De novo genome assembly and annotation of rice sheath rot fungus Sarocladium oryzae reveals genes involved in Helvolic acid and Cerulenin biosynthesis pathways

Evolution and related pathogenic genes of Pseudodiploöspora longispora on Morchella based on genomic characterization and comparative genomic analysis

True morels (Morchella) are globally renowned medicinal and edible mushrooms. White mold disease caused by fungi is the main disease of Morchella, which has the characteristics of wide incidence and strong destructiveness. The disparities observed in the isolation rates of different pathogens indicate their varying degrees of host adaptability and competitive survival abilities. In order to elucidate its potential mechanism, this study, the pathogen of white mold disease from Dafang county, Guizhou Province was isolated and purified, identified as Pseudodiploöspora longispora by morphological, molecular biological and pathogenicity tests. Furthermore, high-quality genome of P. longisporus (40.846 Mb) was assembled N50 of 3.09 Mb, predicts 7381 protein-coding genes. Phylogenetic analysis of single-copy homologous genes showed that P. longispora and Zelopaecilomyces penicillatus have the closest evolutionary relationship, diverging into two branches approximately 50 (44.3-61.4) MYA. Additionally, compared with the other two pathogens causing Morchella disease, Z. penicillatus and Cladobotryum protrusum, it was found that they had similar proportions of carbohydrate enzyme types and encoded abundant cell wall degrading enzymes, such as chitinase and glucanase, indicating their important role in disease development. Moreover, the secondary metabolite gene clusters of P. longispora and Z. penicillatus show a high degree of similarity to leucinostatin A and leucinostatin B (peptaibols). Furthermore, a gene cluster with synthetic toxic substance Ochratoxin A was also identified in P. longispora and C. protrusum, indicating that they may pose a potential threat to food safety. This study provides valuable insights into the genome of P. longispora, contributing to pathogenicity research.

The genome and transcriptome of Sarocladium terricola provide insight into ergosterol biosynthesis

Sarocladium terricola is a species of ascomycete fungus that has been recognized as a biocontrol agent for managing animal and plant pathogens, and exhibits significant potential as a feed additive. In this study, we utilized a combination of short-read Illumina sequencing and long-read PacBio sequencing to sequence, assemble, and analyze the genome of S. terricola. The resulting genome consisted of 11 scaffolds encompassing 30.27 Mb, with a GC content of 54.07%, and 10,326 predicted protein coding gene models. We utilized 268 single-copy ortholog genes to reconstruct the phylogenomic relationships among 26 ascomycetes, and found that S. terricola was closely related to two Acremonium species. We also determined that the ergosterol content of S. terricola was synthesized to nearly double levels when cultured in potato dextrose media compared to bean media (4509 mg/kg vs. 2382 mg/kg). Furthermore, transcriptome analyses of differentially expressed genes suggested that the ergosterol synthesis genes ERG3, ERG5, and ERG25 were significantly up-regulated in potato dextrose media. These results will help us to recognize metabolic pathway of ergosterol biosynthesis of S. terricloa comprehensivelly.

Colorimetric loop-mediated isothermal amplification assay for detection and ecological monitoring of Sarocladium oryzae, an important seed-borne pathogen of rice

Accurate and timely disease detection plays a critical role in achieving sustainable crop protection. Globally, rice has been a staple crop for centuries plagued by the diseases that greatly hamper its productivity. Sheath rot, an emerging disease of rice caused by the seed-borne pathogen Sarocladium oryzae, has reportedly caused heavy losses to agricultural produce in recent years. Our study has led to the development and validation of a LAMP assay for early detection of S. oryzae, the causal agent of sheath rot from the live-infected tissues, seeds, weeds, and environmental samples. The assay could detect as low as 1.6 fg/μl of the pathogen in 15 min. The assay was implemented to bio-surveil the presence of this pathogen by testing it on three weed species (Echinochloa colona, Echinochloa crus-galli, and Cyperus teneriffae) growing around the rice fields. The results showed the presence of the pathogen in two of the weed species viz. E. colona and E. crus-galli. The assay was used to test 13 different rice varieties for the presence of S. oryzae in seeds. In total, three of the varieties did not show the presence of S. oryzae in their seeds while the rest were found to harbor the pathogen. The developed assay can effectively be used to detect and screen the presence of S. oryzae in live samples including seeds and field soil.

Metabolomic and Transcriptomic Changes Induced by Potassium Deficiency During Sarocladium oryzae Infection Reveal Insights into Rice Sheath Rot Disease Resistance

Rice sheath rot disease caused by Sarocladium oryzae (S. oryzae) infection is an emerging disease, and infection can cause yield losses of 20-85%. Adequate potassium (K) application is a feasible strategy for rice tolerance to S. oryzae infection. However, little is known about the metabolic mechanisms regulated by K that allow rice to cope better with S. oryzae infection. The present study performed a comparative metabolome and transcriptome analysis of rice with different K nutrition statuses before and upon S. oryzae infection. Sarocladium oryzae infection triggered a hydrogen peroxide (H₂O₂) burst, and K starvation aggravated the accumulation of H₂O₂ in the flag leaf sheath (FLS), which resulted in lipid peroxidation. Likewise, K deficiency altered the lipid homeostasis of the host plants by hyperaccumulation of 1-alkyl-2-acylglycerophosphoethanolamine. K starvation decreased the content of glycoglycerolipids including monogalactosyldiacyglycerol and digalactosyldoacylglycerol during S. oryzae infection, which destroyed the stability of bilayer membranes. In contrast, sufficient K supply increased antioxidant-related transcript expression (for example, the genes related to glutathione-S-transferase biosynthesis were upregulated), which activated the antioxidant systems. Additionally, upon S. oryzae infection, K starvation amplified the negative impacts of S. oryzae infection on flag leaf photosynthetic potential. These results provide new insight into the role of K in alleviating S. oryzae infection. Adequate K supply decreased the negative impacts of sheath rot disease on rice growth by alleviating lipid peroxidation and maintaining lipid homeostasis.

Survival of the fittest: how the rice microbial community forces Sarocladium oryzae into pathogenicity

The fungus Sarocladium oryzae (Sawada) causes rice sheath rot and produces the phytotoxins cerulenin and helvolic acid. Both toxins show antimicrobial activity but only helvolic acid production in the rice sheath correlates with virulence. Sarocladium oryzae isolates that differ in their toxin production were used to study their interaction with the rice culturable bacterial endophyte community. The diversity and community structure was defined in the edge of sheath rot lesions, followed by a null model-based co-occurrence analysis to discover pairwise interactions. Non-random pairs were co-cultured to study the nature of the interactions and the role of the toxins herein. Compared to healthy sheaths, endophyte diversity strongly increased when infected with the least virulent S. oryzae isolates producing low amounts of toxins. Virulent S. oryzae isolates did not affect diversity but caused strong shifts in species composition. The endophyte community of healthy rice plants was dominated by B. cereus. This bacterium was enriched in lesions produced by low-virulent S. oryzae isolates and caused hyphal lysis. Contrarily, helvolic acid producers eliminated this bacterium from the sheath endosphere. We conclude that S. oryzae needs to produce antibiotics to defend itself against antagonistic rice endophytes to successfully colonize and infect the rice sheath.

Genome Sequencing of Ciboria shiraiana Provides Insights into the Pathogenic Mechanisms of Hypertrophy Sorosis Scleroteniosis

Ciboria shiraiana causes hypertrophy sorosis scleroteniosis in mulberry trees, resulting in huge economic losses, and exploring its pathogenic mechanism at a genomic level is important for developing new control methods. Here, genome sequencing of C. shiraiana based on PacBio RSII and Illumina HiSeq 2500 platform as well as manual gap filling was performed. Synteny analysis with Sclerotinia sclerotiorum revealed 16 putative chromosomes corresponding to 16 chromosomes of C. shiraiana. Screening of rapid-evolution genes revealed that 97 and 2.4% of genes had undergone purifying selection and positive selection, respectively. When compared with S. sclerotiorum, fewer secreted effector proteins were found in C. shiraiana. The number of genes involved in pathogenicity, including secondary metabolites, carbohydrate active enzymes, and P450s, in the C. shiraiana genome was comparable with that of other necrotrophs but higher than that of biotrophs and saprotrophs. The growth-related genes and plant cell-wall-degradation-related genes in C. shiraiana were expressed in different developmental and infection stages, and may be potential targets for prevention and control of this pathogen. These results provide new insights into C. shiraiana pathogenic mechanisms, especially host range and necrotrophy features, and lay the foundation for further study of the underlying molecular mechanisms.[Formula: see text] The author(s) have dedicated the work to the public domain under the Creative Commons CC0 "No Rights Reserved" license by waiving all of his or her rights to the work worldwide under copyright law, including all related and neighboring rights, to the extent allowed by law.

Pathobiomes Revealed that Pseudomonas fuscovaginae and Sarocladium oryzae Are Independently Associated with Rice Sheath Rot

Rice sheath rot has been mainly associated with the bacterial pathogen Pseudomonas fuscovaginae and in some cases to the fungal pathogen Sarocladium oryzae; it is yet unclear if they are part of a complex disease. The bacterial and fungal community associated with rice sheath rot symptomatic and asymptomatic rice plants was determined/studied with the main aim to shed light on the pathogen(s) causing rice sheath rot. Plant samples were collected from different rice varieties in two locations (highland and lowland) in two rice-growing seasons (wet and dry season) in Burundi. Our results showed that the bacterial Pseudomonas genus was prevalent in highland in both rice-growing seasons and was not affected by rice plant varieties. Pseudomonas sequence reads displayed a significant high similarity to Pseudomonas fuscovaginae indicating that it is the causal agent of rice sheath rot as previously reported. The fungal Sarocladium genus was on the other hand prevalent in lowland only in the wet season; the sequence reads were most significantly similar to Sarocladium oryzae. These studies showed that plant microbiome analysis is very useful in determining the microorganisms involved in a plant disease. P. fuscovaginae and S. oryzae were prevalent in symptomatic samples in highland and lowland respectively being present independently and hence are not part of a complex disease. The significant presence of other bacterial and fungal taxa in symptomatic samples is also discussed possibly making this disease more complex. Finally, we also report the microbial communities that are associated with the plant sheath in symptomatic and asymptomatic plants from the same rice fields.

Comparative genomics of rice false smut fungi Ustilaginoidea virens Uv-Gvt strain from India reveals genetic diversity and phylogenetic divergence

False smut disease of rice caused by Ustilaginoidea virens, is an emerging threat to rice cultivation worldwide due to its detrimental effects on grain yield and quality. False smut disease severity was 4.44‒17.22% during a roving survey in Kharif 2016 in the four different rice ecosystems of Karnataka, India. Further, 15 pathogen isolates representing four different ecosystems were studied for their virulence and morphometric diversity. Among the 15 strains studied, most virulent strains Uv-Gvt was selected for whole genome sequencing in Illumina NextSeq 500 platform using 2 × 150 bp sequencing chemistry. The total assembled genome of Uv-Gvt was 26.96 Mb, which comprised of 9157 scaffolds with an N50 value of 15,934 bp and 6628 protein-coding genes. Next, the comparative genomic study revealed a similar gene inventory as UV-8b and MAFF 236576 strains reported from China and Japan, respectively. But, 1756 genes were unique to Uv-Gvt strain. The Uv-Gvt genome harbors 422 putative host-pathogen interacting genes compared to 359 and 520 genes in UV-8b and MAFF 236576 strains, respectively. The variant analysis revealed low genetic diversity (0.073‒0.088%) among U. virens strains. Further, phylogenetic analysis using 250 single copy orthologs genes of U. virens revealed a distinct phylogeny and an approximate divergence time. Our study, report the genomic resource of rice false smut pathogen from India, where the disease originated, and this information will have broader applicability in understanding the pathogen population diversity.

Genome Sequencing and Analysis of the Fungal Symbiont of Sirex noctilio, Amylostereum areolatum: Revealing the Biology of Fungus-Insect Mutualism

Sirex noctilio (F.), together with Amylostereum areolatum, a wood-decaying symbiotic fungus, causes severe damage to Pinus species worldwide. In China, it causes extensive death of Mongolian pine (Pinus sylvestris var. mongolica). There is an obligate dependency mutualism between the woodwasp and its fungus. Studies have suggested that the fungal growth rate affected the size of the wasps: larger adults emerged from sites with a higher fungus growth rate. This genome is the first reported genome sequence of a woodwasp symbiotic fungus. Genome sequence analysis of this fungus would prove the possibility of A. areolatum volatiles affecting the host selection of S. noctilio on a molecular basis. We further clarified that A. areolatum was a strict obligate symbiotic fungus and that it would provide S. noctilio with a suitable environment and with nutrients for the larval growth. These results would lay a foundation for our understanding of the mechanism of this entomogenous symbiosis.

Amylostereum areolatum is the symbiotic fungus of the Eurasian woodwasp, Sirex noctilio, a globally invasive species. The mutualistic symbiont is associated with the woodwasp, assisting the damage process and providing nutrition for its insect partners. Colonization and growth of A. areolatum have essential impacts on the development and spread of S. noctilio, though the mechanism of interaction between the two has been poorly described. In this study, the first genome of this symbiotic fungus was sequenced, assembled, and annotated. The assembled A. areolatum genome was 57.5 Mb (54.51% GC content) with 15,611 protein-coding genes. We identified 580 carbohydrate-active enzymes (CAZymes), 661 genes associated with pathogen-host interactions, and 318 genes encoding transport proteins in total. The genome annotation revealed 10 terpene/phytoene synthases responsible for terpenoid biosynthesis, which could be classified into three clades. Terpene synthase gene clusters in clade II were conserved well across Russulales. In this cluster, genes encoding mevalonate kinase (MK), EGR12 (COG1557), and nonplant terpene cyclases (cd00687) were the known biosynthesis and regulatory genes. Genome sequence analysis of this fungus would prove the possibility of A. areolatum volatiles affecting the host selection of S. noctilio on a molecular basis. We further clarified that A. areolatum was a strict obligate symbiotic fungus. The wasps might protect the fungus before it was introduced into a suitable host substrate by oviposition, while the fungus would provide S. noctilio with a suitable environment and nutrients for the larval growth. These results would lay a foundation for our understanding of the mechanism of this entomogenous symbiosis.

IMPORTANCESirex noctilio (F.), together with Amylostereum areolatum, a wood-decaying symbiotic fungus, causes severe damage to Pinus species worldwide. In China, it causes extensive death of Mongolian pine (Pinus sylvestris var. mongolica). There is an obligate dependency mutualism between the woodwasp and its fungus. Studies have suggested that the fungal growth rate affected the size of the wasps: larger adults emerged from sites with a higher fungus growth rate. This genome is the first reported genome sequence of a woodwasp symbiotic fungus. Genome sequence analysis of this fungus would prove the possibility of A. areolatum volatiles affecting the host selection of S. noctilio on a molecular basis. We further clarified that A. areolatum was a strict obligate symbiotic fungus and that it would provide S. noctilio with a suitable environment and with nutrients for the larval growth. These results would lay a foundation for our understanding of the mechanism of this entomogenous symbiosis.

Morphological, Pathogenic and Toxigenic Variability in the Rice Sheath Rot Pathogen Sarocladium Oryzae

Sheath rot is an emerging rice disease that leads to considerable yield losses. The main causal agent is the fungus Sarocladium oryzae. This pathogen is known to produce the toxins cerulenin and helvolic acid, but their role in pathogenicity has not been clearly established. S. oryzea isolates from different rice-producing regions can be grouped into three phylogenetic lineages. When grown in vitro, isolates from these lineages differed in growth rate, colour and in the ability to form sectors. A diverse selection of isolates from Rwanda and Nigeria, representing these lineages, were used to further study their pathogenicity and toxin production. Liquid chromatography high-resolution mass spectrometry analysis was used to measure cerulenin and helvolic acid production in vitro and in planta. The three lineages clearly differed in pathogenicity on the japonica cultivar Kitaake. Isolates from the least pathogenic lineage produced the highest levels of cerulenin in vitro. Helvolic acid production was not correlated with the lineage. Sectorisation was observed in isolates from the two least pathogenic lineages and resulted in a loss of helvolic acid production. In planta, only the production of helvolic acid, but not of cerulenin, correlated strongly with disease severity. The most pathogenic isolates all belonged to one lineage. They were phenotypically stable, shown by the lack of sectorisation, and therefore maintained high helvolic acid production in planta.

Potassium deficiency aggravates yield loss in rice by restricting the translocation of non-structural carbohydrates under Sarocladium oryzae infection condition

Sheath rot disease (ShR) caused by Sarocladium oryzae (S. oryzae) infection is an emerging disease that causes severe yield loss by restricting the translocation of non-structural carbohydrates (NSC). Potassium (K) nutrition plays a critical role in disease resistance and the exportation of NSC. However, the physiological mechanisms of K with respect to ShR have not been thoroughly elucidated to date. The objectives of this study were to reveal the mechanisms by which K increases ShR resistance by regulating NSC translocation of rice, therefore, a field experiment combined with an inoculation experiment was conducted. We demonstrate that ShR disease incidence and disease index decreased dramatically with an increasing K application. K deficiency sharply induced the accumulation of NSC in the flag leaf (FL) and flag leaf sheath (FLS) under S. oryzae infection condition, which reduced the contribution of transferred NSC to final yield. A permutational multivariate analysis showed that K deficiency had a greater (49.0%, P < 0.001) effect on the NSC content variation in FL than that of S. oryzae infection (15.0%, P < 0.001). S. oryzae infection dramatically increased the difference in apparent transferred mass of NSC and cell membrane injury of diseased organs between K-deficient and K-sufficient rice. Finally, we demonstrate that cell membrane injury was a limiting factor imposed by K deficiency, which restricts the export of NSC from source organs. This work highlights the importance of K in improving ShR resistance by regulating NSC translocation (particularly the stem NSC).

Genomic characteristics and comparative genomics analysis of the endophytic fungus Sarocladium brachiariae

BACKGROUND

Sarocladium brachiariae is a newly identified endophytic fungus isolated from Brachiaria brizantha. A previous study indicated that S. brachiariae had antifungal activity; however, limited genomic information restrains further study. Therefore, we sequenced the genome of S. brachiariae and compared it with the genome of S. oryzae to identify differences between a Sarocladium plant pathogen and an endophyte.

RESULTS

In this study, we reported a gapless genome sequence of a newly identified endophytic fungus Sarocladium brachiariae isolated from Brachiaria brizantha. The genome of S. brachiariae is 31.86 Mb, with a contig N50 of 3.27 Mb and 9903 protein coding genes. Phylogenomic analysis based on single copy orthologous genes provided insights into the evolutionary relationships of S. brachiariae and its closest species was identified as S. oryzae. Comparative genomics analysis revealed that S. brachiaria has 14.9% more plant cell wall degradation related CAZymes to S. oryzae, and 33.3% more fungal cell wall degradation related CAZymes, which could explain the antifungal activity of S. brachiaria. Based on Antibiotics & Secondary Metabolite Analysis Shell (antiSMASH) analysis, we identified a contact helvolic acid biosynthetic gene cluster (BGC) for the first time in S. oryzae. However, S. brachiaria had seven fewer terpene gene clusters, including helvolic acid BGC, compared with S. oryzae and this may be associated with adaptation to an endophytic lifestyle. Synteny analysis of polyketide synthases (PKS), non-ribosomal peptide synthetases (NRPS), and hybrid (PKS-NRPS) gene clusters between S. brachiariae and S. oryzae revealed that just 37.5% of tested clusters have good synteny, while 63.5% have no or poor synteny. This indicated that the S. brachiariae could potentially synthesize a variety of unknown-function secondary metabolites, which may play an important role in adaptation to its endophytic lifestyle and antifungal activity.

CONCLUSIONS

The data provided a better understanding of the Sarocladium brachiariae genome. Further comparative genomic analysis provided insight into the genomic basis of its endophytic lifestyle and antifungal activity.

Extending the Metabolite Diversity of the Endophyte Dimorphosporicola tragani

Fungi are one of the most prolific sources of microbial secondary metabolites. The production of new metabolites can be achieved using multiple fermentation conditions and by adding small-molecule effectors, including epigenetic modifiers. In the framework of our Natural Product screening programme targeting the discovery of new antimicrobial compounds, we applied multiple fermentation conditions and adsorptive polymeric resins on a large collection of fungal endophytes, to increase and stimulate their fungal secondary metabolite production. During this work the endophytic fungus Dimorphosporicola tragani CF-090383 showed antimicrobial activity only when grown in presence of adsorptive polymeric resins. In addition, seven epigenetic modifiers were added to fermentations of this endophytic fungus, in an attempt to activate its cryptic pathways as well as to analyse the metabolites produced under these conditions. D. tragani was seen to produce three different mycotoxin dendrodolides when the epigenetic modifiers 5-azacytidine and valproic acid were added to the fermentations, and these compounds were further characterized. However, the fungus produced the fatty acid synthesis inhibitor cerulenin, a molecule not previously described to be produced by this fungal species, only when cultivated in presence of the XAD-16 resin. We have found that the addition of XAD-16 resin resulted in four-fold higher titers in the production of cerulenin when compared to the best production conditions described in literature for the original fungal producer strain, Cephalosporium caerulens KF-140 (=Sarocladium oryzae), in a zeolite-based fermentation, used as an ammonium ion-trapping agent. The production of cerulenin by this strain of D. tragani, represents an alternative source for the improved production of cerulenin with better yields.

Comparative genomic analysis of monosporidial and monoteliosporic cultures for unraveling the complexity of molecular pathogenesis of Tilletia indica pathogen of wheat

Tilletia indica (Ti) - a quarantined fungal pathogen of wheat and its pathogenesis is chiefly governed by pathogen effectors secreted inside the host plant. The de novo genome sequencing of several field isolates and stages available could be used for understanding the molecular pathogenesis. The presence of gaps and low coverage of assembled genomes poses a problem in accurate functional annotation of such functions. In the present study attempts were made to improve the Ti draft genome through reconciliation of globally available datasets of three highly virulent monoteliospore cultures of Ti field isolates. It has sequence depth of 107x and N50 scaffold size of 80,772 (more than 26 times as large as achieved in the draft assembly) with highest sequence contiguity, more accurate and nearly complete. Functional annotation revealed that Ti genome contains 9209 genes evolved with many expanded gene families and arranged mostly in a cluster. About 79% of Ti genes were orthologous to other basidiomycetes fungi, Around 7.93% proteins were having secretary signals and 6.66% were identified as highly virulent pathogenicity genes. Using improved Ti genome as a reference, the genomic variation was assessed with respect to repeats, SNPs/InDel, gene families and correct set of virulence associated genes during its life cycle. The comparative intra-species, inter-stage and inter-species genomic variation will have broader implications to understand the gene regulatory networks involved in growth, mating and virulence behaviour of Tilletia f. spp. and also for better appreciation of fungal biology and disease management.

Draft Genome Sequence of Phoma arachidicola Wb2 Causing Peanut Web Blotch in China

Peanut web blotch, a peanut disease with both web and blotch symptom leaflets, is an emerging threat for peanut cultivation worldwide and one of the most important fungal diseases in China. However, the limited pieces of information in genomic resources and pathogenesis are the major constraints to integrated disease management. The genome contains a large number of pathogenicity-related genes, but the genomic information of the pathogen is still blank. Considering this fact, current study presented the draft genome sequence of a Phoma arachidicola isolate named Wb2. Strain Wb2 was isolated from peanut leaves with typical web blotch symptoms, and identified as Phoma arachidicola based on morphological characteristics and phylogenic analysis using ITS sequence. The draft genome of Wb2 is about 34.11 Mb and contains 37330 open reading frames (ORFs), with G + C content 49.23%. The strain Wb2 has an abundance of secreted oxidases, peroxidases, and carbohydrate-active enzymes for degrading cell wall polysaccharides and penetrating into the host tissue. The genome information of Wb2 will help to better understand the mechanisms of interaction between P. arachidicola and peanuts. Furthermore, the genome-based plant-pathogen interaction analysis will provide clues for disease control, which is essential to ensure peanut production and food security.

Secondary metabolite arsenal of an opportunistic pathogenic fungus

Aspergillus fumigatus is a versatile fungus able to successfully exploit diverse environments from mammalian lungs to agricultural waste products. Among its many fitness attributes are dozens of genetic loci containing biosynthetic gene clusters (BGCs) producing bioactive small molecules (often referred to as secondary metabolites or natural products) that provide growth advantages to the fungus dependent on environment. Here we summarize the current knowledge of these BGCs-18 of which can be named to product-their expression profiles in vivo, and which BGCs may enhance virulence of this opportunistic human pathogen. Furthermore, we find extensive evidence for the presence of many of these BGCs, or similar BGCs, in distantly related genera including the emerging pathogen Pseudogymnoascus destructans, the causative agent of white-nose syndrome in bats, and suggest such BGCs may be predictive of pathogenic potential in other fungi.This article is part of the themed issue 'Tackling emerging fungal threats to animal health, food security and ecosystem resilience'.

Biosynthesis of helvolic acid and identification of an unusual C-4-demethylation process distinct from sterol biosynthesis

Fusidane-type antibiotics represented by helvolic acid, fusidic acid and cephalosporin P₁ are a class of bacteriostatic agents, which have drawn renewed attention because they have no cross-resistance to commonly used antibiotics. However, their biosynthesis is poorly understood. Here, we perform a stepwise introduction of the nine genes from the proposed gene cluster for helvolic acid into Aspergillus oryzae NSAR1, which enables us to isolate helvolic acid (~20 mg L^-1) and its 21 derivatives. Anti-Staphylococcus aureus assay reveals that the antibacterial activity of three intermediates is even stronger than that of helvolic acid. Notably, we observe an unusual C-4 demethylation process mediated by a promiscuous short-chain dehydrogenase/reductase (HelC) and a cytochrome P450 enzyme (HelB1), which is distinct from the common sterol biosynthesis. These studies have set the stage for using biosynthetic approaches to expand chemical diversity of fusidane-type antibiotics.

Describing Genomic and Epigenomic Traits Underpinning Emerging Fungal Pathogens

An unprecedented number of pathogenic fungi are emerging and causing disease in animals and plants, putting the resilience of wild and managed ecosystems in jeopardy. While the past decades have seen an increase in the number of pathogenic fungi, they have also seen the birth of new big data technologies and analytical approaches to tackle these emerging pathogens. We review how the linked fields of genomics and epigenomics are transforming our ability to address the challenge of emerging fungal pathogens. We explore the methodologies and bioinformatic toolkits that currently exist to rapidly analyze the genomes of unknown fungi, then discuss how these data can be used to address key questions that shed light on their epidemiology. We show how genomic approaches are leading a revolution into our understanding of emerging fungal diseases and speculate on future approaches that will transform our ability to tackle this increasingly important class of emerging pathogens.

Genome and Transcriptome sequence of Finger millet (Eleusine coracana (L.) Gaertn.) provides insights into drought tolerance and nutraceutical properties

Background

Finger millet (Eleusine coracana (L.) Gaertn.) is an important staple food crop widely grown in Africa and South Asia. Among the millets, finger millet has high amount of calcium, methionine, tryptophan, fiber, and sulphur containing amino acids. In addition, it has C4 photosynthetic carbon assimilation mechanism, which helps to utilize water and nitrogen efficiently under hot and arid conditions without severely affecting yield. Therefore, development and utilization of genomic resources for genetic improvement of this crop is immensely useful.

Results

Experimental results from whole genome sequencing and assembling process of ML-365 finger millet cultivar yielded 1196 Mb covering approximately 82% of total estimated genome size. Genome analysis showed the presence of 85,243 genes and one half of the genome is repetitive in nature. The finger millet genome was found to have higher colinearity with foxtail millet and rice as compared to other Poaceae species. Mining of simple sequence repeats (SSRs) yielded abundance of SSRs within the finger millet genome. Functional annotation and mining of transcription factors revealed finger millet genome harbors large number of drought tolerance related genes. Transcriptome analysis of low moisture stress and non-stress samples revealed the identification of several drought-induced candidate genes, which could be used in drought tolerance breeding.

Conclusions

This genome sequencing effort will strengthen plant breeders for allele discovery, genetic mapping, and identification of candidate genes for agronomically important traits. Availability of genomic resources of finger millet will enhance the novel breeding possibilities to address potential challenges of finger millet improvement.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-017-3850-z) contains supplementary material, which is available to authorized users.