101
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Septoria Leaf Blotch and Reduced Nitrogen Availability Alter WRKY Transcription Factor Expression in a Codependent Manner. Int J Mol Sci 2020; 21:ijms21114165. [PMID: 32545181 PMCID: PMC7312603 DOI: 10.3390/ijms21114165] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 06/05/2020] [Accepted: 06/08/2020] [Indexed: 01/03/2023] Open
Abstract
A major cause of yield loss in wheat worldwide is the fungal pathogen Zymoseptoria tritici, a hemibiotrophic fungus which causes Septoria leaf blotch, the most destructive wheat disease in Europe. Resistance in commercial wheat varieties is poor, however, a link between reduced nitrogen availability and increased Septoria tolerance has been observed. We have shown that Septoria load is not affected by nitrogen, whilst the fungus is in its first, symptomless stage of growth. This suggests that a link between nitrogen and Septoria is only present during the necrotrophic phase of Septoria infection. Quantitative real-time PCR data demonstrated that WRKYs, a superfamily of plant-specific transcription factors, are differentially expressed in response to both reduced nitrogen and Septoria. WRKY39 was downregulated over 30-fold in response to necrotrophic stage Septoria, whilst changes in the expression of WRKY68a during the late biotrophic phase were dependent on the concentration of nitrogen under which wheat is grown. WRKY68a may therefore mediate a link between nitrogen and Septoria. The potential remains to identify key regulators in the link between nitrogen and Septoria, and as such, elucidate molecular markers for wheat breeding, or targets for molecular-based breeding approaches.
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102
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Ridenour JB, Möller M, Freitag M. Polycomb Repression without Bristles: Facultative Heterochromatin and Genome Stability in Fungi. Genes (Basel) 2020; 11:E638. [PMID: 32527036 PMCID: PMC7348808 DOI: 10.3390/genes11060638] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 05/27/2020] [Accepted: 06/04/2020] [Indexed: 02/06/2023] Open
Abstract
Genome integrity is essential to maintain cellular function and viability. Consequently, genome instability is frequently associated with dysfunction in cells and associated with plant, animal, and human diseases. One consequence of relaxed genome maintenance that may be less appreciated is an increased potential for rapid adaptation to changing environments in all organisms. Here, we discuss evidence for the control and function of facultative heterochromatin, which is delineated by methylation of histone H3 lysine 27 (H3K27me) in many fungi. Aside from its relatively well understood role in transcriptional repression, accumulating evidence suggests that H3K27 methylation has an important role in controlling the balance between maintenance and generation of novelty in fungal genomes. We present a working model for a minimal repressive network mediated by H3K27 methylation in fungi and outline challenges for future research.
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Affiliation(s)
| | | | - Michael Freitag
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis OR 97331, USA; (J.B.R.); (M.M.)
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103
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Fedoryshchak RO, Ocasio CA, Strutton B, Mattocks J, Corran AJ, Tate EW. Wheat pathogen Zymoseptoria tritici N-myristoyltransferase inhibitors: on-target antifungal activity and an unusual metabolic defense mechanism. RSC Chem Biol 2020; 1:68-78. [PMID: 34458749 PMCID: PMC8341946 DOI: 10.1039/d0cb00020e] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Accepted: 04/27/2020] [Indexed: 12/15/2022] Open
Abstract
Zymoseptoria tritici is the causative agent of Septoria tritici blotch (STB), which costs billions of dollars annually to major wheat-producing countries in terms of both fungicide use and crop loss. Agricultural pathogenic fungi have acquired resistance to most commercially available fungicide classes, and the rate of discovery and development of new fungicides has stalled, demanding new approaches and insights. Here we investigate a potential mechanism of targeting an important wheat pathogen Z. tritici via inhibition of N-myristoyltransferase (NMT). We characterize Z. tritici NMT biochemically for the first time, profile the in vivo Z. tritici myristoylated proteome and identify and validate the first Z. tritici NMT inhibitors. Proteomic investigation of the downstream effects of NMT inhibition identified an unusual and novel mechanism of defense against chemical toxicity in Z. tritici through the application of comparative bioinformatics to deconvolute function from the previously largely unannotated Z. tritici proteome. Research into novel fungicidal modes-of-action is essential to satisfy an urgent unmet need for novel fungicide targets, and we anticipate that this study will serve as a useful proteomics and bioinformatics resource for researchers studying Z. tritici.
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Affiliation(s)
- Roman O Fedoryshchak
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub Wood Lane London W12 0BZ UK
- The Francis Crick Institute 1 Midland Rd London NW1 1AT UK
| | - Cory A Ocasio
- The Francis Crick Institute 1 Midland Rd London NW1 1AT UK
| | | | - Jo Mattocks
- Syngenta AG, Jealott's Hill Research Centre Bracknell UK
| | | | - Edward W Tate
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub Wood Lane London W12 0BZ UK
- The Francis Crick Institute 1 Midland Rd London NW1 1AT UK
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104
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Mekonnen T, Haileselassie T, Goodwin SB, Tesfayea K. Genetic diversity and population structure of Zymoseptoria tritici in Ethiopia as revealed by microsatellite markers. Fungal Genet Biol 2020; 141:103413. [PMID: 32442667 DOI: 10.1016/j.fgb.2020.103413] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2019] [Revised: 02/02/2020] [Accepted: 05/15/2020] [Indexed: 11/17/2022]
Abstract
Septoria tritici blotch (STB), caused by Zymoseptoria tritici (formerly: Mycosphaerella graminicola or Septoria tritici), is one of the most devastating diseases of wheat globally. Understanding genetic diversity of the pathogen has supreme importance in developing best management strategies. However, there is dearth of information on the genetic structure of Z. tritici populations in Ethiopia. Therefore, the present study was targeted to uncover the genetic diversity and population structure of Z. tritici populations from the major wheat-growing areas of Ethiopia. Totally, 182 Z. tritici isolates representing eight populations were analyzed with 14 microsatellite markers. All the microsatellite loci were polymorphic and highly informative, and hence useful genetic tools to depict the genetic diversity and population structure of the pathogen. A wide range of diversity indices including number of observed alleles, effective number of alleles, Shannon's diversity index, number of private alleles, Nei's gene diversity and percentage of polymorphic loci (PPL) were computed to determine genetic variation within populations. A high within-populations genetic diversity was confirmed with gene diversity index and PPL values ranging from 0.34 - 0.58 and 79-100% with overall mean of 0.45 and 94%, respectively. Analysis of molecular variance (AMOVA) revealed a moderate genetic differentiation where 92% of the total genetic variation resides within populations, leaving only 8% among populations. Cluster (UPGMA), PCoA and STRUCTURE analyses did not group the populations into sharply genetically distinct clusters according to their geographical origins, likely due to high gene flow (Nm = 5.66) and reproductive biology of the pathogen. All individual samples shared alleles from two subgroups (K = 2) evidencing high potential of genetic admixture. In conclusion, the microsatellite markers used in the present study were highly informative and thus, helped to dissect the genetic structures of Z. tritici populations in Ethiopia. Among the studied populations, those of East Shewa, Arsi, South West Shewa and Bale showed a high genetic diversity, and hence these areas can be considered as hot spots for investigations planned on the pathogen and host-pathogen interactions. Therefore, the present study not only enriches missing information in Ethiopia but also provides new insights into the epidemiology and genetic structure of Z. tritici in Africa where the agro-climatic conditions and the wheat cropping systems are different from other parts of the world. Such baseline information is useful for designing and implementing durable and effective management strategies.
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Affiliation(s)
- Tilahun Mekonnen
- Institute of Biotechnology, Addis Ababa University, Addis Ababa, Ethiopia.
| | | | - Stephen B Goodwin
- USDA-Agricultural Research Service, Department of Botany and Plant Pathology, Purdue University, 915 West State Street, West Lafayette, IN 47907-2054, USA.
| | - Kassahun Tesfayea
- Institute of Biotechnology, Addis Ababa University, Addis Ababa, Ethiopia; Ethiopian Biotechnology Institute. Affiliated with Institute of Biotechnology, Addis Ababa University, Addis Ababa, Ethiopia.
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105
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Plaumann PL, Koch C. The Many Questions about Mini Chromosomes in Colletotrichum spp. PLANTS 2020; 9:plants9050641. [PMID: 32438596 PMCID: PMC7284448 DOI: 10.3390/plants9050641] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 05/08/2020] [Accepted: 05/14/2020] [Indexed: 11/16/2022]
Abstract
Many fungal pathogens carry accessory regions in their genome, which are not required for vegetative fitness. Often, although not always, these regions occur as relatively small chromosomes in different species. Such mini chromosomes appear to be a typical feature of many filamentous plant pathogens. Since these regions often carry genes coding for effectors or toxin-producing enzymes, they may be directly related to virulence of the respective pathogen. In this review, we outline the situation of small accessory chromosomes in the genus Colletotrichum, which accounts for ecologically important plant diseases. We summarize which species carry accessory chromosomes, their gene content, and chromosomal makeup. We discuss the large variation in size and number even between different isolates of the same species, their potential roles in host range, and possible mechanisms for intra- and interspecies exchange of these interesting genetic elements.
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106
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Carreón-Anguiano KG, Islas-Flores I, Vega-Arreguín J, Sáenz-Carbonell L, Canto-Canché B. EffHunter: A Tool for Prediction of Effector Protein Candidates in Fungal Proteomic Databases. Biomolecules 2020; 10:biom10050712. [PMID: 32375409 PMCID: PMC7277995 DOI: 10.3390/biom10050712] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Revised: 03/17/2020] [Accepted: 03/21/2020] [Indexed: 11/16/2022] Open
Abstract
Pathogens are able to deliver small-secreted, cysteine-rich proteins into plant cells to enable infection. The computational prediction of effector proteins remains one of the most challenging areas in the study of plant fungi interactions. At present, there are several bioinformatic programs that can help in the identification of these proteins; however, in most cases, these programs are managed independently. Here, we present EffHunter, an easy and fast bioinformatics tool for the identification of effectors. This predictor was used to identify putative effectors in 88 proteomes using characteristics such as size, cysteine residue content, secretion signal and transmembrane domains.
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Affiliation(s)
- Karla Gisel Carreón-Anguiano
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, A.C., Calle 43 No. 130 X 32 y 34, Col. Chuburná de Hidalgo, C.P. 97205 Mérida, México
| | - Ignacio Islas-Flores
- Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán, A.C., Calle 43 No. 130 X 32 y 34, Col. Chuburná de Hidalgo, C.P. 97205 Mérida, México
| | - Julio Vega-Arreguín
- Laboratorio de Ciencias AgroGenómicas, Escuela Nacional de Estudios Superiores-UNAM, León, México
| | - Luis Sáenz-Carbonell
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, A.C., Calle 43 No. 130 X 32 y 34, Col. Chuburná de Hidalgo, C.P. 97205 Mérida, México
| | - Blondy Canto-Canché
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, A.C., Calle 43 No. 130 X 32 y 34, Col. Chuburná de Hidalgo, C.P. 97205 Mérida, México
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107
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Wang B, Liang X, Gleason ML, Hsiang T, Zhang R, Sun G. A chromosome-scale assembly of the smallest Dothideomycete genome reveals a unique genome compaction mechanism in filamentous fungi. BMC Genomics 2020; 21:321. [PMID: 32326892 PMCID: PMC7181583 DOI: 10.1186/s12864-020-6732-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 04/14/2020] [Indexed: 11/19/2022] Open
Abstract
Background The wide variation in the size of fungal genomes is well known, but the reasons for this size variation are less certain. Here, we present a chromosome-scale assembly of ectophytic Peltaster fructicola, a surface-dwelling extremophile, based on long-read DNA sequencing technology, to assess possible mechanisms associated with genome compaction. Results At 18.99 million bases (Mb), P. fructicola possesses one of the smallest known genomes sequence among filamentous fungi. The genome is highly compact relative to other fungi, with substantial reductions in repeat content, ribosomal DNA copies, tRNA gene quantity, and intron sizes, as well as intergenic lengths and the size of gene families. Transposons take up just 0.05% of the entire genome, and no full-length transposon was found. We concluded that reduced genome sizes in filamentous fungi such as P. fructicola, Taphrina deformans and Pneumocystis jirovecii occurred through reduction in ribosomal DNA copy number and reduced intron sizes. These dual mechanisms contrast with genome reduction in the yeast fungus Saccharomyces cerevisiae, whose small and compact genome is associated solely with intron loss. Conclusions Our results reveal a unique genomic compaction architecture of filamentous fungi inhabiting plant surfaces, and broaden the understanding of the mechanisms associated with compaction of fungal genomes.
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Affiliation(s)
- Bo Wang
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, 712100, Shaanxi Province, China.,MOE Key Laboratory for Intelligent Networks & Network Security, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, 710049, China
| | - Xiaofei Liang
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, 712100, Shaanxi Province, China.
| | - Mark L Gleason
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, 50011, USA
| | - Tom Hsiang
- School of Environmental Sciences, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| | - Rong Zhang
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, 712100, Shaanxi Province, China
| | - Guangyu Sun
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, 712100, Shaanxi Province, China.
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108
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Queiroz CBD, Santana MF. Prediction of the secretomes of endophytic and nonendophytic fungi reveals similarities in host plant infection and colonization strategies. Mycologia 2020; 112:491-503. [PMID: 32286912 DOI: 10.1080/00275514.2020.1716566] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Endophytic fungi are microorganisms that inhabit internal plant tissues without causing apparent damage. During the infection process, both endophytic and phytopathogenic fungi secrete proteins to resist or supplant the plant's defense mechanisms. This study analyzed the predicted secretomes of six species of endophytic fungi and compared them with predicted secretomes of eight fungal species with different lifestyles: saprophytic, necrotrophic, hemibiotrophic, and biotrophic. The sizes of the predicted secretomes varied from 260 to 1640 proteins, and the predicted secretomes have a wide diversity of CAZymes, proteases, and conserved domains. Regarding the CAZymes in the secretomes of the analyzed fungi, the most abundant CAZyme families were glycosyl hydrolase and serine proteases. Several predicted proteins have characteristics similar to those found in small, secreted proteins with effector characteristics (SSPEC). The most abundant conserved domains, besides those found in the SSPEC, have oxidation activities, indicating that these proteins can protect the fungus against oxidative stress, against domains with protease activity, which may be involved in the mechanisms of nutrition, or against lytic enzymes secreted by the host plant. This study demonstrates that secretomes of endophytic and nonendophytic fungi share an arsenal of proteins important in the process of infection and colonization of host plants.
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Affiliation(s)
- Casley Borges de Queiroz
- Laboratório de Biologia Molecular, Embrapa Amazônia Ocidental , Rodovia AM 10, km 29, s/n, CEP: 69010-970, Manaus, Amazonas, Brazil
| | - Mateus Ferreira Santana
- Departamento de Microbiologia (BIOAGRO), Universidade Federal de Viçosa , CEP: 36570-900, Viçosa, Minas Gerais, Brazil
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109
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Covo S. Genomic Instability in Fungal Plant Pathogens. Genes (Basel) 2020; 11:E421. [PMID: 32295266 PMCID: PMC7230313 DOI: 10.3390/genes11040421] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 03/29/2020] [Accepted: 04/10/2020] [Indexed: 02/07/2023] Open
Abstract
Fungi and fungal-like organisms (oomycetes) that cause diseases in plants have impacted human communities for centuries and probably from the dawn of agriculture. In modern agriculture, there is a constant race between new strategies to manage fungal plant pathogens and their ability to adapt. An important component in this race is fungal genetic diversity. Mechanisms such as sexual and parasexual recombination that contribute to the creation of novel allele combinations in fungal plant pathogens are briefly discussed in the first part of this review. Advances in genomics have enabled the investigation of chromosomal aberrations of agriculturally important fungal isolates at the nucleotide level. Some of these cases are summarized in the second part of this review; it is claimed that the effect of chromosomal aberrations on pathogenicity should be studied mechanistically. More data on the effect of gene copy number variations on phenotypes that are relevant to agriculture are especially needed. Genome rearrangements through translocations have shaped the genome of fungal plant pathogens by creating lineage-specific chromosome territories encoding for genes participating in plant diseases. Pathogenicity chromosomes are unique cases of such lineage-specific genetic elements, interestingly these chromosomes can be transferred horizontally and thus transforming a non-pathogenic strain to a pathogenic one. The third part of this review describes our attempts to reveal mutators in fungal plant pathogens by identifying fungi that lack important DNA repair genes or respond to DNA damage in an unconventional way. We found that a group of fungal plant pathogens lack conserved genes that are needed for an important Holliday junction resolution pathway. In addition, in Fusarium oxysporum, the rate-limiting step in dNTP production is not induced under DNA replication stress. This is very different from organisms from bacteria to humans. It remains to be seen if these mechanisms promote genetic instability in fungal plant pathogens.
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Affiliation(s)
- Shay Covo
- Department of Plant Pathology and Microbiology, Robert H. Smith Faculty of Agriculture, Food and Environment, Hebrew University, Rehovot 76100001, Israel
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110
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Feurtey A, Stevens DM, Stephan W, Stukenbrock EH. Interspecific Gene Exchange Introduces High Genetic Variability in Crop Pathogen. Genome Biol Evol 2020; 11:3095-3105. [PMID: 31603209 PMCID: PMC6836716 DOI: 10.1093/gbe/evz224] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/08/2019] [Indexed: 12/27/2022] Open
Abstract
Genome analyses have revealed a profound role of hybridization and introgression in the evolution of many eukaryote lineages, including fungi. The impact of recurrent introgression on fungal evolution however remains elusive. Here, we analyzed signatures of introgression along the genome of the fungal wheat pathogen Zymoseptoria tritici. We applied a comparative population genomics approach, including genome data from five Zymoseptoria species, to characterize the distribution and composition of introgressed regions representing segments with an exceptional haplotype pattern. These regions are found throughout the genome, comprising 5% of the total genome and overlapping with > 1,000 predicted genes. We performed window-based phylogenetic analyses along the genome to distinguish regions which have a monophyletic or nonmonophyletic origin with Z. tritici sequences. A majority of nonmonophyletic windows overlap with the highly variable regions suggesting that these originate from introgression. We verified that incongruent gene genealogies do not result from incomplete lineage sorting by comparing the observed and expected length distribution of haplotype blocks resulting from incomplete lineage sorting. Although protein-coding genes are not enriched in these regions, we identify 18 that encode putative virulence determinants. Moreover, we find an enrichment of transposable elements in these regions implying that hybridization may contribute to the horizontal spread of transposable elements. We detected a similar pattern in the closely related species Zymoseptoria ardabiliae, suggesting that hybridization is widespread among these closely related grass pathogens. Overall, our results demonstrate a significant impact of recurrent hybridization on overall genome evolution of this important wheat pathogen.
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Affiliation(s)
- Alice Feurtey
- Environmental Genomics, Max Planck Institute for Evolutionary Biology, Plön, Germany.,Botanical Institute, Christian-Albrechts University of Kiel, Germany
| | - Danielle M Stevens
- Environmental Genomics, Max Planck Institute for Evolutionary Biology, Plön, Germany.,Botanical Institute, Christian-Albrechts University of Kiel, Germany.,Department of Plant Pathology, University of California, Davis
| | - Wolfgang Stephan
- Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany
| | - Eva H Stukenbrock
- Environmental Genomics, Max Planck Institute for Evolutionary Biology, Plön, Germany.,Botanical Institute, Christian-Albrechts University of Kiel, Germany
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111
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Demin SY, Berdieva MA, Podlipaeva YI, Goodkov AV. Karyotypic instability of endoprophase and mitotic cells of Amoeba sp. strain Cont from the "proteus-type" group (Amoebozoa, Euamoebida, Amoebidae). Eur J Protistol 2020; 74:125691. [PMID: 32200034 DOI: 10.1016/j.ejop.2020.125691] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 02/21/2020] [Accepted: 03/03/2020] [Indexed: 01/01/2023]
Abstract
We performed karyotyping of Amoeba sp. strain Cont. Based on the results of a cytological analysis, we concluded that the chromosome number of Amoeba sp. strain Cont in mitosis was unstable. In all cases they appeared to be hypergaploid (the basic chromosome number is 30), with monosomy of all chromosomes except four shortest ones. The presence of "extrachromosomes" in the nucleus could prolong until the beginning of the anaphase. It was only then that they were ejected from the nucleus and the euploidy (haploidy) was restored. The stage of endoprophase nucleus was revealed in the cell cycle of Amoeba sp. strain Cont. This stage has not yet been found in other amoebae from the "proteus-type" group that had been previously studied (A. proteus strain B and A. borokensis). The maximum number of endoreplication rounds in the strain Cont amoebae nuclear cycle was 4 or 5. The regular extrusion of chromosomes from the nucleus into the cytoplasm occurred in each of the endoreplication rounds. Comparative cytological analysis of A. proteus strain B, A. borokensis and Amoeba sp. strain Cont karyotypes indicated that strain Cont, though rather close to the former two amoebae, is actually a distinct species.
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Affiliation(s)
- Sergei Yu Demin
- Institute of Cytology, Russian Academy of Sciences, 4 Tikhoretsky Avenue, 194064 St. Petersburg, Russia
| | - Mariia A Berdieva
- Institute of Cytology, Russian Academy of Sciences, 4 Tikhoretsky Avenue, 194064 St. Petersburg, Russia
| | - Yuliya I Podlipaeva
- Institute of Cytology, Russian Academy of Sciences, 4 Tikhoretsky Avenue, 194064 St. Petersburg, Russia
| | - Andrew V Goodkov
- Institute of Cytology, Russian Academy of Sciences, 4 Tikhoretsky Avenue, 194064 St. Petersburg, Russia.
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112
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Chromosomal Differentiation in Genetically Isolated Populations of the Marsh-Specialist Crocidura suaveolens (Mammalia: Soricidae). Genes (Basel) 2020; 11:genes11030270. [PMID: 32131436 PMCID: PMC7140822 DOI: 10.3390/genes11030270] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 02/26/2020] [Accepted: 02/27/2020] [Indexed: 12/12/2022] Open
Abstract
The genus Crocidura represents a remarkable model for the study of chromosome evolution. This is the case of the lesser white-toothed shrew (Crocidura suaveolens), a representative of the Palearctic group. Although continuously distributed from Siberia to Central Europe, C. suaveolens is a rare, habitat-specialist species in the southwesternmost limit of its distributional range, in the Gulf of Cádiz (Iberian Peninsula). In this area, C. suaveolens is restricted to genetically isolated populations associated to the tidal marches of five rivers (Guadiana, Piedras, Odiel, Tinto and Guadalquivir). This particular distributional range provides a unique opportunity to investigate whether genetic differentiation and habitat specialization was accompanied by chromosomal variation. In this context, the main objective of this study was to determinate the chromosomal characteristics of the habitat-specialist C. suaveolens in Southwestern Iberia, as a way to understand the evolutionary history of this species in the Iberian Peninsula. A total of 41 individuals from six different populations across the Gulf of Cádiz were collected and cytogenetically characterized. We detected four different karyotypes, with diploid numbers (2n) ranging from 2n = 40 to 2n = 43. Two of them (2n = 41 and 2n = 43) were characterized by the presence of B-chromosomes. The analysis of karyotype distribution across lineages and populations revealed an association between mtDNA population divergence and chromosomal differentiation. C. suaveolens populations in the Gulf of Cádiz provide a rare example of true karyotypic polymorphism potentially associated to genetic isolation and habitat specialization in which to investigate the evolutionary significance of chromosomal variation in mammals and their contribution to phenotypic and ecological divergence.
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113
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Badet T, Oggenfuss U, Abraham L, McDonald BA, Croll D. A 19-isolate reference-quality global pangenome for the fungal wheat pathogen Zymoseptoria tritici. BMC Biol 2020; 18:12. [PMID: 32046716 PMCID: PMC7014611 DOI: 10.1186/s12915-020-0744-3] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 01/27/2020] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND The gene content of a species largely governs its ecological interactions and adaptive potential. A species is therefore defined by both core genes shared between all individuals and accessory genes segregating presence-absence variation. There is growing evidence that eukaryotes, similar to bacteria, show intra-specific variability in gene content. However, it remains largely unknown how functionally relevant such a pangenome structure is for eukaryotes and what mechanisms underlie the emergence of highly polymorphic genome structures. RESULTS Here, we establish a reference-quality pangenome of a fungal pathogen of wheat based on 19 complete genomes from isolates sampled across six continents. Zymoseptoria tritici causes substantial worldwide losses to wheat production due to rapidly evolved tolerance to fungicides and evasion of host resistance. We performed transcriptome-assisted annotations of each genome to construct a global pangenome. Major chromosomal rearrangements are segregating within the species and underlie extensive gene presence-absence variation. Conserved orthogroups account for only ~ 60% of the species pangenome. Investigating gene functions, we find that the accessory genome is enriched for pathogenesis-related functions and encodes genes involved in metabolite production, host tissue degradation and manipulation of the immune system. De novo transposon annotation of the 19 complete genomes shows that the highly diverse chromosomal structure is tightly associated with transposable element content. Furthermore, transposable element expansions likely underlie recent genome expansions within the species. CONCLUSIONS Taken together, our work establishes a highly complex eukaryotic pangenome providing an unprecedented toolbox to study how pangenome structure impacts crop-pathogen interactions.
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Affiliation(s)
- Thomas Badet
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Ursula Oggenfuss
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Leen Abraham
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Bruce A McDonald
- Plant Pathology, Institute of Integrative Biology, ETH Zürich, Zürich, Switzerland
| | - Daniel Croll
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland.
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Badet T, Oggenfuss U, Abraham L, McDonald BA, Croll D. A 19-isolate reference-quality global pangenome for the fungal wheat pathogen Zymoseptoria tritici. BMC Biol 2020; 18:12. [PMID: 32046716 DOI: 10.1101/803098] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 01/27/2020] [Indexed: 05/26/2023] Open
Abstract
BACKGROUND The gene content of a species largely governs its ecological interactions and adaptive potential. A species is therefore defined by both core genes shared between all individuals and accessory genes segregating presence-absence variation. There is growing evidence that eukaryotes, similar to bacteria, show intra-specific variability in gene content. However, it remains largely unknown how functionally relevant such a pangenome structure is for eukaryotes and what mechanisms underlie the emergence of highly polymorphic genome structures. RESULTS Here, we establish a reference-quality pangenome of a fungal pathogen of wheat based on 19 complete genomes from isolates sampled across six continents. Zymoseptoria tritici causes substantial worldwide losses to wheat production due to rapidly evolved tolerance to fungicides and evasion of host resistance. We performed transcriptome-assisted annotations of each genome to construct a global pangenome. Major chromosomal rearrangements are segregating within the species and underlie extensive gene presence-absence variation. Conserved orthogroups account for only ~ 60% of the species pangenome. Investigating gene functions, we find that the accessory genome is enriched for pathogenesis-related functions and encodes genes involved in metabolite production, host tissue degradation and manipulation of the immune system. De novo transposon annotation of the 19 complete genomes shows that the highly diverse chromosomal structure is tightly associated with transposable element content. Furthermore, transposable element expansions likely underlie recent genome expansions within the species. CONCLUSIONS Taken together, our work establishes a highly complex eukaryotic pangenome providing an unprecedented toolbox to study how pangenome structure impacts crop-pathogen interactions.
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Affiliation(s)
- Thomas Badet
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Ursula Oggenfuss
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Leen Abraham
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Bruce A McDonald
- Plant Pathology, Institute of Integrative Biology, ETH Zürich, Zürich, Switzerland
| | - Daniel Croll
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland.
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115
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Fouché S, Badet T, Oggenfuss U, Plissonneau C, Francisco CS, Croll D. Stress-Driven Transposable Element De-repression Dynamics and Virulence Evolution in a Fungal Pathogen. Mol Biol Evol 2020; 37:221-239. [PMID: 31553475 DOI: 10.1093/molbev/msz216] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Transposable elements (TEs) are drivers of genome evolution and affect the expression landscape of the host genome. Stress is a major factor inducing TE activity; however, the regulatory mechanisms underlying de-repression are poorly understood. Plant pathogens are excellent models to dissect the impact of stress on TEs. The process of plant infection induces stress for the pathogen, and virulence factors (i.e., effectors) located in TE-rich regions become expressed. To dissect TE de-repression dynamics and contributions to virulence, we analyzed the TE expression landscape of four strains of the major wheat pathogen Zymoseptoria tritici. We experimentally exposed strains to nutrient starvation and host infection stress. Contrary to expectations, we show that the two distinct conditions induce the expression of different sets of TEs. In particular, the most highly expressed TEs, including miniature inverted-repeat transposable element and long terminal repeat-Gypsy element, show highly distinct de-repression across stress conditions. Both the genomic context of TEs and the genetic background stress (i.e., different strains harboring the same TEs) were major predictors of de-repression under stress. Gene expression profiles under stress varied significantly depending on the proximity to the closest TEs and genomic defenses against TEs were largely ineffective to prevent de-repression. Next, we analyzed the locus encoding the Avr3D1 effector. We show that the insertion and subsequent silencing of TEs in close proximity likely contributed to reduced expression and virulence on a specific wheat cultivar. The complexity of TE responsiveness to stress across genetic backgrounds and genomic locations demonstrates substantial intraspecific genetic variation to control TEs with consequences for virulence.
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Affiliation(s)
- Simone Fouché
- Plant Pathology, Institute of Integrative Biology, ETH Zürich, Zürich, Switzerland.,Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Thomas Badet
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Ursula Oggenfuss
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Clémence Plissonneau
- Plant Pathology, Institute of Integrative Biology, ETH Zürich, Zürich, Switzerland
| | | | - Daniel Croll
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
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Précigout PA, Claessen D, Makowski D, Robert C. Does the Latent Period of Leaf Fungal Pathogens Reflect Their Trophic Type? A Meta-Analysis of Biotrophs, Hemibiotrophs, and Necrotrophs. PHYTOPATHOLOGY 2020; 110:345-361. [PMID: 31577162 DOI: 10.1094/phyto-04-19-0144-r] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
We performed a meta-analysis to search for a relation between the trophic type and latent period of fungal pathogens. The pathogen incubation period and the level of resistance of the hosts were also investigated. This ecological knowledge would help us to more efficiently regulate crop epidemics for different types of pathogens. We gathered latent period data from 103 studies dealing with 51 fungal pathogens of the three major trophic types (25 biotrophs, 15 hemibiotrophs, and 11 necrotrophs), representing 2,542 mean latent periods. We show that these three trophic types display significantly different latent periods. Necrotrophs exhibited the shortest latent periods (<100 degree-days [DD]), biotrophs had intermediate ones (between 100 and 200 DD), and hemibiotrophs had the longest latent periods (>200 DD). We argue that this relation between trophic type and latent period points to two opposing host exploitation strategies: necrotrophs mount a rapid destructive attack on the host tissue, whereas biotrophs and hemibiotrophs avoid or delay the damaging phase. We query the definition of hemibiotrophic pathogens and discuss whether the length of the latent period is determined by the physiological limits inherent to each trophic type or by the adaptation of pathogens of different trophic types to the contrasting conditions experienced in their interaction with the host.
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Affiliation(s)
- Pierre-Antoine Précigout
- Institut de Biologie de l'Ecole Normale Supérieure, CNRS-ENS-INSERM UMR8197, Ecole Normale Supérieure, 75005 Paris, France
- UMR EcoSys, Institut National de la Recherche Agronomique (INRA), AgroParisTech, 78850 Thiverval-Grignon, France
| | - David Claessen
- Institut de Biologie de l'Ecole Normale Supérieure, CNRS-ENS-INSERM UMR8197, Ecole Normale Supérieure, 75005 Paris, France
| | - David Makowski
- UMR Agronomie, INRA, AgroParisTech, Université Paris-Saclay, 78850 Thiverval-Grignon, France
| | - Corinne Robert
- UMR EcoSys, Institut National de la Recherche Agronomique (INRA), AgroParisTech, 78850 Thiverval-Grignon, France
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117
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Wang M, Liu B, Ruan R, Zeng Y, Luo J, Li H. Genomic Sequencing of Phyllosticta citriasiana Provides Insight Into Its Conservation and Diversification With Two Closely Related Phyllosticta Species Associated With Citrus. Front Microbiol 2020; 10:2979. [PMID: 31998266 PMCID: PMC6965161 DOI: 10.3389/fmicb.2019.02979] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2019] [Accepted: 12/10/2019] [Indexed: 11/25/2022] Open
Abstract
Phyllosticta capitalensis, Phyllosticta citricarpa, and Phyllosticta citriasiana are three very important Phyllosticta species associated with citrus. P. capitalensis is an endophyte fungus of citrus while P. citricarpa can cause black spot of citrus (e.g., oranges and mandarins). P. citriasiana was identified recently which is the causal agent of the pomelo tan spot. Here, we present the ∼34 Mb genome of P. citriasiana. The genome is organized in 92 contigs, encompassing 9202 predicted genes. Comparative genomic analyses with two other Phyllosticta species (P. citricarpa and P. capitalensis) associated with citrus was conducted to understand their evolutionary conservation and diversification. Pair-wise genome alignments revealed that these species are highly syntenic. All species encode similar numbers of CAZymes and secreted proteins. However, the molecular functions of the secretome showed that each species contains some enzymes with distinct activities. The three Phyllosticta species investigated shared a core set of 7261 protein families. P. capitalensis had the largest set of orphan genes (1991), in complete contrast to that of P. citriasiana (364) and P. citricarpa (262). Most of the orphan genes are functionally unknown, but they contain a certain number of species-specific secreted proteins. A total of 23 secondary metabolites biosynthesis clusters were identified in the three Phyllosticta species, 21 of them being highly conserved among these species while the remaining two showed whole cluster gain and loss polymorphisms or gene content polymorphisms. Taken together, our study reveals insights into the genetic mechanisms of host adaptation of three species of Phyllosticta associated with citrus and paves the way to identify effectors that function in infection of citrus plants.
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Affiliation(s)
- Mingshuang Wang
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Bei Liu
- Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Ministry of Agriculture, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Ruoxin Ruan
- Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Ministry of Agriculture, Institute of Biotechnology, Zhejiang University, Hangzhou, China
- Hangzhou Academy of Agricultural Sciences, Hangzhou, China
| | - Yibing Zeng
- Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Ministry of Agriculture, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Jinshui Luo
- Fujian Institute of Tropical Crops, Zhangzhou, China
| | - Hongye Li
- Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Ministry of Agriculture, Institute of Biotechnology, Zhejiang University, Hangzhou, China
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118
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Ma X, Wiedmer J, Palma-Guerrero J. Small RNA Bidirectional Crosstalk During the Interaction Between Wheat and Zymoseptoria tritici. FRONTIERS IN PLANT SCIENCE 2020; 10:1669. [PMID: 31969895 PMCID: PMC6960233 DOI: 10.3389/fpls.2019.01669] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Accepted: 11/27/2019] [Indexed: 05/21/2023]
Abstract
Cross-kingdom RNA interference (RNAi) has been shown to play important roles during plant-pathogen interactions, and both plants and pathogens can use small RNAs (sRNAs) to silence genes in each other. This bidirectional cross-kingdom RNAi was still unexplored in the wheat-Zymoseptoria tritici pathosystem. Here, we performed a detailed analysis of the sRNA bidirectional crosstalk between wheat and Z. tritici. Using a combination of small RNA sequencing (sRNA-seq) and microRNA sequencing (mRNA-seq), we were able to identify known and novel sRNAs and study their expression and their action on putative targets in both wheat and Z. tritici. We predicted the target genes of all the sRNAs in either wheat or Z. tritici transcriptome and used degradome analysis to validate the cleavage of these gene transcripts. We could not find any clear evidence of a cross-kingdom RNAi acting by mRNA cleavage in this pathosystem. We also found that the fungal sRNA enrichment was lower in planta than during in vitro growth, probably due to the lower expression of the only Dicer gene of the fungus during plant infection. Our results support the recent finding that Z. tritici sRNAs cannot play important roles during wheat infection. However, we also found that the fungal infection induced wheat sRNAs regulating the expression of specific wheat genes, including auxin-related genes, as an immune response. These results indicate a role of sRNAs in the regulation of wheat defenses during Z. tritici infection. Our findings contribute to improve our understanding of the interactions between wheat and Z. tritici.
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Affiliation(s)
- Xin Ma
- Plant Pathology, Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland
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119
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Brennan CJ, Zhou B, Benbow HR, Ajaz S, Karki SJ, Hehir JG, O’Driscoll A, Feechan A, Mullins E, Doohan FM. Taxonomically Restricted Wheat Genes Interact With Small Secreted Fungal Proteins and Enhance Resistance to Septoria Tritici Blotch Disease. FRONTIERS IN PLANT SCIENCE 2020; 11:433. [PMID: 32477375 PMCID: PMC7236048 DOI: 10.3389/fpls.2020.00433] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Accepted: 03/24/2020] [Indexed: 05/12/2023]
Abstract
Understanding the nuances of host/pathogen interactions are paramount if we wish to effectively control cereal diseases. In the case of the wheat/Zymoseptoria tritici interaction that leads to Septoria tritici blotch (STB) disease, a 10,000-year-old conflict has led to considerable armaments being developed on both sides which are not reflected in conventional model systems. Taxonomically restricted genes (TRGs) have evolved in wheat to better allow it to cope with stress caused by fungal pathogens, and Z. tritici has evolved specialized effectors which allow it to manipulate its' host. A microarray focused on the latent phase response of a resistant wheat cultivar (cv. Stigg) and susceptible wheat cultivar (cv. Gallant) to Z. tritici infection was mined for TRGs within the Poaceae. From this analysis, we identified two TRGs that were significantly upregulated in response to Z. tritici infection, Septoria-responsive TRG6 and 7 (TaSRTRG6 and TaSRTRG7). Virus induced silencing of these genes resulted in an increased susceptibility to STB disease in cvs. Gallant and Stigg, and significantly so in the latter (2.5-fold increase in STB disease). In silico and localization studies categorized TaSRTRG6 as a secreted protein and TaSRTRG7 as an intracellular protein. Yeast two-hybrid analysis and biofluorescent complementation studies demonstrated that both TaSRTRG6 and TaSRTRG7 can interact with small proteins secreted by Z. tritici (potential effector candidates). Thus we conclude that TRGs are an important part of the wheat-Z. tritici co-evolution story and potential candidates for modulating STB resistance.
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Affiliation(s)
- Ciarán J. Brennan
- UCD School of Biology and Environmental Science and UCD Earth Institute, UCD O’Brien Centre for Science (East), University College Dublin, Belfield, Ireland
| | - Binbin Zhou
- UCD School of Biology and Environmental Science and UCD Earth Institute, UCD O’Brien Centre for Science (East), University College Dublin, Belfield, Ireland
| | - Harriet R. Benbow
- UCD School of Biology and Environmental Science and UCD Earth Institute, UCD O’Brien Centre for Science (East), University College Dublin, Belfield, Ireland
| | - Sobia Ajaz
- UCD School of Biology and Environmental Science and UCD Earth Institute, UCD O’Brien Centre for Science (East), University College Dublin, Belfield, Ireland
| | - Sujit J. Karki
- School of Agriculture and Food Science, University College Dublin, Belfield, Ireland
| | | | | | - Angela Feechan
- School of Agriculture and Food Science, University College Dublin, Belfield, Ireland
| | - Ewen Mullins
- Department of Crop Science, Teagasc, Carlow, Ireland
| | - Fiona M. Doohan
- UCD School of Biology and Environmental Science and UCD Earth Institute, UCD O’Brien Centre for Science (East), University College Dublin, Belfield, Ireland
- *Correspondence: Fiona M. Doohan,
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120
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Chaudhari Y, Cairns TC, Sidhu Y, Attah V, Thomas G, Csukai M, Talbot NJ, Studholme DJ, Haynes K. The Zymoseptoria tritici ORFeome: A Functional Genomics Community Resource. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2019; 32:1564-1570. [PMID: 31272284 DOI: 10.1094/mpmi-05-19-0123-a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Libraries of protein-encoding sequences can be generated by identification of open reading frames (ORFs) from a genome of choice that are then assembled into collections of plasmids termed ORFeome libraries. These represent powerful resources to facilitate functional genomic characterization of genes and their encoded products. Here, we report the generation of an ORFeome for Zymoseptoria tritici, which causes the most serious disease of wheat in temperate regions of the world. We screened the genome of strain IP0323 for high confidence gene models, identifying 4,075 candidates from 10,933 predicted genes. These were amplified from genomic DNA, were cloned into the Gateway entry vector pDONR207, and were sequenced, providing a total of 3,022 quality-controlled plasmids. The ORFeome includes genes predicted to encode effectors (n = 410) and secondary metabolite biosynthetic proteins (n = 171) in addition to genes residing at dispensable chromosomes (n = 122) or those that are preferentially expressed during plant infection (n = 527). The ORFeome plasmid library is compatible with our previously developed suite of Gateway destination vectors, which have various combinations of promoters, selection markers, and epitope tags. The Z. tritici ORFeome constitutes a powerful resource for functional genomics and offers unparalleled opportunities to understand the biology of Z. tritici.[Formula: see text] Copyright © 2019 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.
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Affiliation(s)
| | | | | | | | - Graham Thomas
- Biosciences, University of Exeter, Exeter EX4 4QD, U.K
| | - Michael Csukai
- Syngenta, Jealott's Hill International Research Centre, Bracknell, RG42 6EY, U.K
| | - Nicholas J Talbot
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, NR47UH, U.K
| | | | - Ken Haynes
- Biosciences, University of Exeter, Exeter EX4 4QD, U.K
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121
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Lütkenhaus R, Traeger S, Breuer J, Carreté L, Kuo A, Lipzen A, Pangilinan J, Dilworth D, Sandor L, Pöggeler S, Gabaldón T, Barry K, Grigoriev IV, Nowrousian M. Comparative Genomics and Transcriptomics To Analyze Fruiting Body Development in Filamentous Ascomycetes. Genetics 2019; 213:1545-1563. [PMID: 31604798 PMCID: PMC6893386 DOI: 10.1534/genetics.119.302749] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Accepted: 10/08/2019] [Indexed: 02/08/2023] Open
Abstract
Many filamentous ascomycetes develop three-dimensional fruiting bodies for production and dispersal of sexual spores. Fruiting bodies are among the most complex structures differentiated by ascomycetes; however, the molecular mechanisms underlying this process are insufficiently understood. Previous comparative transcriptomics analyses of fruiting body development in different ascomycetes suggested that there might be a core set of genes that are transcriptionally regulated in a similar manner across species. Conserved patterns of gene expression can be indicative of functional relevance, and therefore such a set of genes might constitute promising candidates for functional analyses. In this study, we have sequenced the genome of the Pezizomycete Ascodesmis nigricans, and performed comparative transcriptomics of developing fruiting bodies of this fungus, the Pezizomycete Pyronema confluens, and the Sordariomycete Sordaria macrospora With only 27 Mb, the A. nigricans genome is the smallest Pezizomycete genome sequenced to date. Comparative transcriptomics indicated that gene expression patterns in developing fruiting bodies of the three species are more similar to each other than to nonsexual hyphae of the same species. An analysis of 83 genes that are upregulated only during fruiting body development in all three species revealed 23 genes encoding proteins with predicted roles in vesicle transport, the endomembrane system, or transport across membranes, and 13 genes encoding proteins with predicted roles in chromatin organization or the regulation of gene expression. Among four genes chosen for functional analysis by deletion in S. macrospora, three were shown to be involved in fruiting body formation, including two predicted chromatin modifier genes.
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Affiliation(s)
- Ramona Lütkenhaus
- Department of Molecular and Cellular Botany, Ruhr-Universität Bochum, 44780 Bochum, Germany
| | - Stefanie Traeger
- Department of Molecular and Cellular Botany, Ruhr-Universität Bochum, 44780 Bochum, Germany
| | - Jan Breuer
- Department of Molecular and Cellular Botany, Ruhr-Universität Bochum, 44780 Bochum, Germany
| | - Laia Carreté
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation, 08003 Barcelona, Spain
| | - Alan Kuo
- US Department of Energy Joint Genome Institute, Walnut Creek, California 94598
| | - Anna Lipzen
- US Department of Energy Joint Genome Institute, Walnut Creek, California 94598
| | - Jasmyn Pangilinan
- US Department of Energy Joint Genome Institute, Walnut Creek, California 94598
| | - David Dilworth
- US Department of Energy Joint Genome Institute, Walnut Creek, California 94598
| | - Laura Sandor
- US Department of Energy Joint Genome Institute, Walnut Creek, California 94598
| | - Stefanie Pöggeler
- Institute of Microbiology and Genetics, Department of Genetics of Eukaryotic Microorganisms, Georg-August University, Göttingen, 37077 Göttingen, Germany
| | - Toni Gabaldón
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation, 08003 Barcelona, Spain
- Universitat Pompeu Fabra, 08002 Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats, 08010 Barcelona, Spain
| | - Kerrie Barry
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation, 08003 Barcelona, Spain
| | - Igor V Grigoriev
- US Department of Energy Joint Genome Institute, Walnut Creek, California 94598
- Department of Plant and Microbial Biology, University of California Berkeley, California 94720
| | - Minou Nowrousian
- Department of Molecular and Cellular Botany, Ruhr-Universität Bochum, 44780 Bochum, Germany
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Ametrano CG, Grewe F, Crous PW, Goodwin SB, Liang C, Selbmann L, Lumbsch HT, Leavitt SD, Muggia L. Genome-scale data resolve ancestral rock-inhabiting lifestyle in Dothideomycetes (Ascomycota). IMA Fungus 2019; 10:19. [PMID: 32647623 PMCID: PMC7325674 DOI: 10.1186/s43008-019-0018-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Accepted: 09/11/2019] [Indexed: 12/31/2022] Open
Abstract
Dothideomycetes is the most diverse fungal class in Ascomycota and includes species with a wide range of lifestyles. Previous multilocus studies have investigated the taxonomic and evolutionary relationships of these taxa but often failed to resolve early diverging nodes and frequently generated inconsistent placements of some clades. Here, we use a phylogenomic approach to resolve relationships in Dothideomycetes, focusing on two genera of melanized, extremotolerant rock-inhabiting fungi, Lichenothelia and Saxomyces, that have been suggested to be early diverging lineages. We assembled phylogenomic datasets from newly sequenced (4) and previously available genomes (238) of 242 taxa. We explored the influence of tree inference methods, supermatrix vs. coalescent-based species tree, and the impact of varying amounts of genomic data. Overall, our phylogenetic reconstructions provide consistent and well-supported topologies for Dothideomycetes, recovering Lichenothelia and Saxomyces among the earliest diverging lineages in the class. In addition, many of the major lineages within Dothideomycetes are recovered as monophyletic, and the phylogenomic approach implemented strongly supports their relationships. Ancestral character state reconstruction suggest that the rock-inhabiting lifestyle is ancestral within the class.
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Affiliation(s)
- Claudio G Ametrano
- Department of Life Sciences, University of Trieste, via Giorgieri 10, 34127 Trieste, Italy
| | - Felix Grewe
- Grainger Bioinformatics Center and Integrative Research Center, Science and Education, Field Museum of Natural History, 1400 S Lake Shore Drive, Chicago, IL 60605 USA
| | - Pedro W Crous
- Westerdijk Fungal Biodiversity Institute, P.O. Box 85176, 3508 AD Utrecht, The Netherlands
| | - Stephen B Goodwin
- USDA-ARS, Crop Production and Pest Control Research Unit and Department of Botany and Plant Pathology, Purdue University, 915 West State Street, West Lafayette, IN 47907-2054 USA
| | - Chen Liang
- College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, 266109 China
| | - Laura Selbmann
- Department of Ecological and Biological Sciences, University of Tuscia, Largo dell' Università, 01100 Viterbo, Italy.,Italian National Antarctic Museum (MNA), Mycological Section, Genoa, Italy
| | - H Thorsten Lumbsch
- Grainger Bioinformatics Center and Integrative Research Center, Science and Education, Field Museum of Natural History, 1400 S Lake Shore Drive, Chicago, IL 60605 USA
| | - Steven D Leavitt
- Department of Biology and M.L. Bean Life Science Museum, Brigham Young University, 4102 Life Science Building, Provo, UT 84602 USA
| | - Lucia Muggia
- Department of Life Sciences, University of Trieste, via Giorgieri 10, 34127 Trieste, Italy
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Chong P, Vichou AE, Schouten HJ, Meijer HJG, Arango Isaza RE, Kema GHJ. Pfcyp51 exclusively determines reduced sensitivity to 14α-demethylase inhibitor fungicides in the banana black Sigatoka pathogen Pseudocercospora fijiensis. PLoS One 2019; 14:e0223858. [PMID: 31622393 PMCID: PMC6797121 DOI: 10.1371/journal.pone.0223858] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2019] [Accepted: 09/30/2019] [Indexed: 11/27/2022] Open
Abstract
The haploid fungus Pseudocercospora fijiensis causes black Sigatoka in banana and is chiefly controlled by extensive fungicide applications, threatening occupational health and the environment. The 14α-Demethylase Inhibitors (DMIs) are important disease control fungicides, but they lose sensitivity in a rather gradual fashion, suggesting an underlying polygenic genetic mechanism. In spite of this, evidence found thus far suggests that P. fijiensis cyp51 gene mutations are the main responsible factor for sensitivity loss in the field. To better understand the mechanisms involved in DMI resistance, in this study we constructed a genetic map using DArTseq markers on two F1 populations generated by crossing two different DMI resistant strains with a sensitive strain. Analysis of the inheritance of DMI resistance in the F1 populations revealed two major and discrete DMI-sensitivity groups. This is an indicative of a single major responsible gene. Using the DMI-sensitivity scorings of both F1 populations and the generation of genetic linkage maps, the sensitivity causal factor was located in a single genetic region. Full agreement was found for genetic markers in either population, underlining the robustness of the approach. The two maps indicated a similar genetic region where the Pfcyp51 gene is found. Sequence analyses of the Pfcyp51 gene of the F1 populations also revealed a matching bimodal distribution with the DMI resistant. Amino acid substitutions in P. fijiensis CYP51 enzyme of the resistant progeny were previously correlated with the loss of DMI sensitivity. In addition, the resistant progeny inherited a Pfcyp51 gene promoter insertion, composed of a repeat element with a palindromic core, also previously correlated with increased gene expression. This genetic approach confirms that Pfcyp51 is the single explanatory gene for reduced sensitivity to DMI fungicides in the analysed P. fijiensis strains. Our study is the first genetic analysis to map the underlying genetic factors for reduced DMI efficacy.
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Affiliation(s)
- Pablo Chong
- ESPOL Polythecnic University, Escuela Superior Politécnica del Litoral, ESPOL, Centro de Investigaciones Biotecnológicas del Ecuador, Laboratorio de Fitopatología, Guayaquil, Ecuador
- Laboratory of Phytopathology, Wageningen University and Research, The Netherlands, Wageningen, the Netherlands
| | - Aikaterini-Eleni Vichou
- Laboratory of Phytopathology, Wageningen University and Research, The Netherlands, Wageningen, the Netherlands
| | - Henk J. Schouten
- Laboratory of Phytopathology, Wageningen University and Research, The Netherlands, Wageningen, the Netherlands
| | - Harold J. G. Meijer
- Laboratory of Phytopathology, Wageningen University and Research, The Netherlands, Wageningen, the Netherlands
| | - Rafael E. Arango Isaza
- Escuela de Biociencias, Faculta de Ciencias, Universidad Nacional de Colombia -Sede Medellín (UNALMED), Medellín, Colombia
- Unidad de biotecnología (UNALMED-CIB), Corporación para Investigaciones Biológicas, Medellín, Colombia
| | - Gert H. J. Kema
- Laboratory of Phytopathology, Wageningen University and Research, The Netherlands, Wageningen, the Netherlands
- * E-mail:
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Richards JK, Stukenbrock EH, Carpenter J, Liu Z, Cowger C, Faris JD, Friesen TL. Local adaptation drives the diversification of effectors in the fungal wheat pathogen Parastagonospora nodorum in the United States. PLoS Genet 2019; 15:e1008223. [PMID: 31626626 PMCID: PMC6821140 DOI: 10.1371/journal.pgen.1008223] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 10/30/2019] [Accepted: 08/25/2019] [Indexed: 12/22/2022] Open
Abstract
Filamentous fungi rapidly evolve in response to environmental selection pressures in part due to their genomic plasticity. Parastagonospora nodorum, a fungal pathogen of wheat and causal agent of septoria nodorum blotch, responds to selection pressure exerted by its host, influencing the gain, loss, or functional diversification of virulence determinants, known as effector genes. Whole genome resequencing of 197 P. nodorum isolates collected from spring, durum, and winter wheat production regions of the United States enabled the examination of effector diversity and genomic regions under selection specific to geographically discrete populations. 1,026,859 SNPs/InDels were used to identify novel loci, as well as SnToxA and SnTox3 as factors in disease. Genes displaying presence/absence variation, predicted effector genes, and genes localized on an accessory chromosome had significantly higher pN/pS ratios, indicating a higher rate of sequence evolution. Population structure analyses indicated two P. nodorum populations corresponding to the Upper Midwest (Population 1) and Southern/Eastern United States (Population 2). Prevalence of SnToxA varied greatly between the two populations which correlated with presence of the host sensitivity gene Tsn1 in the most prevalent cultivars in the corresponding regions. Additionally, 12 and 5 candidate effector genes were observed to be under diversifying selection among isolates from Population 1 and 2, respectively, but under purifying selection or neutrally evolving in the opposite population. Selective sweep analysis revealed 10 and 19 regions that had recently undergone positive selection in Population 1 and 2, respectively, involving 92 genes in total. When comparing genes with and without presence/absence variation, those genes exhibiting this variation were significantly closer to transposable elements. Taken together, these results indicate that P. nodorum is rapidly adapting to distinct selection pressures unique to spring and winter wheat production regions by rapid adaptive evolution and various routes of genomic diversification, potentially facilitated through transposable element activity.
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Affiliation(s)
- Jonathan K. Richards
- Department of Plant Pathology and Crop Physiology, Louisiana State University Agricultural Center, Baton Rouge, Louisiana, United States of America
| | - Eva H. Stukenbrock
- Department of Environmental Genomics, Christian-Albrechts University of Kiel, Kiel, Germany
- Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Jessica Carpenter
- Department of Plant Pathology, North Dakota State University, Fargo, North Dakota, United States of America
| | - Zhaohui Liu
- Department of Plant Pathology, North Dakota State University, Fargo, North Dakota, United States of America
| | - Christina Cowger
- Plant Science Research Unit, USDA-ARS, Raleigh, North Carolina, United States of America
| | - Justin D. Faris
- Cereal Crops Research Unit, Edward T. Schaefer Agricultural Research Center, USDA-ARS, Fargo, North Dakota, United States of America
| | - Timothy L. Friesen
- Department of Plant Pathology, North Dakota State University, Fargo, North Dakota, United States of America
- Cereal Crops Research Unit, Edward T. Schaefer Agricultural Research Center, USDA-ARS, Fargo, North Dakota, United States of America
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Tiley AMM, White HJ, Foster GD, Bailey AM. The ZtvelB Gene Is Required for Vegetative Growth and Sporulation in the Wheat Pathogen Zymoseptoria tritici. Front Microbiol 2019; 10:2210. [PMID: 31632366 PMCID: PMC6779691 DOI: 10.3389/fmicb.2019.02210] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 09/10/2019] [Indexed: 11/13/2022] Open
Abstract
The ascomycete fungus Zymoseptoria tritici is the causal agent of Septoria Tritici Blotch (STB), a major disease of wheat across Europe. Current understanding of the genetic components and the environmental cues which influence development and pathogenicity of this fungus is limited. The velvet B gene, velB, has conserved roles in development, secondary metabolism, and pathogenicity across fungi. The function of this gene is best characterised in the model ascomycete fungus Aspergillus nidulans, where it is involved in co-ordinating the light response with downstream processes. There is limited knowledge of the role of light in Z. tritici, and of the molecular mechanisms underpinning the light response. We show that Z. tritici is able to detect light, and that the vegetative morphology of this fungus is influenced by light conditions. We also identify and characterise the Z. tritici velB gene, ZtvelB, by gene disruption. The ΔztvelB deletion mutants were fixed in a filamentous growth pattern and are unable to form yeast-like vegetative cells. Their morphology was similar under light and dark conditions, showing an impairment in light-responsive growth. In addition, the ΔztvelB mutants produced abnormal pycnidia that were impaired in macropycnidiospore production but could still produce viable infectious micropycnidiospores. Our results show that ZtvelB is required for yeast-like growth and asexual sporulation in Z. tritici, and we provide evidence for a role of ZtvelB in integrating light perception and developmental regulation in this important plant pathogenic fungus.
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Affiliation(s)
- Anna M M Tiley
- Molecular Plant Pathology and Fungal Biology, School of Biological Sciences, University of Bristol, Bristol, United Kingdom
| | - Hannah J White
- School of Biology and Environmental Science, O'Brien Centre for Science, University College Dublin, Dublin, Ireland
| | - Gary D Foster
- Molecular Plant Pathology and Fungal Biology, School of Biological Sciences, University of Bristol, Bristol, United Kingdom
| | - Andy M Bailey
- Molecular Plant Pathology and Fungal Biology, School of Biological Sciences, University of Bristol, Bristol, United Kingdom
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126
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Peng Z, Oliveira-Garcia E, Lin G, Hu Y, Dalby M, Migeon P, Tang H, Farman M, Cook D, White FF, Valent B, Liu S. Effector gene reshuffling involves dispensable mini-chromosomes in the wheat blast fungus. PLoS Genet 2019; 15:e1008272. [PMID: 31513573 PMCID: PMC6741851 DOI: 10.1371/journal.pgen.1008272] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 06/24/2019] [Indexed: 11/28/2022] Open
Abstract
Newly emerged wheat blast disease is a serious threat to global wheat production. Wheat blast is caused by a distinct, exceptionally diverse lineage of the fungus causing rice blast disease. Through sequencing a recent field isolate, we report a reference genome that includes seven core chromosomes and mini-chromosome sequences that harbor effector genes normally found on ends of core chromosomes in other strains. No mini-chromosomes were observed in an early field strain, and at least two from another isolate each contain different effector genes and core chromosome end sequences. The mini-chromosome is enriched in transposons occurring most frequently at core chromosome ends. Additionally, transposons in mini-chromosomes lack the characteristic signature for inactivation by repeat-induced point (RIP) mutation genome defenses. Our results, collectively, indicate that dispensable mini-chromosomes and core chromosomes undergo divergent evolutionary trajectories, and mini-chromosomes and core chromosome ends are coupled as a mobile, fast-evolving effector compartment in the wheat pathogen genome. The emerging blast disease on wheat is proving even harder to control than the ancient, still-problematic rice blast disease. Potential wheat resistance identified using strains isolated soon after disease emergence are no longer effective in controlling recent aggressive field isolates from wheat in South America and South Asia. We construct a high-quality assembly of an aggressive, recently-isolated wheat blast fungal strain and the first assembled mini-chromosome genome sequence of wheat and rice blast pathogens. We report that recent wheat pathogens can contain one or two highly-variable dispensable mini-chromosomes, each with an amalgamation of fungal effector genes and other sequences that are duplicated or absent from indispensable core chromosome ends. Well-studied effectors found on different core chromosomes in rice pathogens appear side-by-side in wheat pathogen mini-chromosomes. The rice pathogen often overcomes deployed resistance genes by deleting triggering effector genes. We propose that the fast-evolving effector-rich compartment of the wheat blast fungus is a combination of core chromosome ends and mobile mini-chromosomes that are easily lost from individual strains. Localization of effectors on mini-chromosomes would therefore accelerate pathogen adaptation in the field.
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Affiliation(s)
- Zhao Peng
- Department of Plant Pathology, Kansas State University, Manhattan, KS, United States of America
- Department of Plant Pathology, University of Florida, Gainesville, FL, United States of America
| | - Ely Oliveira-Garcia
- Department of Plant Pathology, Kansas State University, Manhattan, KS, United States of America
| | - Guifang Lin
- Department of Plant Pathology, Kansas State University, Manhattan, KS, United States of America
| | - Ying Hu
- Department of Plant Pathology, Kansas State University, Manhattan, KS, United States of America
| | - Melinda Dalby
- Department of Plant Pathology, Kansas State University, Manhattan, KS, United States of America
| | - Pierre Migeon
- Department of Plant Pathology, Kansas State University, Manhattan, KS, United States of America
| | - Haibao Tang
- Center for Genomics and Biotechnology and Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fujian, China
| | - Mark Farman
- Department of Plant Pathology, University of Kentucky, Lexington, KY, United States of America
| | - David Cook
- Department of Plant Pathology, Kansas State University, Manhattan, KS, United States of America
| | - Frank F. White
- Department of Plant Pathology, University of Florida, Gainesville, FL, United States of America
| | - Barbara Valent
- Department of Plant Pathology, Kansas State University, Manhattan, KS, United States of America
- * E-mail: (BV); (SL)
| | - Sanzhen Liu
- Department of Plant Pathology, Kansas State University, Manhattan, KS, United States of America
- * E-mail: (BV); (SL)
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127
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Peng Z, Oliveira-Garcia E, Lin G, Hu Y, Dalby M, Migeon P, Tang H, Farman M, Cook D, White FF, Valent B, Liu S. Effector gene reshuffling involves dispensable mini-chromosomes in the wheat blast fungus. PLoS Genet 2019; 15:e1008272. [PMID: 31513573 DOI: 10.1101/359455] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 06/24/2019] [Indexed: 05/26/2023] Open
Abstract
Newly emerged wheat blast disease is a serious threat to global wheat production. Wheat blast is caused by a distinct, exceptionally diverse lineage of the fungus causing rice blast disease. Through sequencing a recent field isolate, we report a reference genome that includes seven core chromosomes and mini-chromosome sequences that harbor effector genes normally found on ends of core chromosomes in other strains. No mini-chromosomes were observed in an early field strain, and at least two from another isolate each contain different effector genes and core chromosome end sequences. The mini-chromosome is enriched in transposons occurring most frequently at core chromosome ends. Additionally, transposons in mini-chromosomes lack the characteristic signature for inactivation by repeat-induced point (RIP) mutation genome defenses. Our results, collectively, indicate that dispensable mini-chromosomes and core chromosomes undergo divergent evolutionary trajectories, and mini-chromosomes and core chromosome ends are coupled as a mobile, fast-evolving effector compartment in the wheat pathogen genome.
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Affiliation(s)
- Zhao Peng
- Department of Plant Pathology, Kansas State University, Manhattan, KS, United States of America
- Department of Plant Pathology, University of Florida, Gainesville, FL, United States of America
| | - Ely Oliveira-Garcia
- Department of Plant Pathology, Kansas State University, Manhattan, KS, United States of America
| | - Guifang Lin
- Department of Plant Pathology, Kansas State University, Manhattan, KS, United States of America
| | - Ying Hu
- Department of Plant Pathology, Kansas State University, Manhattan, KS, United States of America
| | - Melinda Dalby
- Department of Plant Pathology, Kansas State University, Manhattan, KS, United States of America
| | - Pierre Migeon
- Department of Plant Pathology, Kansas State University, Manhattan, KS, United States of America
| | - Haibao Tang
- Center for Genomics and Biotechnology and Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fujian, China
| | - Mark Farman
- Department of Plant Pathology, University of Kentucky, Lexington, KY, United States of America
| | - David Cook
- Department of Plant Pathology, Kansas State University, Manhattan, KS, United States of America
| | - Frank F White
- Department of Plant Pathology, University of Florida, Gainesville, FL, United States of America
| | - Barbara Valent
- Department of Plant Pathology, Kansas State University, Manhattan, KS, United States of America
| | - Sanzhen Liu
- Department of Plant Pathology, Kansas State University, Manhattan, KS, United States of America
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128
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Haddad Momeni M, Bollella P, Ortiz R, Thormann E, Gorton L, Abou Hachem M. A novel starch-binding laccase from the wheat pathogen Zymoseptoria tritici highlights the functional diversity of ascomycete laccases. BMC Biotechnol 2019; 19:61. [PMID: 31426777 PMCID: PMC6700816 DOI: 10.1186/s12896-019-0552-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Accepted: 07/26/2019] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Laccases are multicopper oxidases, which are assigned into auxiliary activity family 1 (AA1) in the CAZy database. These enzymes, catalyzing the oxidation of phenolic and nonphenolic substrates coupled to reduction of O2 to H2O, are increasingly attractive as eco-friendly oxidation biocatalysts. Basidiomycota laccases are well characterized due to their potential in de-lignification of lignocellulose. By contrast, insight into the biochemical diversity of Ascomycota counterparts from saprophytes and plant pathogens is scarce. RESULTS Here, we report the properties of the laccase from the major wheat pathogen Zymoseptoria tritici (ZtrLac1A), distinguished from common plant fungal pathogens by an apoplastic infection strategy. We demonstrate that ZtrLac1A is appended to a functional starch-binding module and displays an activity signature disfavoring relatively apolar phenolic redox mediators as compared to the related biochemically characterized laccases. By contrast, the redox potential of ZtrLac1A (370 mV vs. SHE) is similar to ascomycetes counterparts. The atypical specificity is consistent with distinctive sequence substitutions and insertions in loops flanking the T1 site and the enzyme C-terminus compared to characterized laccases. CONCLUSIONS ZtrLac1A is the first reported modular laccase appended to a functional starch-specific carbohydrate binding module of family 20 (CBM20). The distinct specificity profile of ZtrLac1A correlates to structural differences in the active site region compared to previously described ascomycetes homologues. These differences are also highlighted by the clustering of the sequence of ZtrLac1A in a distinct clade populated predominantly by plant pathogens in the phylogenetic tree of AA1 laccases. The possible role of these laccases in vivo merits further investigations. These findings expand our toolbox of laccases for green oxidation and highlight the binding functionality of CBM-appended laccases as versatile immobilization tags.
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Affiliation(s)
- Majid Haddad Momeni
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, 2800 Kgs, Lyngby, Denmark
| | - Paolo Bollella
- Department of Biochemistry and Structural Biology, Lund University, P.O. Box 124, 221 00 Lund, Sweden
- Department of Chemistry and Drug Technologies, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Roberto Ortiz
- Department of Chemistry, Technical University of Denmark, Kemitorvet 207, 2800 Kgs, Lyngby, Denmark
| | - Esben Thormann
- Department of Chemistry, Technical University of Denmark, Kemitorvet 207, 2800 Kgs, Lyngby, Denmark
| | - Lo Gorton
- Department of Biochemistry and Structural Biology, Lund University, P.O. Box 124, 221 00 Lund, Sweden
| | - Maher Abou Hachem
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, 2800 Kgs, Lyngby, Denmark
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129
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Kettles GJ, Hofinger BJ, Hu P, Bayon C, Rudd JJ, Balmer D, Courbot M, Hammond-Kosack KE, Scalliet G, Kanyuka K. sRNA Profiling Combined With Gene Function Analysis Reveals a Lack of Evidence for Cross-Kingdom RNAi in the Wheat - Zymoseptoria tritici Pathosystem. FRONTIERS IN PLANT SCIENCE 2019; 10:892. [PMID: 31333714 PMCID: PMC6620828 DOI: 10.3389/fpls.2019.00892] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 06/21/2019] [Indexed: 05/19/2023]
Abstract
Cross-kingdom small RNA (sRNA) silencing has recently emerged as a mechanism facilitating fungal colonization and disease development. Here we characterized RNAi pathways in Zymoseptoria tritici, a major fungal pathogen of wheat, and assessed their contribution to pathogenesis. Computational analysis of fungal sRNA and host mRNA sequencing datasets was used to define the global sRNA populations in Z. tritici and predict their mRNA targets in wheat. 389 in planta-induced sRNA loci were identified. sRNAs generated from some of these loci were predicted to target wheat mRNAs including those potentially involved in pathogen defense. However, molecular approaches failed to validate targeting of selected wheat mRNAs by fungal sRNAs. Mutant strains of Z. tritici carrying deletions of genes encoding key components of RNAi such as Dicer-like (DCL) and Argonaute (AGO) proteins were generated, and virulence bioassays suggested that these are dispensable for full infection of wheat. Nonetheless, our results did suggest the existence of non-canonical DCL-independent pathway(s) for sRNA biogenesis in Z. tritici. dsRNA targeting essential fungal genes applied in vitro or generated from an RNA virus vector in planta in a procedure known as HIGS (Host-Induced Gene Silencing) was ineffective in preventing Z. tritici growth or disease. We also demonstrated that Z. tritici is incapable of dsRNA uptake. Collectively, our data suggest that RNAi approaches for gene function analyses in this fungal species and potentially also as a control measure may not be as effective as has been demonstrated for some other plant pathogenic fungi.
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Affiliation(s)
- Graeme J. Kettles
- Biointeractions and Crop Protection, Rothamsted Research, Harpenden, United Kingdom
| | - Bernhard J. Hofinger
- Biointeractions and Crop Protection, Rothamsted Research, Harpenden, United Kingdom
| | - Pingsha Hu
- Syngenta Biotechnology, Inc., Research Triangle Park, NC, United States
| | - Carlos Bayon
- Biointeractions and Crop Protection, Rothamsted Research, Harpenden, United Kingdom
| | - Jason J. Rudd
- Biointeractions and Crop Protection, Rothamsted Research, Harpenden, United Kingdom
| | - Dirk Balmer
- Syngenta Crop Protection AG, Stein, Switzerland
| | | | | | | | - Kostya Kanyuka
- Biointeractions and Crop Protection, Rothamsted Research, Harpenden, United Kingdom
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130
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Kay WT, Fones HN, Gurr SJ. Rapid loss of virulence during submergence of Z. tritici asexual spores. Fungal Genet Biol 2019; 128:14-19. [DOI: 10.1016/j.fgb.2019.03.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 03/08/2019] [Accepted: 03/08/2019] [Indexed: 11/28/2022]
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131
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Thynne E, Mead OL, Chooi YH, McDonald MC, Solomon PS. Acquisition and Loss of Secondary Metabolites Shaped the Evolutionary Path of Three Emerging Phytopathogens of Wheat. Genome Biol Evol 2019; 11:890-905. [PMID: 30793159 PMCID: PMC6431248 DOI: 10.1093/gbe/evz037] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/19/2019] [Indexed: 12/14/2022] Open
Abstract
White grain disorder is a recently emerged wheat disease in Australia, caused by Eutiarosporella darliae, E. pseudodarliae, and E. tritici-australis. The disease cycle of these pathogens and the molecular basis of their interaction with wheat are poorly understood. To address this knowledge gap, we undertook a comparative genomics analysis focused on the secondary metabolite gene repertoire among these three species. This analysis revealed a diverse array of secondary metabolite gene clusters in these pathogens, including modular polyketide synthase genes. These genes have only been previously associated with bacteria and this is the first report of such genes in fungi. Subsequent phylogenetic analyses provided strong evidence that the modular PKS genes were horizontally acquired from a bacterial or a protist species. We also uncovered a secondary metabolite gene cluster with three polyketide/nonribosomal peptide synthase genes (Hybrid-1, -2, and -3) in E. darliae and E. pseudodarliae. In contrast, only remnant and partial genes homologous to this cluster were identified in E. tritici-australis, suggesting loss of this cluster. Homologues of Hybrid-2 in other fungi have been proposed to facilitate disease in woody plants, suggesting a possible alternative host range for E. darliae and E. pseudodarliae. Subsequent assays confirmed that E. darliae and E. pseudodarliae were both pathogenic on woody plants, but E. tritici-australis was not, implicating woody plants as potential host reservoirs for the fungi. Combined, these data have advanced our understanding of the lifestyle and potential host-range of these recently emerged wheat pathogens and shed new light on fungal secondary metabolism.
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Affiliation(s)
- Elisha Thynne
- Division of Plant Sciences, Research School of Biology, The Australian National University, Canberra, Australia
| | - Oliver L Mead
- Division of Plant Sciences, Research School of Biology, The Australian National University, Canberra, Australia
| | - Yit-Heng Chooi
- School of Molecular Sciences, Faculty of Science, The University of Western Australia, Perth, Australia
| | - Megan C McDonald
- Division of Plant Sciences, Research School of Biology, The Australian National University, Canberra, Australia
| | - Peter S Solomon
- Division of Plant Sciences, Research School of Biology, The Australian National University, Canberra, Australia
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132
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van de Vossenberg BTLH, Warris S, Nguyen HDT, van Gent-Pelzer MPE, Joly DL, van de Geest HC, Bonants PJM, Smith DS, Lévesque CA, van der Lee TAJ. Comparative genomics of chytrid fungi reveal insights into the obligate biotrophic and pathogenic lifestyle of Synchytrium endobioticum. Sci Rep 2019; 9:8672. [PMID: 31209237 PMCID: PMC6572847 DOI: 10.1038/s41598-019-45128-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 05/31/2019] [Indexed: 01/09/2023] Open
Abstract
Synchytrium endobioticum is an obligate biotrophic soilborne Chytridiomycota (chytrid) species that causes potato wart disease, and represents the most basal lineage among the fungal plant pathogens. We have chosen a functional genomics approach exploiting knowledge acquired from other fungal taxa and compared this to several saprobic and pathogenic chytrid species. Observations linked to obligate biotrophy, genome plasticity and pathogenicity are reported. Essential purine pathway genes were found uniquely absent in S. endobioticum, suggesting that it relies on scavenging guanine from its host for survival. The small gene-dense and intron-rich chytrid genomes were not protected for genome duplications by repeat-induced point mutation. Both pathogenic chytrids Batrachochytrium dendrobatidis and S. endobioticum contained the largest amounts of repeats, and we identified S. endobioticum specific candidate effectors that are associated with repeat-rich regions. These candidate effectors share a highly conserved motif, and show isolate specific duplications. A reduced set of cell wall degrading enzymes, and LysM protein expansions were found in S. endobioticum, which may prevent triggering plant defense responses. Our study underlines the high diversity in chytrids compared to the well-studied Ascomycota and Basidiomycota, reflects characteristic biological differences between the phyla, and shows commonalities in genomic features among pathogenic fungi.
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Affiliation(s)
- Bart T L H van de Vossenberg
- Wageningen University & Research, Droevendaalsesteeg 1, Plant Science Group, 6708PB, Wageningen, The Netherlands.
- Dutch National Plant Protection Organization, National Reference Centre, Geertjesweg 15, 6706EA, Wageningen, The Netherlands.
| | - Sven Warris
- Wageningen University & Research, Droevendaalsesteeg 1, Plant Science Group, 6708PB, Wageningen, The Netherlands
| | - Hai D T Nguyen
- Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, Canada
| | - Marga P E van Gent-Pelzer
- Wageningen University & Research, Droevendaalsesteeg 1, Plant Science Group, 6708PB, Wageningen, The Netherlands
| | - David L Joly
- Université de Moncton, 18 avenue Antonine-Maillet, Moncton, Canada
| | - Henri C van de Geest
- Wageningen University & Research, Droevendaalsesteeg 1, Plant Science Group, 6708PB, Wageningen, The Netherlands
| | - Peter J M Bonants
- Wageningen University & Research, Droevendaalsesteeg 1, Plant Science Group, 6708PB, Wageningen, The Netherlands
| | - Donna S Smith
- Canadian Food Inspection Agency, 93 Mount Edward Road, Charlottetown, Canada
| | - C André Lévesque
- Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, Canada
| | - Theo A J van der Lee
- Wageningen University & Research, Droevendaalsesteeg 1, Plant Science Group, 6708PB, Wageningen, The Netherlands
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133
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Progress and Challenges: Development and Implementation of CRISPR/Cas9 Technology in Filamentous Fungi. Comput Struct Biotechnol J 2019; 17:761-769. [PMID: 31312414 PMCID: PMC6607083 DOI: 10.1016/j.csbj.2019.06.007] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 06/09/2019] [Accepted: 06/11/2019] [Indexed: 12/13/2022] Open
Abstract
Widely distributed in various environmental niches, filamentous fungi play an important role in industry, drug development, and plant/animal health. Manipulation of the genome and the coding sequences are essential for a better understanding of the function of genes and their regulation, but traditional genetic approaches in some filamentous fungi are either inefficient or nonfunctional. The rapid development and wide implementation of CRISPR/Cas9 (clustered regularly interspaced short palindromic repeats /(CRISPR)-associated protein-9 nuclease) technology for various model and non-model organisms has provided the initial framework to adapt this gene editing technology for filamentous fungi. In this review, an overview of the CRISPR/Cas9 tools and strategies that have been developed for different filamentous fungi is presented, including integration of the CAS9 gene into the genome, transient expression of Cas9/sgRNA, the AMA1-based plasmid approach, and the Cas9 RNP method. The various applications of CRISPR/Cas9 technology in filamentous fungi that have been implemented are explored, with particular emphasis on gene disruption/deletion and precise genome modification through gene tagging and alteration in gene regulation. Potential challenges that are confronted when developing a CRISPR/Cas9 system for filamentous fungi are also discussed such as the nuclear localization sequence for the CAS9 gene, potential off-target effects, and highly efficient transformation methods. Overcoming these obstacles may further facilitate wide application of this technology. As a simple, economical, and powerful tool, CRISPR/Cas9 systems have the potential for future implementation into many molecular aspects of filamentous fungi.
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134
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Grandaubert J, Dutheil JY, Stukenbrock EH. The genomic determinants of adaptive evolution in a fungal pathogen. Evol Lett 2019; 3:299-312. [PMID: 31171985 PMCID: PMC6546377 DOI: 10.1002/evl3.117] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2018] [Revised: 04/02/2019] [Accepted: 04/05/2019] [Indexed: 12/16/2022] Open
Abstract
Unravelling the strength, frequency, and distribution of selective variants along the genome as well as the underlying factors shaping this distribution are fundamental goals of evolutionary biology. Antagonistic host-pathogen coevolution is thought to be a major driver of genome evolution between interacting species. While rapid evolution of pathogens has been documented in several model organisms, the genetic mechanisms of their adaptation are still poorly understood and debated, particularly the role of sexual reproduction. Here, we apply a population genomic approach to infer genome-wide patterns of selection among 13 isolates of Zymoseptoria tritici, a fungal pathogen characterized by extremely high genetic diversity, gene density, and recombination rates. We report that the genome of Z. tritici undergoes a high rate of adaptive substitutions, with 44% of nonsynonymous substitutions being adaptive on average. This fraction reaches 68% in so-called effector genes encoding determinants of pathogenicity, and the distribution of fitness effects differs in this class of genes as they undergo adaptive mutations with stronger positive fitness effects, but also more slightly deleterious mutations. Besides the globally high rate of adaptive substitutions, we report a negative relationship between pN/pS and the fine-scale recombination rate and a strong positive correlation between the rate of adaptive nonsynonymous substitutions (ωa) and recombination rate. This result suggests a pervasive role of both background selection and Hill-Robertson interference even in a species with an exceptionally high recombination rate (60 cM/Mb on average). While transposable elements (TEs) have been suggested to contribute to adaptation by creating compartments of fast-evolving genomic regions, we do not find a significant effect of TEs on the rate of adaptive mutations. Overall our study suggests that sexual recombination is a significant driver of genome evolution, even in rapidly evolving organisms subject to recurrent mutations with large positive effects.
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Affiliation(s)
- Jonathan Grandaubert
- Environmental Genomics GroupMax Planck Institute for Evolutionary BiologyAugust‐Thienemann‐Str. 224306PlönGermany
- Christian‐Albrechts University of KielAm Botanischen Garten 1–924118KielGermany
| | - Julien Y. Dutheil
- Research group Molecular Systems EvolutionMax Planck Institute for Evolutionary BiologyAugust‐Thienemann‐Str. 224306PlönGermany
- UMR 5554 Institut des Sciences de l'Evolution, CNRS, IRD, EPHEUniversité de MontpellierPlace E. Bataillon34095MontpellierFrance
| | - Eva H. Stukenbrock
- Environmental Genomics GroupMax Planck Institute for Evolutionary BiologyAugust‐Thienemann‐Str. 224306PlönGermany
- Christian‐Albrechts University of KielAm Botanischen Garten 1–924118KielGermany
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135
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Bradshaw RE, Sim AD, Chettri P, Dupont P, Guo Y, Hunziker L, McDougal RL, Van der Nest A, Fourie A, Wheeler D, Cox MP, Barnes I. Global population genomics of the forest pathogen Dothistroma septosporum reveal chromosome duplications in high dothistromin-producing strains. MOLECULAR PLANT PATHOLOGY 2019; 20:784-799. [PMID: 30938073 PMCID: PMC6637865 DOI: 10.1111/mpp.12791] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Dothistroma needle blight is one of the most devastating pine tree diseases worldwide. New and emerging epidemics have been frequent over the last 25 years, particularly in the Northern Hemisphere, where they are in part associated with changing weather patterns. One of the main Dothistroma needle blight pathogens, Dothistroma septosporum, has a global distribution but most molecular plant pathology research has been confined to Southern Hemisphere populations that have limited genetic diversity. Extensive genomic and transcriptomic data are available for a D. septosporum reference strain from New Zealand, where an introduced clonal population of the pathogen predominates. Due to the global importance of this pathogen, we determined whether the genome of this reference strain is representative of the species worldwide by sequencing the genomes of 18 strains sampled globally from different pine hosts. Genomic polymorphism shows substantial variation within the species, clustered into two distinct groups of strains with centres of diversity in Central and South America. A reciprocal chromosome translocation uniquely identifies the New Zealand strains. Globally, strains differ in their production of the virulence factor dothistromin, with extremely high production levels in strain ALP3 from Germany. Comparisons with the New Zealand reference revealed that several strains are aneuploids; for example, ALP3 has duplications of three chromosomes. Increased gene copy numbers therefore appear to contribute to increased production of dothistromin, emphasizing that studies of population structure are a necessary adjunct to functional analyses of genetic polymorphisms to identify the molecular basis of virulence in this important forest pathogen.
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Affiliation(s)
- Rosie E. Bradshaw
- School of Fundamental Sciences and Bio‐Protection Research CentreMassey UniversityPalmerston North4410New Zealand
| | - Andre D. Sim
- School of Fundamental Sciences and Bio‐Protection Research CentreMassey UniversityPalmerston North4410New Zealand
| | - Pranav Chettri
- School of Fundamental Sciences and Bio‐Protection Research CentreMassey UniversityPalmerston North4410New Zealand
| | - Pierre‐Yves Dupont
- School of Fundamental Sciences and Bio‐Protection Research CentreMassey UniversityPalmerston North4410New Zealand
- Institute of Environmental Science and ResearchChristchurch8041New Zealand
| | - Yanan Guo
- School of Fundamental Sciences and Bio‐Protection Research CentreMassey UniversityPalmerston North4410New Zealand
| | - Lukas Hunziker
- School of Fundamental Sciences and Bio‐Protection Research CentreMassey UniversityPalmerston North4410New Zealand
| | | | - Ariska Van der Nest
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI)University of PretoriaPretoriaSouth Africa
| | - Arista Fourie
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI)University of PretoriaPretoriaSouth Africa
| | - David Wheeler
- School of Fundamental Sciences and Bio‐Protection Research CentreMassey UniversityPalmerston North4410New Zealand
- NSW Department of Primary IndustriesOrange Agricultural InstituteAustralia
| | - Murray P. Cox
- School of Fundamental Sciences and Bio‐Protection Research CentreMassey UniversityPalmerston North4410New Zealand
| | - Irene Barnes
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI)University of PretoriaPretoriaSouth Africa
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136
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Jehangir M, Ahmad SF, Cardoso AL, Ramos E, Valente GT, Martins C. De novo genome assembly of the cichlid fish Astatotilapia latifasciata reveals a higher level of genomic polymorphism and genes related to B chromosomes. Chromosoma 2019; 128:81-96. [PMID: 31115663 DOI: 10.1007/s00412-019-00707-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 02/27/2019] [Accepted: 05/07/2019] [Indexed: 12/15/2022]
Abstract
Supernumerary B chromosomes (Bs) are accessory elements to the regular chromosome set (As) and have been observed in a huge diversity of eukaryotic species. Although extensively investigated, the biological significance of Bs remains enigmatic. Here, we present de novo genome assemblies for the cichlid fish Astatotilapia latifasciata, a well-known model to study Bs. High coverage data with Illumina sequencing was obtained for males and females with 0B (B-), 1B, and 2B (B+) chromosomes to provide information regarding the diversity among these genomes. The draft assemblies comprised 771 Mb for the B- genome and 781 Mb for the B+ genome. Comparative analysis of the B+ and B- assemblies reveals syntenic discontinuity, duplicated blocks and several insertions, deletions, and inversions indicative of rearrangements in the B+ genome. Hundreds of transposable elements and 1546 protein coding sequences were annotated in the duplicated B+ regions. Our work contributes a list of thousands of genes harbored on the B chromosome, with functions in several biological processes, including the cell cycle.
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Affiliation(s)
- Maryam Jehangir
- Department of Morphology, Institute of Bioscience at Botucatu, São Paulo State University - UNESP, Botucatu, SP, 18618-689, Brazil
| | - Syed F Ahmad
- Department of Morphology, Institute of Bioscience at Botucatu, São Paulo State University - UNESP, Botucatu, SP, 18618-689, Brazil
| | - Adauto L Cardoso
- Department of Morphology, Institute of Bioscience at Botucatu, São Paulo State University - UNESP, Botucatu, SP, 18618-689, Brazil
| | - Erica Ramos
- Department of Morphology, Institute of Bioscience at Botucatu, São Paulo State University - UNESP, Botucatu, SP, 18618-689, Brazil
| | - Guilherme T Valente
- Bioprocess and Biotechnology Department, Agronomical Science Faculty, Sao Paulo State University - UNESP, Botucatu, SP, Brazil
| | - Cesar Martins
- Department of Morphology, Institute of Bioscience at Botucatu, São Paulo State University - UNESP, Botucatu, SP, 18618-689, Brazil.
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137
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van der Nest MA, Steenkamp ET, Roodt D, Soal NC, Palmer M, Chan WY, Wilken PM, Duong TA, Naidoo K, Santana QC, Trollip C, De Vos L, van Wyk S, McTaggart AR, Wingfield MJ, Wingfield BD. Genomic analysis of the aggressive tree pathogen Ceratocystis albifundus. Fungal Biol 2019; 123:351-363. [PMID: 31053324 DOI: 10.1016/j.funbio.2019.02.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 02/08/2019] [Accepted: 02/11/2019] [Indexed: 12/13/2022]
Abstract
The overall goal of this study was to determine whether the genome of an important plant pathogen in Africa, Ceratocystis albifundus, is structured into subgenomic compartments, and if so, to establish how these compartments are distributed across the genome. For this purpose, the publicly available genome of C. albifundus was complemented with the genome sequences for four additional isolates using the Illumina HiSeq platform. In addition, a reference genome for one of the individuals was assembled using both PacBio and Illumina HiSeq technologies. Our results showed a high degree of synteny between the five genomes, although several regions lacked detectable long-range synteny. These regions were associated with the presence of accessory genes, lower genetic similarity, variation in read-map depth, as well as transposable elements and genes associated with host-pathogen interactions (e.g. effectors and CAZymes). Such patterns are regarded as hallmarks of accelerated evolution, particularly of accessory subgenomic compartments in fungal pathogens. Our findings thus showed that the genome of C. albifundus is made-up of core and accessory subgenomic compartments, which is an important step towards characterizing its pangenome. This study also highlights the value of comparative genomics for understanding mechanisms that may underly and influence the biology and evolution of pathogens.
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Affiliation(s)
- Magriet A van der Nest
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa.
| | - Emma T Steenkamp
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Danielle Roodt
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Nicole C Soal
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Marike Palmer
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Wai-Yin Chan
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - P Markus Wilken
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Tuan A Duong
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Kershney Naidoo
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Quentin C Santana
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Conrad Trollip
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Lieschen De Vos
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Stephanie van Wyk
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Alistair R McTaggart
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Michael J Wingfield
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Brenda D Wingfield
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
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138
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Möller M, Schotanus K, Soyer JL, Haueisen J, Happ K, Stralucke M, Happel P, Smith KM, Connolly LR, Freitag M, Stukenbrock EH. Destabilization of chromosome structure by histone H3 lysine 27 methylation. PLoS Genet 2019; 15:e1008093. [PMID: 31009462 PMCID: PMC6510446 DOI: 10.1371/journal.pgen.1008093] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2018] [Revised: 05/10/2019] [Accepted: 03/15/2019] [Indexed: 01/23/2023] Open
Abstract
Chromosome and genome stability are important for normal cell function as instability often correlates with disease and dysfunction of DNA repair mechanisms. Many organisms maintain supernumerary or accessory chromosomes that deviate from standard chromosomes. The pathogenic fungus Zymoseptoria tritici has as many as eight accessory chromosomes, which are highly unstable during meiosis and mitosis, transcriptionally repressed, show enrichment of repetitive elements, and enrichment with heterochromatic histone methylation marks, e.g., trimethylation of H3 lysine 9 or lysine 27 (H3K9me3, H3K27me3). To elucidate the role of heterochromatin on genome stability in Z. tritici, we deleted the genes encoding the methyltransferases responsible for H3K9me3 and H3K27me3, kmt1 and kmt6, respectively, and generated a double mutant. We combined experimental evolution and genomic analyses to determine the impact of these deletions on chromosome and genome stability, both in vitro and in planta. We used whole genome sequencing, ChIP-seq, and RNA-seq to compare changes in genome and chromatin structure, and differences in gene expression between mutant and wildtype strains. Analyses of genome and ChIP-seq data in H3K9me3-deficient strains revealed dramatic chromatin reorganization, where H3K27me3 is mostly relocalized into regions that are enriched with H3K9me3 in wild type. Many genome rearrangements and formation of new chromosomes were found in the absence of H3K9me3, accompanied by activation of transposable elements. In stark contrast, loss of H3K27me3 actually increased the stability of accessory chromosomes under normal growth conditions in vitro, even without large scale changes in gene activity. We conclude that H3K9me3 is important for the maintenance of genome stability because it disallows H3K27me3 in regions considered constitutive heterochromatin. In this system, H3K27me3 reduces the overall stability of accessory chromosomes, generating a "metastable" state for these quasi-essential regions of the genome.
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Affiliation(s)
- Mareike Möller
- Environmental Genomics, Christian-Albrechts University, Kiel, Germany
- Max Planck Fellow Group Environmental Genomics, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Klaas Schotanus
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC, United States of America
| | - Jessica L. Soyer
- UMR BIOGER, INRA, AgroParisTech, Université Paris-Saclay, Thiverval-Grignon, France
| | - Janine Haueisen
- Environmental Genomics, Christian-Albrechts University, Kiel, Germany
- Max Planck Fellow Group Environmental Genomics, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Kathrin Happ
- Environmental Genomics, Christian-Albrechts University, Kiel, Germany
| | - Maja Stralucke
- Environmental Genomics, Christian-Albrechts University, Kiel, Germany
| | - Petra Happel
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Kristina M. Smith
- Department of Biology, Oregon State University—Cascades, Bend, OR, United States of America
| | - Lanelle R. Connolly
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR, United States of America
| | - Michael Freitag
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR, United States of America
| | - Eva H. Stukenbrock
- Environmental Genomics, Christian-Albrechts University, Kiel, Germany
- Max Planck Fellow Group Environmental Genomics, Max Planck Institute for Evolutionary Biology, Plön, Germany
- * E-mail:
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139
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Anasontzis GE, Lebrun MH, Haon M, Champion C, Kohler A, Lenfant N, Martin F, O'Connell RJ, Riley R, Grigoriev IV, Henrissat B, Berrin JG, Rosso MN. Broad-specificity GH131 β-glucanases are a hallmark of fungi and oomycetes that colonize plants. Environ Microbiol 2019; 21:2724-2739. [PMID: 30887618 DOI: 10.1111/1462-2920.14596] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 02/17/2019] [Accepted: 03/17/2019] [Indexed: 12/21/2022]
Abstract
Plant-tissue-colonizing fungi fine-tune the deconstruction of plant-cell walls (PCW) using different sets of enzymes according to their lifestyle. However, some of these enzymes are conserved among fungi with dissimilar lifestyles. We identified genes from Glycoside Hydrolase family GH131 as commonly expressed during plant-tissue colonization by saprobic, pathogenic and symbiotic fungi. By searching all the publicly available genomes, we found that GH131-coding genes were widely distributed in the Dikarya subkingdom, except in Taphrinomycotina and Saccharomycotina, and in phytopathogenic Oomycetes, but neither other eukaryotes nor prokaryotes. The presence of GH131 in a species was correlated with its association with plants as symbiont, pathogen or saprobe. We propose that GH131-family expansions and horizontal-gene transfers contributed to this adaptation. We analysed the biochemical activities of GH131 enzymes whose genes were upregulated during plant-tissue colonization in a saprobe (Pycnoporus sanguineus), a plant symbiont (Laccaria bicolor) and three hemibiotrophic-plant pathogens (Colletotrichum higginsianum, C. graminicola, Zymoseptoria tritici). These enzymes were all active on substrates with β-1,4, β-1,3 and mixed β-1,4/1,3 glucosidic linkages. Combined with a cellobiohydrolase, GH131 enzymes enhanced cellulose degradation. We propose that secreted GH131 enzymes unlock the PCW barrier and allow further deconstruction by other enzymes during plant tissue colonization by symbionts, pathogens and saprobes.
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Affiliation(s)
- George E Anasontzis
- INRA, Aix-Marseille Univ, UMR1163, Biodiversité et Biotechnologie Fongiques, BBF, Marseille, France.,CNRS, Aix-Marseille Univ, UMR7257, Architecture et Fonction des Macromolecules Biologiques, Marseille, France
| | - Marc-Henri Lebrun
- INRA, AgroParisTech, Université Paris-Saclay, BIOGER, Thiverval-Grignon, France
| | - Mireille Haon
- INRA, Aix-Marseille Univ, UMR1163, Biodiversité et Biotechnologie Fongiques, BBF, Marseille, France
| | - Charlotte Champion
- INRA, Aix-Marseille Univ, UMR1163, Biodiversité et Biotechnologie Fongiques, BBF, Marseille, France
| | - Annegret Kohler
- INRA, University of Lorraine, Laboratory of Excellence Advanced Research on the Biology of Tree and Forest Ecosystems (ARBRE), UMR 1136, Champenoux, France
| | - Nicolas Lenfant
- CNRS, Aix-Marseille Univ, UMR7257, Architecture et Fonction des Macromolecules Biologiques, Marseille, France
| | - Francis Martin
- INRA, University of Lorraine, Laboratory of Excellence Advanced Research on the Biology of Tree and Forest Ecosystems (ARBRE), UMR 1136, Champenoux, France
| | - Richard J O'Connell
- INRA, AgroParisTech, Université Paris-Saclay, BIOGER, Thiverval-Grignon, France
| | - Robert Riley
- US Department of Energy Joint Genome Institute (JGI), Walnut Creek, CA, 94598, USA
| | - Igor V Grigoriev
- US Department of Energy Joint Genome Institute (JGI), Walnut Creek, CA, 94598, USA.,Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, 94598, USA
| | - Bernard Henrissat
- CNRS, Aix-Marseille Univ, UMR7257, Architecture et Fonction des Macromolecules Biologiques, Marseille, France.,INRA, USC 1408, AFMB, Marseille, France
| | - Jean-Guy Berrin
- INRA, Aix-Marseille Univ, UMR1163, Biodiversité et Biotechnologie Fongiques, BBF, Marseille, France
| | - Marie-Noëlle Rosso
- INRA, Aix-Marseille Univ, UMR1163, Biodiversité et Biotechnologie Fongiques, BBF, Marseille, France
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140
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Wheeler DL, Dung JKS, Johnson DA. From pathogen to endophyte: an endophytic population of Verticillium dahliae evolved from a sympatric pathogenic population. THE NEW PHYTOLOGIST 2019; 222:497-510. [PMID: 30372525 DOI: 10.1111/nph.15567] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 10/18/2018] [Indexed: 05/27/2023]
Abstract
The fungus Verticillium dahliae causes wilts of several hundred plant species, including potato and mint. Verticillium spp. also colonize sympatric hosts such as mustards and grasses as endophytes. The evolutionary history of and interactions between pathogenic and endophytic of this fungus are unknown. Verticillium dahliae isolates recovered from sympatric potato, mint, mustard and grasses were characterized genotypically with microsatellite markers and phenotypically for pathogenicity. The evolutionary history of pathogenic and endophytic populations was reconstructed and gene flow between populations quantified. Verticillium dahliae was recovered from all hosts. Endophytic populations were genetically and genotypically similar to but marginally differentiated from the potato population, from which they evolved. Bidirectional migration was detected between these populations and endophytic isolates were pathogenic to potato and behaved as endophytes in mustard and barley. Verticillium dahliae colonizes plants as both endophytes and pathogens. A historical host-range expansion together with endophytic and pathogenic capabilities are likely to have enabled infection of and gene flow between asymptomatic and symptomatic host populations despite minor differentiation. The ability of hosts to harbor asymptomatic infections and the stability of asymptomatic infections over time warrants investigation to elucidate the mechanisms involved in the maintenance of endophytism and pathogenesis.
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Affiliation(s)
| | - Jeremiah Kam Sung Dung
- Department of Botany and Plant Pathology, Oregon State University, Madras, OR, 97741, USA
| | - Dennis Allen Johnson
- Department of Plant Pathology, Washington State University, Pullman, WA, 99164, USA
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141
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Decoupling a novel Trichormus variabilis-Synechocystis sp. interaction to boost phycoremediation. Sci Rep 2019; 9:2511. [PMID: 30792472 PMCID: PMC6385349 DOI: 10.1038/s41598-019-38997-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 12/18/2018] [Indexed: 11/24/2022] Open
Abstract
To conserve freshwater resources, domestic and industrial wastewater is recycled. Algal systems have emerged as an efficient, low-cost option for treatment (phycoremediation) of nutrient-rich wastewater and environmental protection. However, industrial wastewater may contain growth inhibitory compounds precluding algal use in phycoremediation. Therefore, extremophyte strains, which thrive in hostile environments, are sought-after. Here, we isolated such an alga - a strain of Synechocystis sp. we found to be capable of switching from commensal exploitation of the nitrogen-fixing Trichormus variabilis, for survival in nitrogen-deficient environments, to free-living growth in nitrate abundance. In nitrogen depletion, the cells are tethered to polysaccharide capsules of T. variabilis using nanotubular structures, presumably for nitrate acquisition. The composite culture failed to establish in industrial/domestic waste effluent. However, gradual exposure to increasing wastewater strength over time untethered Synechocystis cells and killed off T. variabilis. This switched the culture to a stress-acclimated monoculture of Synechocystis sp., which rapidly grew and flourished in wastewater, with ammonium and phosphate removal efficiencies of 99.4% and 97.5%, respectively. Therefore, this strain of Synechocystis sp. shows great promise for use in phycoremediation, with potential to rapidly generate biomass that can find use as a green feedstock for valuable bio-products in industrial applications.
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142
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Dalla Benetta E, Akbari OS, Ferree PM. Sequence Expression of Supernumerary B Chromosomes: Function or Fluff? Genes (Basel) 2019; 10:E123. [PMID: 30744010 PMCID: PMC6409846 DOI: 10.3390/genes10020123] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Revised: 02/01/2019] [Accepted: 02/05/2019] [Indexed: 12/25/2022] Open
Abstract
B chromosomes are enigmatic heritable elements found in the genomes of numerous plant and animal species. Contrary to their broad distribution, most B chromosomes are non-essential. For this reason, they are regarded as genome parasites. In order to be stably transmitted through generations, many B chromosomes exhibit the ability to "drive", i.e., they transmit themselves at super-Mendelian frequencies to progeny through directed interactions with the cell division apparatus. To date, very little is understood mechanistically about how B chromosomes drive, although a likely scenario is that expression of B chromosome sequences plays a role. Here, we highlight a handful of previously identified B chromosome sequences, many of which are repetitive and non-coding in nature, that have been shown to be expressed at the transcriptional level. We speculate on how each type of expressed sequence could participate in B chromosome drive based on known functions of RNA in general chromatin- and chromosome-related processes. We also raise some challenges to functionally testing these possible roles, a goal that will be required to more fully understand whether and how B chromosomes interact with components of the cell for drive and transmission.
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Affiliation(s)
- Elena Dalla Benetta
- W. M. Keck Science Department of Claremont McKenna, Pitzer, and Scripps Colleges, Claremont, CA 91711, USA.
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA 92093, USA.
| | - Omar S Akbari
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA 92093, USA.
| | - Patrick M Ferree
- W. M. Keck Science Department of Claremont McKenna, Pitzer, and Scripps Colleges, Claremont, CA 91711, USA.
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143
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Haueisen J, Möller M, Eschenbrenner CJ, Grandaubert J, Seybold H, Adamiak H, Stukenbrock EH. Highly flexible infection programs in a specialized wheat pathogen. Ecol Evol 2019; 9:275-294. [PMID: 30680113 PMCID: PMC6342133 DOI: 10.1002/ece3.4724] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Revised: 10/04/2018] [Accepted: 10/05/2018] [Indexed: 12/21/2022] Open
Abstract
Many filamentous plant pathogens exhibit high levels of genomic variability, yet the impact of this variation on host-pathogen interactions is largely unknown. We have addressed host specialization in the wheat pathogen Zymoseptoria tritici. Our study builds on comparative analyses of infection and gene expression phenotypes of three isolates and reveals the extent to which genomic variation translates into phenotypic variation. The isolates exhibit genetic and genomic variation but are similarly virulent. By combining confocal microscopy, disease monitoring, staining of ROS, and comparative transcriptome analyses, we conducted a detailed comparison of the infection processes of these isolates in a susceptible wheat cultivar. We characterized four core infection stages: establishment, biotrophic growth, lifestyle transition, and necrotrophic growth and asexual reproduction that are shared by the three isolates. However, we demonstrate differentiated temporal and spatial infection development and significant differences in the expression profiles of the three isolates during the infection stages. More than 20% of the genes were differentially expressed and these genes were located significantly closer to transposable elements, suggesting an impact of epigenetic regulation. Further, differentially expressed genes were enriched in effector candidates suggesting that isolate-specific strategies for manipulating host defenses are present in Z. tritici. We demonstrate that individuals of a host-specialized pathogen have highly differentiated infection programs characterized by flexible infection development and functional redundancy. This illustrates how high genetic diversity in pathogen populations results in highly differentiated infection phenotypes, which fact needs to be acknowledged to understand host-pathogen interactions and pathogen evolution.
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Affiliation(s)
- Janine Haueisen
- Environmental Genomics GroupMax Planck Institute for Evolutionary BiologyPlönGermany
- Environmental Genomics GroupChristian‐Albrechts University KielKielGermany
| | - Mareike Möller
- Environmental Genomics GroupMax Planck Institute for Evolutionary BiologyPlönGermany
- Environmental Genomics GroupChristian‐Albrechts University KielKielGermany
| | - Christoph J. Eschenbrenner
- Environmental Genomics GroupMax Planck Institute for Evolutionary BiologyPlönGermany
- Environmental Genomics GroupChristian‐Albrechts University KielKielGermany
| | - Jonathan Grandaubert
- Environmental Genomics GroupMax Planck Institute for Evolutionary BiologyPlönGermany
- Fungal Biology and PathogenicityInstitute PasteurParisFrance
| | - Heike Seybold
- Environmental Genomics GroupMax Planck Institute for Evolutionary BiologyPlönGermany
- Environmental Genomics GroupChristian‐Albrechts University KielKielGermany
| | - Holger Adamiak
- Environmental Genomics GroupChristian‐Albrechts University KielKielGermany
| | - Eva H. Stukenbrock
- Environmental Genomics GroupMax Planck Institute for Evolutionary BiologyPlönGermany
- Environmental Genomics GroupChristian‐Albrechts University KielKielGermany
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144
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Habig M, Kema GHJ, Holtgrewe Stukenbrock E. Meiotic drive of female-inherited supernumerary chromosomes in a pathogenic fungus. eLife 2018; 7:e40251. [PMID: 30543518 PMCID: PMC6331196 DOI: 10.7554/elife.40251] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 12/13/2018] [Indexed: 01/03/2023] Open
Abstract
Meiosis is a key cellular process of sexual reproduction that includes pairing of homologous sequences. In many species however, meiosis can also involve the segregation of supernumerary chromosomes, which can lack a homolog. How these unpaired chromosomes undergo meiosis is largely unknown. In this study we investigated chromosome segregation during meiosis in the haploid fungus Zymoseptoria tritici that possesses a large complement of supernumerary chromosomes. We used isogenic whole chromosome deletion strains to compare meiotic transmission of chromosomes when paired and unpaired. Unpaired chromosomes inherited from the male parent as well as paired supernumerary chromosomes in general showed Mendelian inheritance. In contrast, unpaired chromosomes inherited from the female parent showed non-Mendelian inheritance but were amplified and transmitted to all meiotic products. We concluded that the supernumerary chromosomes of Z. tritici show a meiotic drive and propose an additional feedback mechanism during meiosis, which initiates amplification of unpaired female-inherited chromosomes.
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Affiliation(s)
- Michael Habig
- Environmental GenomicsChristian-Albrechts University of KielKielGermany
- Max Planck Institute for Evolutionary BiologyPlönGermany
| | - Gert HJ Kema
- Wageningen Plant ResearchWageningen University and ResearchWageningenThe Netherlands
- Laboratory of PhytopathologyWageningen University and ResearchWageningenThe Netherlands
| | - Eva Holtgrewe Stukenbrock
- Environmental GenomicsChristian-Albrechts University of KielKielGermany
- Max Planck Institute for Evolutionary BiologyPlönGermany
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145
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Maxwell CS, Mattox K, Turissini DA, Teixeira MM, Barker BM, Matute DR. Gene exchange between two divergent species of the fungal human pathogen, Coccidioides. Evolution 2018; 73:42-58. [PMID: 30414183 DOI: 10.1111/evo.13643] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Revised: 10/15/2018] [Accepted: 10/18/2018] [Indexed: 12/12/2022]
Abstract
The fungal genus Coccidioides is composed of two species, Coccidioides immitis and Coccidioides posadasii. These two species are the causal agents of coccidioidomycosis, a pulmonary disease also known as valley fever. The two species are thought to have shared genetic material due to gene exchange in spite of their long divergence. To quantify the magnitude of shared ancestry between them, we analyzed the genomes of a population sample from each species. Next, we inferred what is the expected size of shared haplotypes that might be inherited from the last common ancestor of the two species and find a cutoff to find what haplotypes have conclusively been exchanged between species. Finally, we precisely identified the breakpoints of the haplotypes that have crossed the species boundary and measure the allele frequency of each introgression in this sample. We find that introgressions are not uniformly distributed across the genome. Most, but not all, of the introgressions segregate at low frequency. Our results show that divergent species can share alleles, that species boundaries can be porous, and highlight the need for a systematic exploration of gene exchange in fungal species.
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Affiliation(s)
- Colin S Maxwell
- Biology Department, University of North Carolina, Chapel Hill, North Carolina
| | - Kathleen Mattox
- Biology Department, University of North Carolina, Chapel Hill, North Carolina
| | - David A Turissini
- Biology Department, University of North Carolina, Chapel Hill, North Carolina
| | - Marcus M Teixeira
- Núcleo de Medicina Tropical, Faculdade de Medicina, University of Brasília, Brasília, Brazil
| | - Bridget M Barker
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona
| | - Daniel R Matute
- Biology Department, University of North Carolina, Chapel Hill, North Carolina
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146
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Chen ECH, Morin E, Beaudet D, Noel J, Yildirir G, Ndikumana S, Charron P, St-Onge C, Giorgi J, Krüger M, Marton T, Ropars J, Grigoriev IV, Hainaut M, Henrissat B, Roux C, Martin F, Corradi N. High intraspecific genome diversity in the model arbuscular mycorrhizal symbiont Rhizophagus irregularis. THE NEW PHYTOLOGIST 2018; 220:1161-1171. [PMID: 29355972 DOI: 10.1111/nph.14989] [Citation(s) in RCA: 126] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Accepted: 12/03/2017] [Indexed: 05/20/2023]
Abstract
Arbuscular mycorrhizal fungi (AMF) are known to improve plant fitness through the establishment of mycorrhizal symbioses. Genetic and phenotypic variations among closely related AMF isolates can significantly affect plant growth, but the genomic changes underlying this variability are unclear. To address this issue, we improved the genome assembly and gene annotation of the model strain Rhizophagus irregularis DAOM197198, and compared its gene content with five isolates of R. irregularis sampled in the same field. All isolates harbor striking genome variations, with large numbers of isolate-specific genes, gene family expansions, and evidence of interisolate genetic exchange. The observed variability affects all gene ontology terms and PFAM protein domains, as well as putative mycorrhiza-induced small secreted effector-like proteins and other symbiosis differentially expressed genes. High variability is also found in active transposable elements. Overall, these findings indicate a substantial divergence in the functioning capacity of isolates harvested from the same field, and thus their genetic potential for adaptation to biotic and abiotic changes. Our data also provide a first glimpse into the genome diversity that resides within natural populations of these symbionts, and open avenues for future analyses of plant-AMF interactions that link AMF genome variation with plant phenotype and fitness.
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Affiliation(s)
- Eric C H Chen
- Department of Biology, University of Ottawa, Ottawa, ON, K1N9A7, Canada
| | - Emmanuelle Morin
- Institut National de la Recherche Agronomique (INRA), Unité Mixte de Recherche 1136 Interactions Arbres/Microorganismes, Laboratoire D'excellence Recherches Avancées sur la Biologie de l'Arbre et les Ecosystèmes Forestiers (ARBRE), Centre INRA-Grand Est-Nancy, Champenoux, 54280, France
| | - Denis Beaudet
- Department of Biology, University of Ottawa, Ottawa, ON, K1N9A7, Canada
| | - Jessica Noel
- Department of Biology, University of Ottawa, Ottawa, ON, K1N9A7, Canada
| | - Gokalp Yildirir
- Department of Biology, University of Ottawa, Ottawa, ON, K1N9A7, Canada
| | - Steve Ndikumana
- Department of Biology, University of Ottawa, Ottawa, ON, K1N9A7, Canada
| | - Philippe Charron
- Department of Biology, University of Ottawa, Ottawa, ON, K1N9A7, Canada
| | - Camille St-Onge
- Department of Biology, University of Ottawa, Ottawa, ON, K1N9A7, Canada
| | - John Giorgi
- Department of Biology, University of Ottawa, Ottawa, ON, K1N9A7, Canada
| | - Manuela Krüger
- Department of Biology, University of Ottawa, Ottawa, ON, K1N9A7, Canada
| | - Timea Marton
- Department of Biology, University of Ottawa, Ottawa, ON, K1N9A7, Canada
| | - Jeanne Ropars
- Department of Biology, University of Ottawa, Ottawa, ON, K1N9A7, Canada
| | - Igor V Grigoriev
- US Department of Energy Joint Genome Institute (JGI), Walnut Creek, CA, 94598, USA
| | - Matthieu Hainaut
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille Université, Marseille, 13288, France
- INRA, USC 1408 AFMB, Marseille, F-13288, France
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille Université, Marseille, 13288, France
- INRA, USC 1408 AFMB, Marseille, F-13288, France
- Department of Biological Sciences, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
| | - Christophe Roux
- Laboratoire de Recherche en Sciences Végétales, UPS, CNRS 24 Chemin de Borde Rouge-Auzeville, Université de Toulouse, Castanet-Tolosan, 31326, France
| | - Francis Martin
- Institut National de la Recherche Agronomique (INRA), Unité Mixte de Recherche 1136 Interactions Arbres/Microorganismes, Laboratoire D'excellence Recherches Avancées sur la Biologie de l'Arbre et les Ecosystèmes Forestiers (ARBRE), Centre INRA-Grand Est-Nancy, Champenoux, 54280, France
| | - Nicolas Corradi
- Department of Biology, University of Ottawa, Ottawa, ON, K1N9A7, Canada
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147
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Stam R, Münsterkötter M, Pophaly SD, Fokkens L, Sghyer H, Güldener U, Hückelhoven R, Hess M. A New Reference Genome Shows the One-Speed Genome Structure of the Barley Pathogen Ramularia collo-cygni. Genome Biol Evol 2018; 10:3243-3249. [PMID: 30371775 PMCID: PMC6301796 DOI: 10.1093/gbe/evy240] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/26/2018] [Indexed: 01/17/2023] Open
Abstract
Ramularia leaf spot has recently emerged as a major threat to barley production world-wide, causing 25% yield loss in many barley growing regions. Here, we provide a new reference genome of the causal agent, the Dothideomycete Ramularia collo-cygni. The assembly of 32 Mb consists of 78 scaffolds. We used RNA-seq to identify 11,622 genes of which 1,303 and 282 are coding for predicted secreted proteins and putative effectors respectively. The pathogen separated from its nearest sequenced relative, Zymoseptoria tritici ∼27 Ma. We calculated the divergence of the two species on protein level and see remarkably high synonymous and nonsynonymous divergence. Unlike in many other plant pathogens, the comparisons of transposable elements and gene distributions, show a very homogeneous genome for R. collo-cygni. We see no evidence for higher selective pressure on putative effectors or other secreted proteins and repetitive sequences are spread evenly across the scaffolds. These findings could be associated to the predominantly endophytic life-style of the pathogen. We hypothesize that R. collo-cygni only recently became pathogenic and that therefore its genome does not yet show the typical pathogen characteristics. Because of its high scaffold length and improved CDS annotations, our new reference sequence provides a valuable resource for the community for future comparative genomics and population genetics studies.
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Affiliation(s)
- Remco Stam
- Chair of Phytopathology, School of Life Sciences Weihenstephan, Technische University Munich, Germany
| | - Martin Münsterkötter
- Functional Genomics and Bioinformatics, Research Centre for Forestry and Wood Industry, University of Sopron, Hungary.,Institute of Bioinformatics and Systems Biology, Helmholtz Centre Munich, Germany
| | - Saurabh Dilip Pophaly
- Section of Population Genetics, School of Life Sciences Weihenstephan, Technische Universität München, Germany.,Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Sweden and Division of Evolutionary Biology, Faculty of Biology II, Ludwig-Maximilians-Universität München, Germany
| | - Like Fokkens
- Molecular Plant Pathology, Swammerdam Institute for Life Sciences, University of Amsterdam, The Netherlands
| | - Hind Sghyer
- Chair of Phytopathology, School of Life Sciences Weihenstephan, Technische University Munich, Germany
| | - Ulrich Güldener
- Department of Bioinformatics, School of Life Sciences Weihenstephan, Technische University Munich, Germany
| | - Ralph Hückelhoven
- Chair of Phytopathology, School of Life Sciences Weihenstephan, Technische University Munich, Germany
| | - Michael Hess
- Chair of Phytopathology, School of Life Sciences Weihenstephan, Technische University Munich, Germany
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148
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Derbyshire MC, Gohari AM, Mehrabi R, Kilaru S, Steinberg G, Ali S, Bailey A, Hammond-Kosack K, Kema GHJ, Rudd JJ. Phosphopantetheinyl transferase (Ppt)-mediated biosynthesis of lysine, but not siderophores or DHN melanin, is required for virulence of Zymoseptoria tritici on wheat. Sci Rep 2018; 8:17069. [PMID: 30459352 PMCID: PMC6244202 DOI: 10.1038/s41598-018-35223-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Accepted: 10/30/2018] [Indexed: 12/19/2022] Open
Abstract
Zymoseptoria tritici is the causal agent of Septoria tritici blotch (STB) disease of wheat. Z. tritici is an apoplastic fungal pathogen, which does not penetrate plant cells at any stage of infection, and has a long initial period of symptomless leaf colonisation. During this phase it is unclear to what extent the fungus can access host plant nutrients or communicate with plant cells. Several important primary and secondary metabolite pathways in fungi are regulated by the post-translational activator phosphopantetheinyl transferase (Ppt) which provides an essential co-factor for lysine biosynthesis and the activities of non-ribosomal peptide synthases (NRPS) and polyketide synthases (PKS). To investigate the relative importance of lysine biosynthesis, NRPS-based siderophore production and PKS-based DHN melanin biosynthesis, we generated deletion mutants of ZtPpt. The ∆ZtPpt strains were auxotrophic for lysine and iron, non-melanised and non-pathogenic on wheat. Deletion of the three target genes likely affected by ZtPpt loss of function (Aar- lysine; Nrps1-siderophore and Pks1- melanin), highlighted that lysine auxotrophy was the main contributing factor for loss of virulence, with no reduction caused by loss of siderophore production or melanisation. This reveals Ppt, and the lysine biosynthesis pathway, as potential targets for fungicides effective against Z. tritici.
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Affiliation(s)
- Mark C Derbyshire
- BioIntercations and Crop Protection, Rothamsted Research, Harpenden, Hertfordshire, UK.,Centre for Crop and Disease Management, Curtin University, Perth, Australia
| | - Amir Mirzadi Gohari
- Department of Plant Pathology, Faculty of Agricultural Sciences and Engineering, College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran.,Wageningen University and Research, Wageningen Plant Research, PO Box 16, 6700AA, Wageningen, The Netherlands
| | - Rahim Mehrabi
- Department of Biotechnology, College of Agriculture, Isfahan University of Technology, Isfahan, 84156-83111, Iran
| | | | | | - Solaf Ali
- Technical College of Health, Sulaimani Polytechnic University, Qrga, Wrme Street, Mardin 327, Alley 76, Sulaimaniyah, Kurdistan Region of Iraq, Sulaimani Governorate, Iraq
| | - Andy Bailey
- School of Biological Sciences, Bristol University, 24 Tyndall Avenue, Bristol, UK
| | - Kim Hammond-Kosack
- BioIntercations and Crop Protection, Rothamsted Research, Harpenden, Hertfordshire, UK
| | - Gert H J Kema
- Wageningen University and Research, Wageningen Plant Research, PO Box 16, 6700AA, Wageningen, The Netherlands. .,Wageningen University and Research, Laboratory of Phytopathology, PO box 16, 6700AA, Wageningen, The Netherlands.
| | - Jason J Rudd
- BioIntercations and Crop Protection, Rothamsted Research, Harpenden, Hertfordshire, UK.
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149
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150
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Winter DJ, Ganley ARD, Young CA, Liachko I, Schardl CL, Dupont PY, Berry D, Ram A, Scott B, Cox MP. Repeat elements organise 3D genome structure and mediate transcription in the filamentous fungus Epichloë festucae. PLoS Genet 2018; 14:e1007467. [PMID: 30356280 PMCID: PMC6218096 DOI: 10.1371/journal.pgen.1007467] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Revised: 11/05/2018] [Accepted: 08/27/2018] [Indexed: 11/18/2022] Open
Abstract
Structural features of genomes, including the three-dimensional arrangement of DNA in the nucleus, are increasingly seen as key contributors to the regulation of gene expression. However, studies on how genome structure and nuclear organisation influence transcription have so far been limited to a handful of model species. This narrow focus limits our ability to draw general conclusions about the ways in which three-dimensional structures are encoded, and to integrate information from three-dimensional data to address a broader gamut of biological questions. Here, we generate a complete and gapless genome sequence for the filamentous fungus, Epichloë festucae. We use Hi-C data to examine the three-dimensional organisation of the genome, and RNA-seq data to investigate how Epichloë genome structure contributes to the suite of transcriptional changes needed to maintain symbiotic relationships with the grass host. Our results reveal a genome in which very repeat-rich blocks of DNA with discrete boundaries are interspersed by gene-rich sequences that are almost repeat-free. In contrast to other species reported to date, the three-dimensional structure of the genome is anchored by these repeat blocks, which act to isolate transcription in neighbouring gene-rich regions. Genes that are differentially expressed in planta are enriched near the boundaries of these repeat-rich blocks, suggesting that their three-dimensional orientation partly encodes and regulates the symbiotic relationship formed by this organism.
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Affiliation(s)
- David J. Winter
- Statistics and Bioinformatics Group, Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand
- The Bio-Protection Research Centre, Massey University, Palmerston North, New Zealand
| | - Austen R. D. Ganley
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Carolyn A. Young
- Noble Research Institute, LLC, Ardmore, Oklahoma, United States of America
| | - Ivan Liachko
- Phase Genomics Inc, Seattle, Washington, United States of America
| | - Christopher L. Schardl
- Department of Plant Pathology, University of Kentucky, Lexington, Kentucky, United States of America
| | - Pierre-Yves Dupont
- Genetics Group, Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Daniel Berry
- Genetics Group, Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Arvina Ram
- Genetics Group, Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Barry Scott
- The Bio-Protection Research Centre, Massey University, Palmerston North, New Zealand
- Genetics Group, Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Murray P. Cox
- Statistics and Bioinformatics Group, Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand
- The Bio-Protection Research Centre, Massey University, Palmerston North, New Zealand
- * E-mail:
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