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1.
Arch Virol ; 165(4): 1011-1014, 2020 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-32040623

RESUMO

The complete genome of a novel fungal virus, Puccinia striiformis narnavirus 1 (PsNV1), was sequenced and analyzed. The full-length cDNA sequence is 2340 bp in length with a GC content of 50.04%. PsNV1 contains a single open reading frame (ORF), which encodes a putative RNA-dependent RNA polymerase (RdRp) of 741 amino acids with a molecular mass of 81.8 kDa. RdRp phylogeny showed that PsNV1 grouped together with Fusarium poae narnavirus 1 (FpNV1) as a sister branch of narnaviruses, forming a distinct clade. The results of genome sequence comparisons and phylogenetic analysis indicate that PsNV1 is a new member in the genus Narnavirus. To our knowledge, this is the first report of a narnavirus genome sequence in the obligately parasitic fungus Puccinia striiformis f. sp. tritici.


Assuntos
Basidiomycota/virologia , Micovírus/isolamento & purificação , Vírus de RNA/isolamento & purificação , Sequência de Bases , Basidiomycota/genética , Basidiomycota/isolamento & purificação , Basidiomycota/fisiologia , Micovírus/classificação , Micovírus/genética , Micovírus/fisiologia , Genoma Viral , Fases de Leitura Aberta , Filogenia , Doenças das Plantas/microbiologia , Vírus de RNA/classificação , Vírus de RNA/genética , Vírus de RNA/fisiologia , Triticum/microbiologia
2.
Mol Biotechnol ; 62(2): 132-141, 2020 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-31897972

RESUMO

A farnesyl diphosphate synthase (FPS) cDNA and promoter region was cloned from Sanghuangporus baumii. The gene contains a 150-bp 5'-untranslated region (UTR), a 154-bp 3'-UTR, and a 1062-bp open reading frame (ORF) encoding a 354 amino acid polypeptide. The FPS-DNA includes three exons (nucleotides 1 -123, 184-321, and 505-1305) and two introns (nucleotides 124-183 and 322-504). The FPS protein has a molecular weight of 40.73 kDa, it is hydrophilic with a theoretical isoelectric point of 5.13, and the secondary and three-dimensional structure were analysed. There is a transcription start site at nucleotides 1318-1368 of the promoter, which includes typical eukaryotic promoter elements (TATA Box, CAAT Box, ARBE, AT-rich element, G-box, MBS, Sp1, LTR). FPS was expressed in Escherichia coli BL21, and the recombinant protein (63.41 kDa) was subjected to dodecyl sulphate, sodium salt-polyacrylamide gel electrophoresis (SDS-PAGE). FPS transcription was measured during different developmental stages, and expression in 11 and 13 days mycelia was upregulated 49.3-fold and 125.4-fold, respectively, compared with 9 days mycelia controls. Through analysing, S. baumii triterpenoid content was correlated with the transcription level of FPS during different development stages, and the triterpenoid content peaked at day 15 (7.21 mg/g).


Assuntos
Basidiomycota/enzimologia , Geraniltranstransferase/metabolismo , Triterpenos/metabolismo , Regiões 3' não Traduzidas , Regiões 5' não Traduzidas , Sequência de Aminoácidos/genética , Basidiomycota/genética , Basidiomycota/crescimento & desenvolvimento , Clonagem Molecular , Escherichia coli , Éxons , Expressão Gênica , Geraniltranstransferase/química , Geraniltranstransferase/genética , Íntrons , Filogenia , Regiões Promotoras Genéticas , Proteínas Recombinantes/genética , Proteínas Recombinantes/metabolismo , Triterpenos/farmacologia
3.
PLoS One ; 15(1): e0227923, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-31978083

RESUMO

Genome sequencing of Tricholoma matsutake revealed its unusually large size as 189.0 Mbp, which is a consequence of extraordinarily high transposable element (TE) content. We identified that 702 genes were surrounded by TEs, and 83.2% of these genes were not transcribed at any developmental stage. This observation indicated that the insertion of TEs alters the transcription of the genes neighboring these TEs. Repeat-induced point mutation, such as C to T hypermutation with a bias over "CpG" dinucleotides, was also recognized in this genome, representing a typical defense mechanism against TEs during evolution. Many transcription factor genes were activated in both the primordia and fruiting body stages, which indicates that many regulatory processes are shared during the developmental stages. Small secreted protein genes (<300 aa) were dominantly transcribed in the hyphae, where symbiotic interactions occur with the hosts. Comparative analysis with 37 Agaricomycetes genomes revealed that IstB-like domains (PF01695) were conserved across taxonomically diverse mycorrhizal genomes, where the T. matsutake genome contained four copies of this domain. Three of the IstB-like genes were overexpressed in the hyphae. Similar to other ectomycorrhizal genomes, the CAZyme gene set was reduced in T. matsutake, including losses in the glycoside hydrolase genes. The T. matsutake genome sequence provides insight into the causes and consequences of genome size inflation.


Assuntos
Elementos de DNA Transponíveis/genética , Genoma Fúngico/genética , Transcrição Genética , Tricholoma/genética , Ascomicetos/genética , Basidiomycota/genética , Regulação Fúngica da Expressão Gênica/genética , Anotação de Sequência Molecular , Micorrizas/genética , Simbiose/genética , Sequenciamento Completo do Genoma
4.
Mol Biol Evol ; 37(1): 44-57, 2020 Jan 01.
Artigo em Inglês | MEDLINE | ID: mdl-31504747

RESUMO

The mitochondrial genomes (mitogenomes) of plants are known to incorporate and accumulate DNA from intra- and extracellular donors. Despite the intimate relationships formed between flowing plants (angiosperms) and fungi, lengthy fungal-like sequence has not been identified in angiosperm mitogenomes to date. Here, we present multiple lines of evidence documenting horizontal gene transfer (HGT) between the mitogenomes of fungi and the ancestors of the orchids, plants that are obligate parasites of fungi during their early development. We show that the ancestor of the orchids acquired an ∼270-bp fungal mitogenomic region containing three transfer RNA genes. We propose that the short HGT was later replaced by a second HGT event transferring >8 kb and 14 genes from a fungal mitogenome to that of the ancestor of the largest orchid subfamily, Epidendroideae. Our results represent the first evidence of genomic-scale HGT between fungal and angiosperm mitogenomes and demonstrate that the length intergenic spacer regions of angiosperm mitogenomes can effectively fossilize the genomic remains of ancient, nonplant organisms.


Assuntos
Basidiomycota/genética , Transferência Genética Horizontal , Genoma Mitocondrial , Orchidaceae/genética , Genoma de Planta , Filogenia , Análise de Sequência de RNA
5.
J Ind Microbiol Biotechnol ; 47(1): 145-154, 2020 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-31734813

RESUMO

Putative iron-reductase (IR) genes from Serpula lacrymans with similarity to the conserved iron-binding domains of cellobiose dehydrogenase (CDH) enzymes have been identified. These genes were cloned and expressed to functionally characterize their activity and role in the decomposition of lignocellulose. The results show that IR1 and IR2 recombinant enzymes have the ability to depolymerize both lignin and cellulose, are capable of the reduction of ferric iron to the ferrous form, and are capable of the degradation of nitrated lignin. Expression of these genes during wheat straw solid-state fermentation was shown to correlate with the release of compounds associated with lignin decomposition. The results suggest that both IR enzymes mediate a non-enzymatic depolymerisation of lignocellulose and highlight the potential of chelator-mediated Fenton systems in the industrial pre-treatment of biomass.


Assuntos
Basidiomycota/metabolismo , FMN Redutase/metabolismo , Lignina/metabolismo , Basidiomycota/genética , Fenômenos Bioquímicos , Fermentação , Triticum/metabolismo
6.
Biosci Biotechnol Biochem ; 84(3): 433-444, 2020 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-31738699

RESUMO

Ascomycota and basidiomycota fungi are prolific sources of biologically active natural products. Recent genomic data and bioinformatic analysis indicate that fungi possess a large number of biosynthetic gene clusters for bioactive natural products but more than 90% are silent. Heterologous expression in the filamentous fungi as hosts is one of the powerful tools to expression of the silent gene clusters. This review introduces recent studies on the total biosynthesis of representative family members via common platform intermediates, genome mining of novel di- and sesterterpenoids including detailed cyclization pathway, and development of expression host for basidiomycota genes with efficient genome editing method. In addition, this review will discuss the several strategies, for the generation of structural diversity, which are found through these studies.


Assuntos
Ascomicetos/metabolismo , Basidiomycota/metabolismo , Produtos Biológicos/metabolismo , Ascomicetos/genética , Basidiomycota/genética , Vias Biossintéticas/genética , Genes Fúngicos , Família Multigênica
7.
Ecotoxicol Environ Saf ; 188: 109935, 2020 Jan 30.
Artigo em Inglês | MEDLINE | ID: mdl-31740233

RESUMO

Chromium (Cr) is one of the most toxic heavy metals and a health hazard to millions of people worldwide. Ectomycorrhizal (ECM) fungi can assist plants in phytoremediation of heavy metal contaminated soil. Cr tolerance differs among ECM fungal varieties, but the underlying molecular mechanisms of Cr tolerance in ECM fungi are not clear. This study identified, analysed and compared the Cr(VI)-induced transcriptional changes between Cr(VI)-tolerant strain (Pisolithus sp. 1 LS-2017) and Cr(VI)-sensitive strain (Pisolithus sp. 2 LS-2017) by de novo transcriptomic analysis. The results showed that 93,642 assembled unique transcripts representing the 22,353 (46.76%) unigenes matched the proteins we have known in the Nr database and 47,801 unigenes were got from the Pisolithus spp. For DEGs between the control and 10 mg/L Cr(VI) treatment, cyanoamino acid metabolic, type I diabetes mellitus metabolism, nitrogen metabolism and beta-Alanine metabolism pathways were significantly enriched (p < 0.05) in Pisolithus sp. 1 LS-2017. Two nitrate reductase family genes (nidD, niiA) provide Cr(VI) tolerance for Pisolithus sp. 1 LS-2017 by regulating Cr(VI) reduction. In addition, NO produced by nidD, niiA regulated denitrification can alleviate Cr(VI) induced oxidative stress. In Pisolithus sp. 2 LS-2017, the alcC, aldA and lcf2 gene may alleviate Cr(VI) induced oxidative stress by protecting SH groups and increasing secondary metabolism, reducing detoxify aldehydes to carboxylic acids and producing LCPUFAs respectively; .T gene regulate Cr(VI) induced wound healing by pigmentation and stability of melanin in spore; MKP2 gene accelerate Cr(VI) induced cell death and gpmA gene regulated Cr(VI) induced energy emergency.


Assuntos
Basidiomycota/genética , Cromo/toxicidade , Genes Fúngicos , Micorrizas/genética , Poluentes do Solo/toxicidade , Transcriptoma/efeitos dos fármacos , Adaptação Fisiológica , Basidiomycota/metabolismo , Biodegradação Ambiental , Desnitrificação , Perfilação da Expressão Gênica , Micorrizas/metabolismo , Estresse Oxidativo/efeitos dos fármacos , Estresse Oxidativo/genética , Solo/química , Microbiologia do Solo/normas
8.
Syst Biol ; 69(1): 17-37, 2020 01 01.
Artigo em Inglês | MEDLINE | ID: mdl-31062852

RESUMO

Resolving deep divergences in the tree of life is challenging even for analyses of genome-scale phylogenetic data sets. Relationships between Basidiomycota subphyla, the rusts and allies (Pucciniomycotina), smuts and allies (Ustilaginomycotina), and mushroom-forming fungi and allies (Agaricomycotina) were found particularly recalcitrant both to traditional multigene and genome-scale phylogenetics. Here, we address basal Basidiomycota relationships using concatenated and gene tree-based analyses of various phylogenomic data sets to examine the contribution of several potential sources of bias. We evaluate the contribution of biological causes (hard polytomy, incomplete lineage sorting) versus unmodeled evolutionary processes and factors that exacerbate their effects (e.g., fast-evolving sites and long-branch taxa) to inferences of basal Basidiomycota relationships. Bayesian Markov Chain Monte Carlo and likelihood mapping analyses reject the hard polytomy with confidence. In concatenated analyses, fast-evolving sites and oversimplified models of amino acid substitution favored the grouping of smuts with mushroom-forming fungi, often leading to maximal bootstrap support in both concatenation and coalescent analyses. On the contrary, the most conserved data subsets grouped rusts and allies with mushroom-forming fungi, although this relationship proved labile, sensitive to model choice, to different data subsets and to missing data. Excluding putative long-branch taxa, genes with high proportions of missing data and/or with strong signal failed to reveal a consistent trend toward one or the other topology, suggesting that additional sources of conflict are at play. While concatenated analyses yielded strong but conflicting support, individual gene trees mostly provided poor support for any resolution of rusts, smuts, and mushroom-forming fungi, suggesting that the true Basidiomycota tree might be in a part of tree space that is difficult to access using both concatenation and gene tree-based approaches. Inference-based assessments of absolute model fit strongly reject best-fit models for the vast majority of genes, indicating a poor fit of even the most commonly used models. While this is consistent with previous assessments of site-homogenous models of amino acid evolution, this does not appear to be the sole source of confounding signal. Our analyses suggest that topologies uniting smuts with mushroom-forming fungi can arise as a result of inappropriate modeling of amino acid sites that might be prone to systematic bias. We speculate that improved models of sequence evolution could shed more light on basal splits in the Basidiomycota, which, for now, remain unresolved despite the use of whole genome data.


Assuntos
Basidiomycota/classificação , Classificação/métodos , Modelos Genéticos , Filogenia , Basidiomycota/genética , Genes Fúngicos/genética
10.
PLoS One ; 14(12): e0226106, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31830116

RESUMO

Secreted effectors of fungal pathogens are essential elements for disease development. However, lack of sequence conservation among identified effectors has long been a problem for predicting effector complements in fungi. Here we have explored the expression characteristics of avirulence (Avr) genes and candidate effectors of the flax rust fungus, Melampsora lini. We performed transcriptome sequencing and real-time quantitative PCR (qPCR) on RNA extracted from ungerminated spores, germinated spores, isolated haustoria and flax seedlings inoculated with M. lini isolate CH5 during plant infection. Genes encoding two categories of M. lini proteins, namely Avr proteins and plant cell wall degrading enzymes (CWDEs), were investigated in detail. Analysis of the expression profiles of 623 genes encoding predicted secreted proteins in the M. lini transcriptome shows that the six known Avr genes (i.e. AvrM (avrM), AvrM14, AvrL2, AvrL567, AvrP123 (AvrP) and AvrP4) fall within a group of 64 similarly expressed genes that are induced in planta and show a peak of expression early in infection with a subsequent decline towards sporulation. Other genes within this group include two paralogues of AvrL2, an AvrL567 virulence allele, and a number of genes encoding putative effector proteins. By contrast, M. lini genes encoding CWDEs fall into different expression clusters with their distribution often unrelated to their catalytic activity or substrate targets. These results suggest that synthesis of M. lini Avr proteins may be regulated in a coordinated fashion and that the expression profiling-based analysis has significant predictive power for the identification of candidate Avr genes.


Assuntos
Basidiomycota/genética , Basidiomycota/patogenicidade , Linho/genética , Linho/microbiologia , Interações Hospedeiro-Patógeno/genética , Doenças das Plantas/microbiologia , Fatores de Virulência/genética , Biologia Computacional , Proteínas Fúngicas/genética , Perfilação da Expressão Gênica , Regulação Fúngica da Expressão Gênica , Genes Fúngicos , Micoses/genética , Micoses/microbiologia , Doenças das Plantas/genética , Folhas de Planta/microbiologia , Esporos Fúngicos/genética , Transcriptoma/fisiologia , Virulência/genética
11.
Nat Commun ; 10(1): 5571, 2019 12 05.
Artigo em Inglês | MEDLINE | ID: mdl-31804478

RESUMO

Chloroplasts are important for photosynthesis and for plant immunity against microbial pathogens. Here we identify a haustorium-specific protein (Pst_12806) from the wheat stripe rust fungus, Puccinia striiformis f. sp. tritici (Pst), that is translocated into chloroplasts and affects chloroplast function. Transient expression of Pst_12806 inhibits BAX-induced cell death in tobacco plants and reduces Pseudomonas-induced hypersensitive response in wheat. It suppresses plant basal immunity by reducing callose deposition and the expression of defense-related genes. Pst_12806 is upregulated during infection, and its knockdown (by host-induced gene silencing) reduces Pst growth and development, likely due to increased ROS accumulation. Pst_12806 interacts with the C-terminal Rieske domain of the wheat TaISP protein (a putative component of the cytochrome b6-f complex). Expression of Pst_12806 in plants reduces electron transport rate, photosynthesis, and production of chloroplast-derived ROS. Silencing TaISP by virus-induced gene silencing in a susceptible wheat cultivar reduces fungal growth and uredinium development, suggesting an increase in resistance against Pst infection.


Assuntos
Basidiomycota/metabolismo , Cloroplastos/metabolismo , Proteínas Fúngicas/metabolismo , Espécies Reativas de Oxigênio/metabolismo , Basidiomycota/genética , Basidiomycota/imunologia , Cloroplastos/imunologia , Cloroplastos/microbiologia , Resistência à Doença/genética , Resistência à Doença/imunologia , Proteínas Fúngicas/genética , Proteínas Fúngicas/imunologia , Regulação Fúngica da Expressão Gênica/imunologia , Inativação Gênica , Glucanos/imunologia , Glucanos/metabolismo , Interações Hospedeiro-Patógeno/genética , Interações Hospedeiro-Patógeno/imunologia , Doenças das Plantas/genética , Doenças das Plantas/imunologia , Doenças das Plantas/microbiologia , Imunidade Vegetal/genética , Imunidade Vegetal/imunologia , Folhas de Planta/genética , Folhas de Planta/metabolismo , Folhas de Planta/microbiologia , Proteínas de Plantas/genética , Proteínas de Plantas/metabolismo , Ligação Proteica , Pseudomonas syringae/imunologia , Pseudomonas syringae/fisiologia , Espécies Reativas de Oxigênio/imunologia , Triticum/genética , Triticum/microbiologia
12.
Int J Mol Sci ; 20(23)2019 Nov 28.
Artigo em Inglês | MEDLINE | ID: mdl-31795104

RESUMO

Nitrilases participate in the nitrile metabolism in microbes and plants. They are widely used to produce carboxylic acids from nitriles. Nitrilases were described in bacteria, Ascomycota and plants. However, they remain unexplored in Basidiomycota. Yet more than 200 putative nitrilases are found in this division via GenBank. The majority of them occur in the subdivision Agaricomycotina. In this work, we analyzed their sequences and classified them into phylogenetic clades. Members of clade 1 (61 proteins) and 2 (25 proteins) are similar to plant nitrilases and nitrilases from Ascomycota, respectively, with sequence identities of around 50%. The searches also identified five putative cyanide hydratases (CynHs). Representatives of clade 1 and 2 (NitTv1 from Trametes versicolor and NitAg from Armillaria gallica, respectively) and a putative CynH (NitSh from Stereum hirsutum) were overproduced in Escherichia coli. The substrates of NitTv1 were fumaronitrile, 3-phenylpropionitrile, ß-cyano-l-alanine and 4-cyanopyridine, and those of NitSh were hydrogen cyanide (HCN), 2-cyanopyridine, fumaronitrile and benzonitrile. NitAg only exhibited activities for HCN and fumaronitrile. The substrate specificities of these nitrilases were largely in accordance with substrate docking in their homology models. The phylogenetic distribution of each type of nitrilase was determined for the first time.


Assuntos
Aminoidrolases/genética , Basidiomycota/genética , Proteínas Fúngicas/genética , Aminoidrolases/química , Aminoidrolases/metabolismo , Basidiomycota/classificação , Basidiomycota/enzimologia , Sítios de Ligação , Fumaratos/metabolismo , Proteínas Fúngicas/química , Proteínas Fúngicas/metabolismo , Cianeto de Hidrogênio/metabolismo , Simulação de Acoplamento Molecular , Filogenia , Ligação Proteica , Piridinas/metabolismo , Especificidade por Substrato
13.
BMC Genomics ; 20(1): 985, 2019 Dec 16.
Artigo em Inglês | MEDLINE | ID: mdl-31842749

RESUMO

BACKGROUND: Stem rust is an economically important disease of wheat and barley. However, studies to gain insight into the molecular basis of these host-pathogen interactions have primarily focused on wheat because of its importance in human sustenance. This is the first extensive study utilizing a transcriptome-wide association mapping approach to identify candidate Puccinia graminis f. sp. tritici (Pgt) effectors/suppressors that elicit or suppress barley stem rust resistance genes. Here we focus on identifying Pgt elicitors that interact with the rpg4-mediated resistance locus (RMRL), the only effective source of Pgt race TTKSK resistance in barley. RESULTS: Thirty-seven Pgt isolates showing differential responses on RMRL were genotyped using Restriction Site Associated DNA-Genotyping by Sequencing (RAD-GBS), identifying 24 diverse isolates that were used for transcript analysis during the infection process. In planta RNAseq was conducted with the 24 diverse isolates on the susceptible barley variety Harrington, 5 days post inoculation. The transcripts were mapped to the Pgt race SCCL reference genome identifying 114 K variants in predicted genes that would result in nonsynonymous amino acid substitutions. Transcriptome wide association analysis identified 33 variants across 28 genes that were associated with dominant RMRL virulence, thus, representing candidate suppressors of resistance. Comparative transcriptomics between the 9 RMRL virulent -vs- the 15 RMRL avirulent Pgt isolates identified 44 differentially expressed genes encoding candidate secreted effector proteins (CSEPs), among which 38 were expressed at lower levels in virulent isolates suggesting that they may represent RMRL avirulence genes. Barley transcript analysis after colonization with 9 RMRL virulent and 15 RMRL avirulent isolates inoculated on the susceptible line Harrington showed significantly lower expression of host biotic stress responses specific to RMRL virulent isolates suggesting virulent isolates harbor effectors that suppress resistance responses. CONCLUSIONS: This transcriptomic study provided novel findings that help fill knowledge gaps in the understanding of stem rust virulence/avirulence and host resistance in barley. The pathogen transcriptome analysis suggested RMRL virulence might depend on the lack of avirulence genes, but evidence from pathogen association mapping analysis and host transcriptional analysis also suggested the alternate hypothesis that RMRL virulence may be due to the presence of suppressors of defense responses.


Assuntos
Basidiomycota/patogenicidade , Resistência à Doença , Proteínas Fúngicas/genética , Perfilação da Expressão Gênica/métodos , Hordeum/microbiologia , Proteínas de Plantas/genética , Substituição de Aminoácidos , Basidiomycota/genética , Proteínas Fúngicas/metabolismo , Regulação Fúngica da Expressão Gênica , Regulação da Expressão Gênica de Plantas , Estudos de Associação Genética , Hordeum/genética , Interações Hospedeiro-Patógeno , Doenças das Plantas/microbiologia , Proteínas de Plantas/metabolismo , Análise de Sequência de DNA , Análise de Sequência de RNA , Virulência
14.
Genome Biol Evol ; 11(12): 3436-3444, 2019 12 01.
Artigo em Inglês | MEDLINE | ID: mdl-31764979

RESUMO

Horizontal gene transfer (HGT) has been identified as an important source of genomic innovation in fungi. However, how HGT drove the evolution of Alternaria alternata, a necrotrophic fungus which can be ubiquitously isolated from soil and various plants and decaying plant materials is largely known. In this study, we identified 12 protein-encoding genes that are likely acquired from lineages outside Pezizomycotina. Phylogenetic trees and approximately unbiased comparative topology tests strongly supported the evolutionary origin of these genes. According to their predicted functions, these HGT candidates are involved in nitrogen and carbohydrate metabolism. Especially, five genes of them were likely transferred as a physically linked cluster from Tremellales (Basidiomycota). Functionally knocking out the five-gene cluster in an A. alternata isolate causing citrus brown spot resulted in an 80% decrease in asexual spore production in the deletion mutant. We further knocked out each of these five genes in this cluster and the resultant single-gene deletion mutants exhibited a various degree of reduction in spore production. Except for conidiation, functions of these genes associated with vegetative growth, stress tolerance, and virulence are very limited. Our results provide new evidence that HGT has played important roles over the course of the evolution of filamentous fungi.


Assuntos
Alternaria/fisiologia , Proteínas Fúngicas/genética , Proteínas Fúngicas/metabolismo , Transferência Genética Horizontal , Família Multigênica , Alternaria/classificação , Alternaria/genética , Ascomicetos/classificação , Ascomicetos/genética , Basidiomycota/classificação , Basidiomycota/genética , Citrus/microbiologia , Evolução Molecular , Deleção de Genes , Filogenia , Doenças das Plantas/microbiologia , Esporos Fúngicos/classificação , Esporos Fúngicos/genética , Esporos Fúngicos/fisiologia
15.
Nat Commun ; 10(1): 5068, 2019 11 07.
Artigo em Inglês | MEDLINE | ID: mdl-31699975

RESUMO

Parasexuality contributes to diversity and adaptive evolution of haploid (monokaryotic) fungi. However, non-sexual genetic exchange mechanisms are not defined in dikaryotic fungi (containing two distinct haploid nuclei). Newly emerged strains of the wheat stem rust pathogen, Puccinia graminis f. sp. tritici (Pgt), such as Ug99, are a major threat to global food security. Here, we provide genomics-based evidence supporting that Ug99 arose by somatic hybridisation and nuclear exchange between dikaryons. Fully haplotype-resolved genome assembly and DNA proximity analysis reveal that Ug99 shares one haploid nucleus genotype with a much older African lineage of Pgt, with no recombination or chromosome reassortment. These findings indicate that nuclear exchange between dikaryotes can generate genetic diversity and facilitate the emergence of new lineages in asexual fungal populations.


Assuntos
Basidiomycota/genética , Genoma Fúngico/genética , Basidiomycota/fisiologia , Evolução Molecular , Variação Genética , Haplótipos , Reprodução , Homologia de Sequência do Ácido Nucleico , Triticum/microbiologia
16.
BMC Genomics ; 20(1): 723, 2019 Oct 09.
Artigo em Inglês | MEDLINE | ID: mdl-31597570

RESUMO

BACKGROUND: Gymnosporangium spp. are fungal plant pathogens causing rust disease and most of them are known to infect two different host plants (heteroecious) with four spore stages (demicyclic). In the present study, we sequenced the transcriptome of G. japonicum teliospores on its host plant Juniperus chinensis and we performed comparison to the transcriptomes of G. yamadae and G. asiaticum at the same life stage, that happens in the same host but on different organs. RESULTS: Functional annotation for the three Gymnosporangium species showed the expression of a conserved genetic program with the top abundant cellular categories corresponding to energy, translation and signal transduction processes, indicating that this life stage is particularly active. Moreover, the survey of predicted secretomes in the three Gymnosporangium transcriptomes revealed shared and specific genes encoding carbohydrate active enzymes and secreted proteins of unknown function that could represent candidate pathogenesis effectors. A transcript encoding a hemicellulase of the glycoside hydrolase 26 family, previously identified in other rust fungi, was particularly highly expressed suggesting a general role in rust fungi. The comparison between the transcriptomes of the three Gymnosporangium spp. and selected Pucciniales species in different taxonomical families allowed to identify lineage-specific protein families that may relate to the biology of teliospores in rust fungi. Among clustered gene families, 205, 200 and 152 proteins were specifically identified in G. japonicum, G. yamadae and G. asiaticum, respectively, including candidate effectors expressed in teliospores. CONCLUSIONS: This comprehensive comparative transcriptomics study of three Gymnosporangium spp. identified gene functions and metabolic pathways particularly expressed in teliospores, a stage of the life cycle that is mostly overlooked in rust fungi. Secreted protein encoding transcripts expressed in teliospores may reveal new candidate effectors related to pathogenesis. Although this spore stage is not involved in host plant infection but in the production of basidiospores infecting plants in the Amygdaloideae, we speculate that candidate effectors may be expressed as early as the teliospore stage for preparing further infection by basidiospores.


Assuntos
Basidiomycota/genética , Proteínas Fúngicas/genética , Perfilação da Expressão Gênica/métodos , Traqueófitas/microbiologia , Basidiomycota/classificação , Basidiomycota/patogenicidade , Regulação Fúngica da Expressão Gênica , Estágios do Ciclo de Vida , Família Multigênica , Filogenia , Análise de Sequência de RNA , Esporos Fúngicos/genética
17.
BMC Genomics ; 20(1): 765, 2019 Oct 22.
Artigo em Inglês | MEDLINE | ID: mdl-31640544

RESUMO

BACKGROUND: Hypsizygus marmoreus, a high value commercialized edible mushroom is widely cultivated in East Asia, and has become one of the most popular edible mushrooms because of its rich nutritional and medicinal value. Mitochondria are vital organelles, and play various essential roles in eukaryotic cells. RESULTS: In this study, we provide the Hypsizygus marmoreus mitochondrial (mt) genome assembly: the circular sequence is 102,752 bp in size and contains 15 putative protein-coding genes, 2 ribosomal RNAs subunits and 28 tRNAs. We compared the mt genomes of the 27 fungal species in the Pezizomycotina and Basidiomycotina subphyla, with the results revealing that H. marmoreus is a sister to Tricholoma matsutake and the phylogenetic distribution of this fungus based on the mt genome. Phylogenetic analysis shows that Ascomycetes mitochondria started to diverge earlier than that of Basidiomycetes and supported the robustness of the hyper metric tree. The fungal sequences are highly polymorphic and gene order varies significantly in the dikarya data set, suggesting a correlation between the gene order and divergence time in the fungi mt genome. To detect the mt genome variations in H. marmoreus, we analyzed the mtDNA sequences of 48 strains. The phylogeny and variation sited type statistics of H. marmoreus provide clear-cut evidence for the existence of four well-defined cultivations isolated lineages, suggesting female ancestor origin of H. marmoreus. Furthermore, variations on two loci were further identified to be molecular markers for distinguishing the subgroup containing 32 strains of other strains. Fifteen conserved protein-coding genes of mtDNAs were analyzed, with fourteen revealed to be under purifying selection in the examined fungal species, suggesting the rapid evolution was caused by positive selection of this gene. CONCLUSIONS: Our studies have provided new reference mt genomes and comparisons between species and intraspecies with other strains, and provided future perspectives for assessing diversity and origin of H. marmoreus.


Assuntos
Agaricales/genética , Evolução Molecular , Genoma Mitocondrial/genética , Agaricales/classificação , Ascomicetos/classificação , Ascomicetos/genética , Basidiomycota/classificação , Basidiomycota/genética , DNA Mitocondrial/genética , Proteínas Fúngicas/genética , Ordem dos Genes , Variação Genética , Filogenia , Seleção Genética , Especificidade da Espécie
18.
Virol J ; 16(1): 118, 2019 10 17.
Artigo em Inglês | MEDLINE | ID: mdl-31623644

RESUMO

BACKGROUND: Mycoviruses were recently discovered in the white pine blister rust (WPBR) fungus Cronartium ribicola (J.C. Fisch.). Detection and characterization of their double stranded RNA (dsRNA) would facilitate understanding of pathogen virulence and disease pathogenesis in WPBR systems. METHODS: Full-length cDNAs were cloned from the dsRNAs purified from viral-infected C. ribicola, and their cDNA sequences were determined by DNA sequencing. Evolutionary relationships of the dsRNAs with related mycoviruses were determined by phylogenetic analysis. Dynamic distributions of the viral RNAs within samples of their fungal host C. ribicola were investigated by measurement of viral genome prevalence and viral gene expression. RESULTS: In this study we identified and characterized five novel dsRNAs from C. ribicola, designated as Cronartium ribicola totivirus 1-5 (CrTV1 to CrTV5). These dsRNA sequences encode capsid protein and RNA-dependent RNA polymerase with significant homologies to dsRNA viruses of the family Totiviridae. Phylogenetic analysis showed that the CrTVs were grouped into two distinct clades. CrTV2 through CrTV5 clustered within the genus Totivirus. CrTV1 along with a few un-assigned dsRNAs constituted a distinct phyletic clade that is genetically distant from presently known genera in the Totiviridae family, indicating that CrTV1 represents a novel genus in the Totiviridae family. The CrTVs were prevalent in fungal samples obtained from infected western white pine, whitebark pine, and limber pines. Viral RNAs were generally expressed at higher levels during in planta mycelium growth than in aeciospores and urediniospores. CrTV4 was significantly associated with C. ribicola virulent pathotype and specific C. ribicola host tree species, suggesting dsRNAs as potential tools for dissection of pathogenic mechanisms of C. ribicola and diagnosis of C. ribicola pathotypes. CONCLUSION: Phylogenetic and expression analyses of viruses in the WPBR pathogen, C. ribicola, have enchanced our understanding of virus diversity in the family Totiviridae, and provided a potential strategy to utilize pathotype-associated mycoviruses to control fungal forest diseases.


Assuntos
Basidiomycota/virologia , Micélio/patogenicidade , Pinus/microbiologia , Doenças das Plantas/microbiologia , RNA de Cadeia Dupla/fisiologia , Totiviridae/fisiologia , Basidiomycota/genética , Basidiomycota/crescimento & desenvolvimento , Basidiomycota/patogenicidade , Genoma Viral/genética , Micélio/genética , Micélio/crescimento & desenvolvimento , Micélio/virologia , Filogenia , Pinus/classificação , RNA de Cadeia Dupla/classificação , RNA de Cadeia Dupla/genética , RNA Viral/genética , Totiviridae/classificação , Totiviridae/genética , Transcrição Genética , Proteínas Virais/genética , Virulência
19.
Mycologia ; 111(5): 782-792, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31545143

RESUMO

We present an account of Rhizopogon introduced from plantings of exotic pine plantations in Argentine Patagonia. Nuc rDNA internal transcribed spacer ITS1-5.8S-ITS2 (ITS) and nuc 28S rDNA (28S) sequences were used to identify specimens from Argentina and examine their relationships with geographically different Rhizopogon species. Based on phylogenetic analyses, we confirm that four species of Rhizopogon occur in pine plantations across Patagonia. Several Rhizopogon collections from Pinus ponderosa plantations across different provinces cluster with R. arctostaphyli, a species within R. subg. Amylopogon. The majority of Patagonian Rhizopogon, however, form three different lineages in R. subg. Roseoli. The first of these, R. roseolus sensu Trappe, includes numerous collections from Pinus ponderosa, P. contorta, and P. radiata stands of North American affiliation. The second, R. roseolus sensu Martin and Garcia from P. ponderosa plantations, clusters in clade IIIa of the R. roseolus complex, which also includes the holotype collection of R. mohelnensis from the Czech Republic. The third species in R. subg. Roseoli, and fourth species overall from Patagonia, is R. granuloflavus from Pinus ponderosa plantations. Multiplex polymerase chain reaction (PCR) of numerous Roseoli samples failed to produce an amplicon indicative of either Japanese or New Zealand shoro.


Assuntos
Basidiomycota/classificação , Basidiomycota/isolamento & purificação , Variação Genética , Filogenia , Pinus ponderosa/microbiologia , Argentina , Basidiomycota/genética , Análise por Conglomerados , DNA Fúngico/química , DNA Fúngico/genética , DNA Ribossômico/química , DNA Ribossômico/genética , DNA Espaçador Ribossômico/química , DNA Espaçador Ribossômico/genética , RNA Ribossômico 28S/genética , Análise de Sequência de DNA
20.
J Genet ; 982019 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-31544783

RESUMO

Thirty-nine wheat genotypes were studied to estimate their partial resistance levels to leaf rust at Behira governortae during three growing seasons, i.e. 2016/2017, 2017/2018 and 2018/2019. In these genotypes, partial resistance was characterized using final leaf rust severity (FRS %) and area under disease progress curve (AUDPC). Of the tested genotypes, only three wheat varieties; Giza 171, Misr 3 and Sohag 5 showed complete resistance. Further, 28 of the 39 genotypes had partial resistance as they revealed low and/or moderate values of FRS (%) and AUDPC (not exceeding 30% and 300, respectively). The other eight varieties were fast rusting, as they displayed the maximum values of FRS (%) and AUDPC. The four monogenic lines; Lr 34, Lr 46, Lr 67 and Lr 68 were identified in the wheat varieties using linked molecular markers; csLV34, Xgwm259, CFD71 and csGSR. Phenotypic results of the wheat varieties were confirmed by molecular marker analysis.


Assuntos
Basidiomycota , Resistência à Doença/genética , Doenças das Plantas/genética , Triticum/genética , Basidiomycota/genética , Mapeamento Cromossômico , Genes de Plantas , Estudos de Associação Genética , Marcadores Genéticos , Genótipo , Fenótipo , Doenças das Plantas/microbiologia
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