Intraspecific comparative genomics of isolates of the Norway spruce pathogen (Heterobasidion parviporum) and identification of its potential virulence factors

Background: Heterobasidion parviporum is an economically most important fungal forest pathogen in northern Europe, causing root and butt rot disease of Norway spruce (Picea abies (L.) Karst.). The mechanisms underlying the pathogenesis and virulence of this species remain elusive. No reference genome to facilitate functional analysis is available for this species. Results: To better understand the virulence factor at both phenotypic and genomic level, we characterized 15 H. parviporum isolates originating from different locations across Finland for virulence, vegetative growth, sporulation and saprotrophic wood decay. Wood decay capability and latitude of fungal origins exerted interactive effects on their virulence and appeared important for H. parviporum virulence. We sequenced the most virulent isolate, the first full genome sequences of H. parviporum as a reference genome, and re-sequenced the remaining 14 H. parviporum isolates. Genome-wide alignments and intrinsic polymorphism analysis showed that these isolates exhibited overall high genomic similarity with an average of at least 96% nucleotide identity when compared to the reference, yet had remarkable intra-specific level of polymorphism with a bias for CpG to TpG mutations. Reads mapping coverage analysis enabled the classification of all predicted genes into five groups and uncovered two genomic regions exclusively present in the reference with putative contribution to its higher virulence. Genes enriched for copy number variations (deletions and duplications) and nucleotide polymorphism were involved in oxidation-reduction processes and encoding domains relevant to transcription factors. Some secreted protein coding genes based on the genome-wide selection pressure, or the presence of variants were proposed as potential virulence candidates. Conclusion: Our study reported on the first reference genome sequence for this Norway spruce pathogen (H. parviporum). Comparative genomics analysis gave insight into the overall genomic variation among this fungal species and also facilitated the identification of several secreted protein coding genes as putative virulence factors for the further functional analysis. We also analyzed and identified phenotypic traits potentially linked to its virulence.Peer reviewe

Obligate Biotrophy Features Unraveled by the Genomic Analysis of the Rust Fungi, Melampsora larici-populina and Puccinia graminis f. sp. tritici

Rust fungi are some of the most devastating pathogens of crop plants. They are obligate biotrophs, which extract nutrients only from living plant tissues and cannot grow apart from their hosts. Their lifestyle has slowed the dissection of molecular mechanisms underlying host invasion and avoidance or suppression of plant innate immunity. We sequenced the 101 mega base pair genome of Melampsora larici-populina, the causal agent of poplar leaf rust, and the 89 mega base pair genome of Puccinia graminis f. sp. tritici, the causal agent of wheat and barley stem rust. We then compared the 16,841 predicted proteins of M. larici-populina to the 18,241 predicted proteins of P. graminis f. sp tritici. Genomic features related to their obligate biotrophic life-style include expanded lineage-specific gene families, a large repertoire of effector-like small secreted proteins (SSPs), impaired nitrogen and sulfur assimilation pathways, and expanded families of amino-acid, oligopeptide and hexose membrane transporters. The dramatic upregulation of transcripts coding for SSPs, secreted hydrolytic enzymes, and transporters in planta suggests that they play a role in host infection and nutrient acquisition. Some of these genomic hallmarks are mirrored in the genomes of other microbial eukaryotes that have independently evolved to infect plants, indicating convergent adaptation to a biotrophic existence inside plant cell

Obligate Biotrophy Features Unraveled by the Genomic Analysis of the Rust Fungi, Melampsora larici-populina and Puccinia graminis f. sp. tritici

Rust fungi are some of the most devastating pathogens of crop plants. They are obligate biotrophs, which extract nutrients only from living plant tissues and cannot grow apart from their hosts. Their lifestyle has slowed the dissection of molecular mechanisms underlying host invasion and avoidance or suppression of plant innate immunity. We sequenced the 101 mega base pair genome of Melampsora larici-populina, the causal agent of poplar leaf rust, and the 89 mega base pair genome of Puccinia graminis f. sp. tritici, the causal agent of wheat and barley stem rust. We then compared the 16,841 predicted proteins of M. larici-populina to the 18,241 predicted proteins of P. graminis f. sp tritici. Genomic features related to their obligate biotrophic life-style include expanded lineage-specific gene families, a large repertoire of effector-like small secreted proteins (SSPs), impaired nitrogen and sulfur assimilation pathways, and expanded families of amino-acid, oligopeptide and hexose membrane transporters. The dramatic upregulation of transcripts coding for SSPs, secreted hydrolytic enzymes, and transporters in planta suggests that they play a role in host infection and nutrient acquisition. Some of these genomic hallmarks are mirrored in the genomes of other microbial eukaryotes that have independently evolved to infect plants, indicating convergent adaptation to a biotrophic existence inside plant cell

CARACTERISATION PAR INGENIERIE GENOMIQUE DES PROFILS D'EXPRESSION GENIQUE DE PISOLITHUS TINCTORIUS ET D'EUCALYPTUS GLOBULUS AU COURS DU DEVELOPPEMENT DE LA SYMBIOSE ECTOMYCORHIZIENNE

LES ECTOMYCORHIZES SONT DES ASSOCIATIONS SYMBIOTIQUES ETABLIES ENTRE LES RACINES DES ARBRES ET CERTAINS CHAMPIGNONS DU SOL. CES RELATIONS MUTUALISTES, DONT LES BENEFICES SONT AVANT TOUT TROPHIQUES, ENTRAINENT DES MODIFICATIONS MORPHOLOGIQUES ET METABOLIQUES IMPORTANTES CHEZ LES DEUX PARTENAIRES. LA FORMATION DE L'ECTOMYCORHIZE EUCALYPTUS GLOBULUS-PISOLITHUS TINCTORIUS, S'ACCOMPAGNE EGALEMENT D'UN CHANGEMENT DU PROTEOME ET DE L'EXPRESSION GENIQUE DES RACINES ET DU CHAMPIGNON. AFIN D'ACQUERIR UNE VISION GLOBALE DES GENES EXPRIMES ET REGULES AU COURS DE LA FORMATION DE L'ECTOMYCORHIZE E. GLOBULUS-P. TINCTORIUS, NOUS AVONS DEVELOPPE UNE ANALYSE DE L'EXPRESSION GENIQUE DANS L'ORGANE SYMBIOTIQUE VIA L'ANALYSE DU TRANSCRIPTOME. UNE PREMIERE ETUDE, NOUS A PERMIS D'OBTENIR LES PROFILS D'EXPRESSION DE 400 ESTS (EXPRESSED SEQUENCE TAGS) DANS UNE ECTOMYCORHIZE EN FORMATION. NOUS AVONS AINSI PU IDENTIFIER 17% DES ESTS QUI SONT REGULES PAR LA SYMBIOSE. NOUS AVONS POURSUIVI NOTRE ANALYSE SUR PLUS DE 700 ESTS AU COURS DU DEVELOPPEMENT DE L'ORGANE SYMBIOTIQUE, DEPUIS LES PREMIERS CONTACTS ENTRE LES SYMBIOTES JUSQU'A LA MISE EN PLACE DE L'ECTOMYCORHIZE FONCTIONNELLE. L'ANALYSE STATISTIQUE DES PROFILS D'EXPRESSION NOUS A PERMIS DE METTRE EN EVIDENCE (I) DES ENSEMBLES DE GENES CO-REGULES (REGULONS) ET (II) UNE CHRONOSEQUENCE DANS L'EXPRESSION GENIQUE. PARMI LES GENES FORTEMENT REGULES, NOUS AVONS IDENTIFIE : CEUX CODANT LES PROTEINES PARIETALES FONGIQUES (HYDROPHOBINES ET SRAP32), PLUSIEURS FAMILLES DE METALLOTHIONEINES, DES PROTEINES DE SIGNALISATION, DES PROTEINES DE STRESS HYDRIQUE ET DES ENZYMES DE LA RESPIRATION MITOCHONDRIALE. PARMI CES GENES REGULES, NOUS AVONS CARACTERISE EN DETAIL, UN GENE CODANT UNE NOUVELLE HYDROPHOBINE, HYDPT-3, ET PLUSIEURS GENES DE COMMUNICATION FONGIQUES (RAS, RAF, CALCINEURINE).NANCY1-SCD Sciences & Techniques (545782101) / SudocSudocFranceF

Genomics Research on Non-Model Plant Pathogens: Delivering Novel Insights into Rust Fungus Biology

Fungi of the order Pucciniales cause rust diseases on many plants including important crops and trees widely used in agriculture, forestry and bioenergy programs; these encompass gymnosperms and angiosperms, monocots and dicots, perennial and annual plant species. These fungi are obligate biotrophs and -except for a few cases- cannot be cultivated outside their hosts in a laboratory. For this reason, standard functional and molecular genetic approaches to study these pathogens are very challenging and the means to study their biology, i.e. how they infect, develop and reproduce on plant hosts, are rather limited, even though they rank among the most devastating pathogens. Among fungal plant pathogens, rust fungi display the most complex lifecycles with up to five different spore forms and for many rust fungi, unrelated alternate hosts on which sexual and clonal reproduction are achieved. The genomics revolution and particularly the application of new generation sequencing technologies have greatly changed the way we now address biological studies and has in particular accelerated and made feasible, molecular studies on non-model species, such as rust fungi. The goal of this research topic is to gather articles that present recent advances in the understanding of rust fungi biology, their complex lifecycles and obligate biotrophic interactions with their hosts, through the means of genomics. This includes genome sequencing and/or resequencing of isolates, RNA-Seq or large-scale transcriptome analyses, genome-scale detailed annotation of gene families, and comparative analyses among the various rust fungi and, where feasible, with other obligate biotrophs or fungi displaying distinct trophic modes. This Research Topic provides a great opportunity to provide an up-to-date account of rust fungus biology through the lens of genomics, including state-of-the-art technologies developed to achieve this knowledge

Genomics Research on Non-Model Plant Pathogens: Delivering Novel Insights into Rust Fungus Biology

Fungi of the order Pucciniales cause rust diseases on many plants including important crops and trees widely used in agriculture, forestry and bioenergy programs; these encompass gymnosperms and angiosperms, monocots and dicots, perennial and annual plant species. These fungi are obligate biotrophs and -except for a few cases- cannot be cultivated outside their hosts in a laboratory. For this reason, standard functional and molecular genetic approaches to study these pathogens are very challenging and the means to study their biology, i.e. how they infect, develop and reproduce on plant hosts, are rather limited, even though they rank among the most devastating pathogens. Among fungal plant pathogens, rust fungi display the most complex lifecycles with up to five different spore forms and for many rust fungi, unrelated alternate hosts on which sexual and clonal reproduction are achieved. The genomics revolution and particularly the application of new generation sequencing technologies have greatly changed the way we now address biological studies and has in particular accelerated and made feasible, molecular studies on non-model species, such as rust fungi. The goal of this research topic is to gather articles that present recent advances in the understanding of rust fungi biology, their complex lifecycles and obligate biotrophic interactions with their hosts, through the means of genomics. This includes genome sequencing and/or resequencing of isolates, RNA-Seq or large-scale transcriptome analyses, genome-scale detailed annotation of gene families, and comparative analyses among the various rust fungi and, where feasible, with other obligate biotrophs or fungi displaying distinct trophic modes. This Research Topic provides a great opportunity to provide an up-to-date account of rust fungus biology through the lens of genomics, including state-of-the-art technologies developed to achieve this knowledge

Genetically-clustered antifungal phytocytokines and receptor proteins function together to trigger plant immune signaling

SummaryPhytocytokines regulate plant immunity via cell-surface receptors.Populus trichocarpaRUST INDUCED SECRETED PEPTIDE 1 (PtRISP1) exhibits an elicitor activity in poplar, as well as a direct antimicrobial activity against rust fungi.PtRISP1gene directly clusters with a gene encoding a leucine-rich repeat receptor protein (LRR-RP), that we termed RISP- ASSOCIATED LRR-RP (PtRALR).In this study, we used phylogenomics to characterize the RISP and RALR gene families, and functional assays to characterize RISP/RALR pairs.BothRISPandRALRgene families specifically evolved in Salicaceae species (poplar and willow), and systematically cluster in the genomes. Two divergent RISPs, PtRISP1 andSalix purpureaRISP1 (SpRISP1), induced a reactive oxygen species (ROS) burst and mitogen- activated protein kinases (MAPKs) phosphorylation inNicotiana benthamianaleaves expressing the respective clustered RALR. PtRISP1 triggers a rapid stomatal closure in poplar, and both PtRISP1 and SpRISP1 directly inhibit rust pathogen growth.Altogether, these results suggest that plants evolved phytocytokines with direct antimicrobial activities, and that the genes coding these phytocytokines co-evolved and physically cluster with their cognate receptors

Transcript Profiling Reveals Novel Marker Genes Involved in Fruiting Body Formation in Tuber borchii

cDNA arrays were used to explore mechanisms controlling fruiting body development in the truffle Tuber borchii. Differences in gene expression were higher between reproductive and vegetative stage than between two stages of fruiting body maturation. We suggest hypotheses about the importance of various physiological processes during the development of fruiting bodies