fungi as organisms and their influence on the environment lies in their ability to span multiple dimensions of time, space, and biological interactions, that is not rivalled by other organism groups. There is also growing evidence that fungi mediate links between different organisms and ecosystems, with the potential to affect the macroecology and evolution of those organisms. This suggests that fungal interactions are an ecological driving force, interconnecting different levels of biological and ecological organisation of their hosts, competitors, and antagonists with the environment and ecosystem functioning. Here we review these emerging lines of evidence by focusing on the dynamics of fungal interactions with other organism groups across various ecosystems. We conclude that the mediating role of fungi through their complex and dynamic ecological interactions underlie their importance and ubiquity across Earth's ecosystems.
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Affiliation(s)
- Mohammad Bahram
- Department of Ecology, Swedish University of Agricultural Sciences, Uppsala, Ulls väg 16, 756 51 Sweden.,Institute of Ecology and Earth Sciences, University of Tartu, Tartu, 40 Lai St. Estonia
| | - Tarquin Netherway
- Department of Ecology, Swedish University of Agricultural Sciences, Uppsala, Ulls väg 16, 756 51 Sweden
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40
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Dallaire A, Manley BF, Wilkens M, Bista I, Quan C, Evangelisti E, Bradshaw CR, Ramakrishna NB, Schornack S, Butter F, Paszkowski U, Miska EA. Transcriptional activity and epigenetic regulation of transposable elements in the symbiotic fungus Rhizophagus irregularis. Genome Res 2021; 31:2290-2302. [PMID: 34772700 PMCID: PMC8647823 DOI: 10.1101/gr.275752.121] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 09/16/2021] [Indexed: 11/29/2022]
Abstract
Arbuscular mycorrhizal (AM) fungi form mutualistic relationships with most land plant species. AM fungi have long been considered as ancient asexuals. Long-term clonal evolution would be remarkable for a eukaryotic lineage and suggests the importance of alternative mechanisms to promote genetic variability facilitating adaptation. Here, we assessed the potential of transposable elements for generating such genomic diversity. The dynamic expression of TEs during Rhizophagus irregularis spore development suggests ongoing TE activity. We find Mutator-like elements located near genes belonging to highly expanded gene families. Whole-genome epigenomic profiling of R. irregularis provides direct evidence of DNA methylation and small RNA production occurring at TE loci. Our results support a model in which TE activity shapes the genome, while DNA methylation and small RNA-mediated silencing keep their overproliferation in check. We propose that a well-controlled TE activity directly contributes to genome evolution in AM fungi.
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Affiliation(s)
- Alexandra Dallaire
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, United Kingdom
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, United Kingdom
- Tree of Life, Wellcome Sanger Institute, Cambridge CB10 1SA, United Kingdom
| | - Bethan F Manley
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, United Kingdom
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, United Kingdom
- Tree of Life, Wellcome Sanger Institute, Cambridge CB10 1SA, United Kingdom
| | - Maya Wilkens
- Quantitative Proteomics, Institute of Molecular Biology, 55128 Mainz, Germany
| | - Iliana Bista
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, United Kingdom
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, United Kingdom
- Tree of Life, Wellcome Sanger Institute, Cambridge CB10 1SA, United Kingdom
| | - Clement Quan
- Sainsbury Laboratory, University of Cambridge, Cambridge CB2 1LR, United Kingdom
| | - Edouard Evangelisti
- Sainsbury Laboratory, University of Cambridge, Cambridge CB2 1LR, United Kingdom
| | - Charles R Bradshaw
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, United Kingdom
| | - Navin B Ramakrishna
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, United Kingdom
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, United Kingdom
| | - Sebastian Schornack
- Sainsbury Laboratory, University of Cambridge, Cambridge CB2 1LR, United Kingdom
| | - Falk Butter
- Quantitative Proteomics, Institute of Molecular Biology, 55128 Mainz, Germany
| | - Uta Paszkowski
- Crop Science Centre, University of Cambridge, Cambridge CB3 0LE, United Kingdom
| | - Eric A Miska
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, United Kingdom
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, United Kingdom
- Tree of Life, Wellcome Sanger Institute, Cambridge CB10 1SA, United Kingdom
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41
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Andler R, D'Afonseca V, Pino J, Valdés C, Salazar-Viedma M. Assessing the Biodegradation of Vulcanised Rubber Particles by Fungi Using Genetic, Molecular and Surface Analysis. Front Bioeng Biotechnol 2021; 9:761510. [PMID: 34733834 PMCID: PMC8558253 DOI: 10.3389/fbioe.2021.761510] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 10/06/2021] [Indexed: 11/13/2022] Open
Abstract
Millions of tonnes of tyre waste are discarded annually and are considered one of the most difficult solid wastes to recycle. A sustainable alternative for the treatment of vulcanised rubber is the use of microorganisms that can biotransform polymers and aromatic compounds and then assimilate and mineralise some of the degradation products. However, vulcanised rubber materials present great resistance to biodegradation due to the presence of highly hydrophobic cross-linked structures that are provided by the additives they contain and the vulcanisation process itself. In this work, the biodegradation capabilities of 10 fungal strains cultivated in PDA and EM solid medium were studied over a period of 4 weeks. The growth of the strains, the mass loss of the vulcanised rubber particles and the surface structure were analysed after the incubation period. With the white rot fungi Trametes versicolor and Pleurotus ostreatus, biodegradation percentages of 7.5 and 6.1%, respectively, were achieved. The FTIR and SEM-EDS analyses confirmed a modification of the abundance of functional groups and elements arranged on the rubber surface, such as C, O, S, Si, and Zn, due to the biological treatment employed. The availability of genomic sequences of P. ostreatus and T. versicolor in public repositories allowed the analysis of the genetic content, genomic characteristics and specific components of both fungal species, determining some similarities between both species and their relationship with rubber biodegradation. Both fungi presented a higher number of sequences for laccases and manganese peroxidases, two extracellular enzymes responsible for many of the oxidative reactions reported in the literature. This was confirmed by measuring the laccase and peroxidase activity in cultures of T. versicolor and P. ostreatus with rubber particles, reaching between 2.8 and 3.3-times higher enzyme activity than in the absence of rubber. The integrative analysis of the results, supported by genetic and bioinformatics tools, allowed a deeper analysis of the biodegradation processes of vulcanised rubber. It is expected that this type of analysis can be used to find more efficient biotechnological solutions in the future.
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Affiliation(s)
- R Andler
- Escuela de Ingeniería en Biotecnología, Centro de Biotecnología de los Recursos Naturales (Cenbio), Universidad Católica del Maule, Talca, Chile
| | - V D'Afonseca
- Centro de Investigación de Estudios Avanzados del Maule, Vicerrectoría de Investigación y Postgrado, Universidad Católica del Maule, Talca, Chile
| | - J Pino
- Escuela de Ingeniería en Biotecnología, Centro de Biotecnología de los Recursos Naturales (Cenbio), Universidad Católica del Maule, Talca, Chile
| | - C Valdés
- Centro de Investigación de Estudios Avanzados del Maule, Vicerrectoría de Investigación y Postgrado, Universidad Católica del Maule, Talca, Chile
| | - M Salazar-Viedma
- Laboratorio de Genética y Microevolución, Facultad de Ciencias Básicas, Universidad Católica del Maule, Talca, Chile
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42
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Pérez G, Lopez-Moya F, Chuina E, Ibañez-Vea M, Garde E, López-Llorca LV, Pisabarro AG, Ramírez L. Strain Degeneration in Pleurotus ostreatus: A Genotype Dependent Oxidative Stress Process Which Triggers Oxidative Stress, Cellular Detoxifying and Cell Wall Reshaping Genes. J Fungi (Basel) 2021; 7:jof7100862. [PMID: 34682283 PMCID: PMC8537115 DOI: 10.3390/jof7100862] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 10/08/2021] [Accepted: 10/09/2021] [Indexed: 12/13/2022] Open
Abstract
Strain degeneration has been defined as a decrease or loss in the yield of important commercial traits resulting from subsequent culture, which ultimately leads to Reactive Oxygen Species (ROS) production. Pleurotus ostreatus is a lignin-producing nematophagous edible mushroom. Mycelia for mushroom production are usually maintained in subsequent culture in solid media and frequently show symptoms of strain degeneration. The dikaryotic strain P. ostreatus (DkN001) has been used in our lab as a model organism for different purposes. Hence, different tools have been developed to uncover genetic and molecular aspects of this fungus. In this work, strain degeneration was studied in a full-sib monokaryotic progeny of the DkN001 strain with fast (F) and slow (S) growth rates by using different experimental approaches (light microscopy, malondialdehyde levels, whole-genome transcriptome analysis, and chitosan effect on monokaryotic mycelia). The results obtained showed that: (i) strain degeneration in P. ostreatus is linked to oxidative stress, (ii) the oxidative stress response in monokaryons is genotype dependent, (iii) stress and detoxifying genes are highly expressed in S monokaryons with symptoms of strain degeneration, (iv) chitosan addition to F and S monokaryons uncovered the constitutive expression of both oxidative stress and cellular detoxifying genes in S monokaryon strains which suggest their adaptation to oxidative stress, and (v) the overexpression of the cell wall genes, Uap1 and Cda1, in S monokaryons with strain degeneration phenotype indicates cell wall reshaping and the activation of High Osmolarity Glycerol (HOG) and Cell Wall Integrity (CWI) pathways. These results could constitute a hallmark for mushroom producers to distinguish strain degeneration in commercial mushrooms.
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Affiliation(s)
- Gumer Pérez
- Genetics, Genomics and Microbiology Research Group, Institute for Multidisciplinary Research in Applied Biology (IMAB), Public University of Navarre (UPNA), 31006 Pamplona, Spain; (G.P.); (E.C.); (M.I.-V.); (E.G.); (A.G.P.)
| | - Federico Lopez-Moya
- Laboratory of Plant Pathology, Department of Marine Sciences and Applied Biology, University of Alicante, 03690 Alicante, Spain; (F.L.-M.); (L.V.L.-L.)
| | - Emilia Chuina
- Genetics, Genomics and Microbiology Research Group, Institute for Multidisciplinary Research in Applied Biology (IMAB), Public University of Navarre (UPNA), 31006 Pamplona, Spain; (G.P.); (E.C.); (M.I.-V.); (E.G.); (A.G.P.)
| | - María Ibañez-Vea
- Genetics, Genomics and Microbiology Research Group, Institute for Multidisciplinary Research in Applied Biology (IMAB), Public University of Navarre (UPNA), 31006 Pamplona, Spain; (G.P.); (E.C.); (M.I.-V.); (E.G.); (A.G.P.)
| | - Edurne Garde
- Genetics, Genomics and Microbiology Research Group, Institute for Multidisciplinary Research in Applied Biology (IMAB), Public University of Navarre (UPNA), 31006 Pamplona, Spain; (G.P.); (E.C.); (M.I.-V.); (E.G.); (A.G.P.)
| | - Luis V. López-Llorca
- Laboratory of Plant Pathology, Department of Marine Sciences and Applied Biology, University of Alicante, 03690 Alicante, Spain; (F.L.-M.); (L.V.L.-L.)
| | - Antonio G. Pisabarro
- Genetics, Genomics and Microbiology Research Group, Institute for Multidisciplinary Research in Applied Biology (IMAB), Public University of Navarre (UPNA), 31006 Pamplona, Spain; (G.P.); (E.C.); (M.I.-V.); (E.G.); (A.G.P.)
| | - Lucía Ramírez
- Genetics, Genomics and Microbiology Research Group, Institute for Multidisciplinary Research in Applied Biology (IMAB), Public University of Navarre (UPNA), 31006 Pamplona, Spain; (G.P.); (E.C.); (M.I.-V.); (E.G.); (A.G.P.)
- Correspondence:
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43
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Genetic Linkage and Physical Mapping for an Oyster Mushroom ( Pleurotus cornucopiae) and Quantitative Trait Locus Analysis for Cap Color. Appl Environ Microbiol 2021; 87:e0095321. [PMID: 34406836 DOI: 10.1128/aem.00953-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Oyster mushrooms are grown commercially worldwide, especially in many developing countries, for their easy cultivation and high biological efficiency. Pleurotus cornucopiae is one of the main oyster mushroom species because of its gastronomic value and nutraceutical properties. Cap color is an important trait, since consumers prefer dark mushrooms, which are now represented by only a small portion of the commercial varieties. Breeding efforts are required to improve quality-related traits to satisfy various demands of consumers. Here, we present a saturated genetic linkage map of P. cornucopiae constructed by using a segregating population of 122 monokaryons and 3,449 single nucleotide polymorphism (SNP) markers generated by the 2b-RAD approach. The map contains 11 linkage groups covering 961.6 centimorgans (cM), with an average marker spacing of 0.27 cM. The genome of P. cornucopiae was de novo sequenced, resulting in 425 scaffolds (>1,000 bp) with a total genome size of 35.1 Mb. The scaffolds were assembled to the pseudochromosome level with the assistance of the genetic linkage map. A total of 97% SNP markers (3,357) were physically localized on 140 scaffolds that were assigned to 11 pseudochromosomes, with a total of 32.5 Mb, representing 92.5% of the whole genome. Six quantitative trait loci (QTL) controlling cap color of P. cornucopiae were detected, accounting for a total phenotypic variation of 65.6%, with the highest value for the QTL on pseudochromosome 5 (18%). The results of our study provide a solid base for marker-assisted breeding for agronomic traits and especially for studies on biological mechanisms controlling cap color in oyster mushrooms. IMPORTANCE Oyster mushrooms are produced and consumed all over the world. Pleurotus cornucopiae is one of the main oyster mushroom species. Dark-cap oyster mushrooms are becoming more and more popular with consumers, but dark varieties are rare on the market. Prerequisites for efficient breeding programs are the availability of high-quality whole genomes and genetic linkage maps. Genetic studies to fulfill some of these prerequisites have hardly been done for P. cornucopiae. In this study, we de novo sequenced the genome and constructed a saturated genetic linkage map for P. cornucopiae. The genetic linkage map was effectively used to assist the genome assembly and identify QTL that genetically control the trait cap color. As well, the genome characteristics of P. cornucopiae were compared to the closely related species Pleurotus ostreatus. The results provided a basis for understanding the genetic background and marker-assisted breeding of this economically important mushroom species.
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44
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Deshmukh R, Tiwari S. Molecular interaction of charcoal rot pathogenesis in soybean: a complex interaction. PLANT CELL REPORTS 2021; 40:1799-1812. [PMID: 34232377 DOI: 10.1007/s00299-021-02747-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 06/28/2021] [Indexed: 06/13/2023]
Abstract
Charcoal rot (CR) is a major disease of soybean, which is caused by Macrophomina phaseolina (Mp). Increasing temperatures and low rainfall in recent years have immensely benefitted the pathogen. Hence, the search for genetically acquired resistance to this pathogen is essential. The pathogen is a hemibiotroph, which germinates on the root surface and colonizes epidermal tissue. Several surface receptors initiate pathogenesis, followed by the secretion of various enzymes that provide entry to host tissue. Several enzymes and other converging cascades in the pathogen participate against host defensive responses. β-glucan of the fungal cell wall is recognized as MAMPs (microbe-associated molecular patterns) in plants, which trigger host immune responses. Kinase receptors, resistance, and pathogenesis-related genes correspond to host defense response. They work in conjunction with hormone-mediated defense pathway especially, the systemic acquired resistance, calcium-signaling, and production of phytoalexins. Due to its quantitative nature, limited QTLs have been identified in soybean for CR resistance. The present review attempts to provide a functional link between M. phaseolina pathogenicity and soybean responses. Elucidation of CR resistance responses would facilitate improved designing of breeding programs, and may help in the selection of corresponding genes to introgress CR resistant traits.
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Affiliation(s)
- Reena Deshmukh
- Biotechnology Centre, Jawaharlal Nehru Agriculture University, Jabalpur, India.
- Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal, India.
| | - Sharad Tiwari
- Biotechnology Centre, Jawaharlal Nehru Agriculture University, Jabalpur, India
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45
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Lorrain C, Feurtey A, Möller M, Haueisen J, Stukenbrock E. Dynamics of transposable elements in recently diverged fungal pathogens: lineage-specific transposable element content and efficiency of genome defenses. G3-GENES GENOMES GENETICS 2021; 11:6173990. [PMID: 33724368 PMCID: PMC8759822 DOI: 10.1093/g3journal/jkab068] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 02/19/2021] [Indexed: 01/29/2023]
Abstract
Transposable elements (TEs) impact genome plasticity, architecture, and evolution in fungal plant pathogens. The wide range of TE content observed in fungal genomes reflects diverse efficacy of host-genome defense mechanisms that can counter-balance TE expansion and spread. Closely related species can harbor drastically different TE repertoires. The evolution of fungal effectors, which are crucial determinants of pathogenicity, has been linked to the activity of TEs in pathogen genomes. Here, we describe how TEs have shaped genome evolution of the fungal wheat pathogen Zymoseptoria tritici and four closely related species. We compared de novo TE annotations and repeat-induced point mutation signatures in 26 genomes from the Zymoseptoria species-complex. Then, we assessed the relative insertion ages of TEs using a comparative genomics approach. Finally, we explored the impact of TE insertions on genome architecture and plasticity. The 26 genomes of Zymoseptoria species reflect different TE dynamics with a majority of recent insertions. TEs associate with accessory genome compartments, with chromosomal rearrangements, with gene presence/absence variation, and with effectors in all Zymoseptoria species. We find that the extent of RIP-like signatures varies among Z. tritici genomes compared to genomes of the sister species. The detection of a reduction of RIP-like signatures and TE recent insertions in Z. tritici reflects ongoing but still moderate TE mobility.
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Affiliation(s)
- Cécile Lorrain
- Environmental Genomics, Max Planck Institute for Evolutionary Biology, Plön 24306, Germany.,Environmental Genomics, Christian-Albrechts University of Kiel, Kiel 24118, Germany.,Université de Lorraine/INRAE, UMR 1136 Interactions Arbres/Microorganismes, INRAE Centre Grand Est-Nancy, Champenoux 54280, France
| | - Alice Feurtey
- Environmental Genomics, Max Planck Institute for Evolutionary Biology, Plön 24306, Germany.,Environmental Genomics, Christian-Albrechts University of Kiel, Kiel 24118, Germany
| | - Mareike Möller
- Environmental Genomics, Max Planck Institute for Evolutionary Biology, Plön 24306, Germany.,Environmental Genomics, Christian-Albrechts University of Kiel, Kiel 24118, Germany
| | - Janine Haueisen
- Environmental Genomics, Max Planck Institute for Evolutionary Biology, Plön 24306, Germany.,Environmental Genomics, Christian-Albrechts University of Kiel, Kiel 24118, Germany
| | - Eva Stukenbrock
- Environmental Genomics, Max Planck Institute for Evolutionary Biology, Plön 24306, Germany.,Environmental Genomics, Christian-Albrechts University of Kiel, Kiel 24118, Germany
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46
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Hiltunen M, Ament-Velásquez SL, Johannesson H. The Assembled and Annotated Genome of the Fairy-Ring Fungus Marasmius oreades. Genome Biol Evol 2021; 13:evab126. [PMID: 34051082 PMCID: PMC8290104 DOI: 10.1093/gbe/evab126] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/27/2021] [Indexed: 01/07/2023] Open
Abstract
Marasmius oreades is a basidiomycete fungus that grows in so called "fairy rings," which are circular, underground mycelia common in lawns across temperate areas of the world. Fairy rings can be thought of as natural, long-term evolutionary experiments. As each ring has a common origin and expands radially outwards over many years, different sectors will independently accumulate mutations during growth. The genotype can be followed to the next generation, as mushrooms producing the sexual spores are formed seasonally at the edge of the ring. Here, we present new genomic data from 95 single-spore isolates of the species, which we used to construct a genetic linkage map and an updated version of the genome assembly. The 44-Mb assembly was anchored to 11 linkage groups, producing chromosome-length scaffolds. Gene annotation revealed 13,891 genes, 55% of which contained a pfam domain. The repetitive fraction of the genome was 22%, and dominated by retrotransposons and DNA elements of the KDZ and Plavaka groups. The level of assembly contiguity we present is so far rare in mushroom-forming fungi, and we expect studies of genomics, transposons, phylogenetics, and evolution to be facilitated by the data we present here of the iconic fairy-ring mushroom.
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Affiliation(s)
- Markus Hiltunen
- Department of Organismal Biology, Uppsala University, Sweden
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47
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Lee YY, Vidal-Diez de Ulzurrun G, Schwarz EM, Stajich JE, Hsueh YP. Genome sequence of the oyster mushroom Pleurotus ostreatus strain PC9. G3-GENES GENOMES GENETICS 2021; 11:6044136. [PMID: 33585864 PMCID: PMC8022983 DOI: 10.1093/g3journal/jkaa008] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 10/01/2020] [Indexed: 01/07/2023]
Abstract
The oyster mushroom Pleurotus ostreatus is a basidiomycete commonly found in the rotten wood and it is one of the most cultivated edible mushrooms globally. Pleurotus ostreatus is also a carnivorous fungus, which can paralyze and kill nematodes within minutes. However, the molecular mechanisms of the predator-prey interactions between P. ostreatus and nematodes remain unclear. PC9 and PC15 are two model strains of P. ostreatus and the genomes of both strains have been sequenced and deposited at the Joint Genome Institute (JGI). These two monokaryotic strains exhibit dramatic differences in growth, but because PC9 grows more robustly in laboratory conditions, it has become the strain of choice for many studies. Despite the fact that PC9 is the common strain for investigation, its genome is fragmentary and incomplete relative to that of PC15. To overcome this problem, we used PacBio long reads and Illumina sequencing to assemble and polish a more integrated genome for PC9. Our PC9 genome assembly, distributed across 17 scaffolds, is highly contiguous and includes five telomere-to-telomere scaffolds, dramatically improving the genome quality. We believe that our PC9 genome resource will be useful to the fungal research community investigating various aspects of P. ostreatus biology.
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Affiliation(s)
- Yi-Yun Lee
- Institute of Molecular Biology, Academia Sinica, Nangang, Taipei 115, Taiwan.,Genome and Systems Biology Degree Program, National Taiwan University and Academic Sinica, Taipei, Taiwan
| | | | - Erich M Schwarz
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853-2703, USA
| | - Jason E Stajich
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA 92521, USA
| | - Yen-Ping Hsueh
- Institute of Molecular Biology, Academia Sinica, Nangang, Taipei 115, Taiwan.,Genome and Systems Biology Degree Program, National Taiwan University and Academic Sinica, Taipei, Taiwan.,Department of Biochemical Science and Technology, National Taiwan University, Taipei 106, Taiwan
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48
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Torres DE, Thomma BPHJ, Seidl MF. Transposable Elements Contribute to Genome Dynamics and Gene Expression Variation in the Fungal Plant Pathogen Verticillium dahliae. Genome Biol Evol 2021; 13:evab135. [PMID: 34100895 PMCID: PMC8290119 DOI: 10.1093/gbe/evab135] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/04/2021] [Indexed: 12/12/2022] Open
Abstract
Transposable elements (TEs) are a major source of genetic and regulatory variation in their host genome and are consequently thought to play important roles in evolution. Many fungal and oomycete plant pathogens have evolved dynamic and TE-rich genomic regions containing genes that are implicated in host colonization and adaptation. TEs embedded in these regions have typically been thought to accelerate the evolution of these genomic compartments, but little is known about their dynamics in strains that harbor them. Here, we used whole-genome sequencing data of 42 strains of the fungal plant pathogen Verticillium dahliae to systematically identify polymorphic TEs that may be implicated in genomic as well as in gene expression variation. We identified 2,523 TE polymorphisms and characterize a subset of 8% of the TEs as polymorphic elements that are evolutionary younger, less methylated, and more highly expressed when compared with the remaining 92% of the total TE complement. As expected, the polyrmorphic TEs are enriched in the adaptive genomic regions. Besides, we observed an association of polymorphic TEs with pathogenicity-related genes that localize nearby and that display high expression levels. Collectively, our analyses demonstrate that TE dynamics in V. dahliae contributes to genomic variation, correlates with expression of pathogenicity-related genes, and potentially impacts the evolution of adaptive genomic regions.
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Affiliation(s)
- David E Torres
- Theoretical Biology and Bioinformatics Group, Department of Biology, Utrecht University, The Netherlands
- Laboratory of Phytopathology, Wageningen University and Research, The Netherlands
| | - Bart P H J Thomma
- Laboratory of Phytopathology, Wageningen University and Research, The Netherlands
- Cluster of Excellence on Plant Sciences (CEPLAS), Institute for Plant Sciences, University of Cologne, Germany
| | - Michael F Seidl
- Theoretical Biology and Bioinformatics Group, Department of Biology, Utrecht University, The Netherlands
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49
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Elfstrand M, Chen J, Cleary M, Halecker S, Ihrmark K, Karlsson M, Davydenko K, Stenlid J, Stadler M, Durling MB. Comparative analyses of the Hymenoscyphus fraxineus and Hymenoscyphus albidus genomes reveals potentially adaptive differences in secondary metabolite and transposable element repertoires. BMC Genomics 2021; 22:503. [PMID: 34217229 PMCID: PMC8254937 DOI: 10.1186/s12864-021-07837-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 06/24/2021] [Indexed: 11/29/2022] Open
Abstract
Background The dieback epidemic decimating common ash (Fraxinus excelsior) in Europe is caused by the invasive fungus Hymenoscyphus fraxineus. In this study we analyzed the genomes of H. fraxineus and H. albidus, its native but, now essentially displaced, non-pathogenic sister species, and compared them with several other members of Helotiales. The focus of the analyses was to identify signals in the genome that may explain the rapid establishment of H. fraxineus and displacement of H. albidus. Results The genomes of H. fraxineus and H. albidus showed a high level of synteny and identity. The assembly of H. fraxineus is 13 Mb longer than that of H. albidus’, most of this difference can be attributed to higher dispersed repeat content (i.e. transposable elements [TEs]) in H. fraxineus. In general, TE families in H. fraxineus showed more signals of repeat-induced point mutations (RIP) than in H. albidus, especially in Long-terminal repeat (LTR)/Copia and LTR/Gypsy elements. Comparing gene family expansions and 1:1 orthologs, relatively few genes show signs of positive selection between species. However, several of those did appeared to be associated with secondary metabolite genes families, including gene families containing two of the genes in the H. fraxineus-specific, hymenosetin biosynthetic gene cluster (BGC). Conclusion The genomes of H. fraxineus and H. albidus show a high degree of synteny, and are rich in both TEs and BGCs, but the genomic signatures also indicated that H. albidus may be less well equipped to adapt and maintain its ecological niche in a rapidly changing environment. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07837-2.
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Affiliation(s)
- Malin Elfstrand
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Almas Allé 5, Box 7026, SE-750 07, Uppsala, Sweden.
| | - Jun Chen
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Almas Allé 5, Box 7026, SE-750 07, Uppsala, Sweden.,Systematic & Evolutionary Botany and Biodiversity group, MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Michelle Cleary
- Southern Swedish Forest Research Centre, Swedish University of Agricultural Sciences, Sundsvägen 3, Box 49, SE-230 53, Alnarp, Sweden
| | - Sandra Halecker
- Dept. Microbial Drugs, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, D-38124, Braunschweig, Germany
| | - Katarina Ihrmark
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Almas Allé 5, Box 7026, SE-750 07, Uppsala, Sweden
| | - Magnus Karlsson
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Almas Allé 5, Box 7026, SE-750 07, Uppsala, Sweden
| | - Kateryna Davydenko
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Almas Allé 5, Box 7026, SE-750 07, Uppsala, Sweden.,Ukrainian research Institute of Forestry and Forest Melioration, 62458, Kharkov, Ukraine
| | - Jan Stenlid
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Almas Allé 5, Box 7026, SE-750 07, Uppsala, Sweden
| | - Marc Stadler
- Dept. Microbial Drugs, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, D-38124, Braunschweig, Germany
| | - Mikael Brandström Durling
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Almas Allé 5, Box 7026, SE-750 07, Uppsala, Sweden
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50
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Miyauchi S, Hage H, Drula E, Lesage-Meessen L, Berrin JG, Navarro D, Favel A, Chaduli D, Grisel S, Haon M, Piumi F, Levasseur A, Lomascolo A, Ahrendt S, Barry K, LaButti KM, Chevret D, Daum C, Mariette J, Klopp C, Cullen D, de Vries RP, Gathman AC, Hainaut M, Henrissat B, Hildén KS, Kües U, Lilly W, Lipzen A, Mäkelä MR, Martinez AT, Morel-Rouhier M, Morin E, Pangilinan J, Ram AFJ, Wösten HAB, Ruiz-Dueñas FJ, Riley R, Record E, Grigoriev IV, Rosso MN. Conserved white-rot enzymatic mechanism for wood decay in the Basidiomycota genus Pycnoporus. DNA Res 2021; 27:5856740. [PMID: 32531032 PMCID: PMC7406137 DOI: 10.1093/dnares/dsaa011] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 06/05/2020] [Indexed: 12/12/2022] Open
Abstract
White-rot (WR) fungi are pivotal decomposers of dead organic matter in forest ecosystems and typically use a large array of hydrolytic and oxidative enzymes to deconstruct lignocellulose. However, the extent of lignin and cellulose degradation may vary between species and wood type. Here, we combined comparative genomics, transcriptomics and secretome proteomics to identify conserved enzymatic signatures at the onset of wood-decaying activity within the Basidiomycota genus Pycnoporus. We observed a strong conservation in the genome structures and the repertoires of protein-coding genes across the four Pycnoporus species described to date, despite the species having distinct geographic distributions. We further analysed the early response of P. cinnabarinus, P. coccineus and P. sanguineus to diverse (ligno)-cellulosic substrates. We identified a conserved set of enzymes mobilized by the three species for breaking down cellulose, hemicellulose and pectin. The co-occurrence in the exo-proteomes of H2O2-producing enzymes with H2O2-consuming enzymes was a common feature of the three species, although each enzymatic partner displayed independent transcriptional regulation. Finally, cellobiose dehydrogenase-coding genes were systematically co-regulated with at least one AA9 lytic polysaccharide monooxygenase gene, indicative of enzymatic synergy in vivo. This study highlights a conserved core white-rot fungal enzymatic mechanism behind the wood-decaying process.
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Affiliation(s)
- Shingo Miyauchi
- INRAE, UMR1163, Biodiversity and Biotechnology of Fungi, Aix Marseille University, 13009 Marseille, France.,INRAE, UMR1136, Interactions Arbres/Microorganismes, Université de Lorraine, Nancy, France
| | - Hayat Hage
- INRAE, UMR1163, Biodiversity and Biotechnology of Fungi, Aix Marseille University, 13009 Marseille, France
| | - Elodie Drula
- INRAE, UMR1163, Biodiversity and Biotechnology of Fungi, Aix Marseille University, 13009 Marseille, France
| | - Laurence Lesage-Meessen
- INRAE, UMR1163, Biodiversity and Biotechnology of Fungi, Aix Marseille University, 13009 Marseille, France.,INRAE, CIRM-CF, UMR1163, Aix Marseille University, Marseille, France
| | - Jean-Guy Berrin
- INRAE, UMR1163, Biodiversity and Biotechnology of Fungi, Aix Marseille University, 13009 Marseille, France
| | - David Navarro
- INRAE, UMR1163, Biodiversity and Biotechnology of Fungi, Aix Marseille University, 13009 Marseille, France.,INRAE, CIRM-CF, UMR1163, Aix Marseille University, Marseille, France
| | - Anne Favel
- INRAE, UMR1163, Biodiversity and Biotechnology of Fungi, Aix Marseille University, 13009 Marseille, France.,INRAE, CIRM-CF, UMR1163, Aix Marseille University, Marseille, France
| | - Delphine Chaduli
- INRAE, UMR1163, Biodiversity and Biotechnology of Fungi, Aix Marseille University, 13009 Marseille, France.,INRAE, CIRM-CF, UMR1163, Aix Marseille University, Marseille, France
| | - Sacha Grisel
- INRAE, UMR1163, Biodiversity and Biotechnology of Fungi, Aix Marseille University, 13009 Marseille, France
| | - Mireille Haon
- INRAE, UMR1163, Biodiversity and Biotechnology of Fungi, Aix Marseille University, 13009 Marseille, France
| | - François Piumi
- INRAE, UMR1163, Biodiversity and Biotechnology of Fungi, Aix Marseille University, 13009 Marseille, France
| | | | - Anne Lomascolo
- INRAE, UMR1163, Biodiversity and Biotechnology of Fungi, Aix Marseille University, 13009 Marseille, France
| | - Steven Ahrendt
- US Department of Energy, Joint Genome Institute, Walnut Creek, CA, USA
| | - Kerrie Barry
- US Department of Energy, Joint Genome Institute, Walnut Creek, CA, USA
| | - Kurt M LaButti
- US Department of Energy, Joint Genome Institute, Walnut Creek, CA, USA
| | - Didier Chevret
- INRAE, UMR1319, Micalis, Plateforme d'Analyse Protéomique de Paris Sud-Ouest, Jouy-en-Josas, France
| | - Chris Daum
- US Department of Energy, Joint Genome Institute, Walnut Creek, CA, USA
| | - Jérôme Mariette
- INRAE, Genotoul Bioinfo, UR875, Mathématiques et Informatique Appliquées de Toulouse, Castanet-Tolosan, France
| | - Christophe Klopp
- INRAE, Genotoul Bioinfo, UR875, Mathématiques et Informatique Appliquées de Toulouse, Castanet-Tolosan, France
| | | | - Ronald P de Vries
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute and Fungal Molecular Physiology, Utrecht University, Utrecht, The Netherlands.,Department of Microbiology, University of Helsinki, Helsinki, Finland
| | - Allen C Gathman
- Department of Biology, Southeast Missouri State University, Cape Girardeau, MI, USA
| | - Matthieu Hainaut
- CNRS, UMR7257, AFMB, Aix Marseille University, Marseille, France.,INRAE, USC1408, AFMB, Marseille, France
| | - Bernard Henrissat
- CNRS, UMR7257, AFMB, Aix Marseille University, Marseille, France.,INRAE, USC1408, AFMB, Marseille, France
| | | | - Ursula Kües
- Department of Molecular Wood Biotechnology and Technical Mycology, Büsgen-Institute, Georg-August-University Göttingen, Göttingen, Germany.,Center for Molecular Biosciences (GZMB), Georg-August-University Göttingen, Göttingen, Germany
| | - Walt Lilly
- Department of Biology, Southeast Missouri State University, Cape Girardeau, MI, USA
| | - Anna Lipzen
- US Department of Energy, Joint Genome Institute, Walnut Creek, CA, USA
| | - Miia R Mäkelä
- Department of Microbiology, University of Helsinki, Helsinki, Finland
| | | | - Mélanie Morel-Rouhier
- INRAE, UMR1136, Interactions Arbres/Microorganismes, Université de Lorraine, Nancy, France
| | - Emmanuelle Morin
- INRAE, UMR1136, Interactions Arbres/Microorganismes, Université de Lorraine, Nancy, France
| | - Jasmyn Pangilinan
- US Department of Energy, Joint Genome Institute, Walnut Creek, CA, USA
| | - Arthur F J Ram
- Molecular Microbiology and Biotechnology, Institute of Biology Leiden, Leiden University, Leiden, The Netherlands
| | - Han A B Wösten
- Microbiology, Utrecht University, Utrecht, The Netherlands
| | | | - Robert Riley
- US Department of Energy, Joint Genome Institute, Walnut Creek, CA, USA
| | - Eric Record
- INRAE, UMR1163, Biodiversity and Biotechnology of Fungi, Aix Marseille University, 13009 Marseille, France
| | - Igor V Grigoriev
- US Department of Energy, Joint Genome Institute, Walnut Creek, CA, USA.,Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, USA
| | - Marie-Noëlle Rosso
- INRAE, UMR1163, Biodiversity and Biotechnology of Fungi, Aix Marseille University, 13009 Marseille, France
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