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Scleromitrula shiraiana is a necrotrophic fungus with a narrow host range, and is one of the main causal pathogens of mulberry sclerotial disease. However, its molecular mechanisms and pathogenesis are unclear. Here, we report a 39.0 Mb high-quality genome sequence for S. shiraiana strain SX-001. The S. shiraiana genome contains 11,327 protein-codi...
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Ciboria carunculoides is the dominant causal agent of mulberry sclerotial disease, and it is a necrotrophic fungal pathogen with a narrow host range that causes devastating diseases in mulberry fruit. However, little is known about the interaction between C. carunculoides and mulberry. Here, our transcriptome sequencing results showed that the tran...
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... Intestinal fungi are an integral part of the gut microbiota. Scleromitrula and Neoascochyta are necrotic fungi with a narrow host range and have negative effects on plants [68,69]. Members of the genus Periconia are commonly found in plants or soil with notable antioxidant and antibacterial activities [70]. ...
The yak (Bos grunniens) exhibits exceptional regional adaptability, enabling it to thrive in the distinctive ecological niches of the Qinghai–Tibet Plateau. Its survival relies on the intricate balance of its intestinal microbiome, essential for adapting to harsh environmental conditions. Despite the documented significance of bacteria and fungi in maintaining intestinal homeostasis and supporting immune functions, there is still a substantial gap in understanding how the composition and functionality of yak gut microbiota vary along altitude–temperature gradients. This study aims to fill this gap by employing 16S rRNA and ITS amplicon sequencing techniques to analyze and compare the intestinal microbiome of yaks residing at different elevations and exposed to varying temperatures. The findings demonstrate subtle variations in the diversity of intestinal bacteria and fungi, accompanied by significant changes in taxonomic composition across various altitudes and temperature gradients. Notably, Firmicutes, Actinobacteriota, and Bacteroidota emerged as the dominant phyla across all groups, with Actinobacteriota exhibiting the highest proportion (35.77%) in the LZF group. Functional prediction analysis revealed significant associations between the LZF group and metabolic pathways related to amino acid metabolism and biosynthesis. This suggests a potential role for actinomycetes in enhancing nutrient absorption and metabolism in yaks. Furthermore, our findings suggest that the microbiota of yaks may enhance energy metabolism and catabolism by modulating the Firmicutes-to-Bacteroidota ratio, potentially mitigating the effects of temperature variations. Variations in gut bacterial and fungal communities among three distinct groups were analyzed using metagenomic techniques. Our findings indicate that microbial genera exhibiting significant increases in yaks at lower altitudes are largely beneficial. To sum up, our research investigated the changes in gut bacterial and fungal populations of yaks residing across diverse altitude and temperature ranges. Moreover, these results enhance comprehension of gut microbial makeup and variability, offering perspectives on the environmental resilience of dry lot feeding yaks from a microbial angle.
... Sclerotiniose thus severely impacts mulberry fruit quality and yield. Although a recent report indicated that Sclerotinia sclerotiorum can infect mulberry, three fungi in the Sclerotiniaceae family, namely Ciboria carunculoides, Ciboria shiraiana, and Scleromitrula shiraiana, were reported to be the causal agents of mulberry sclerotial disease [10][11][12][13][14]. ...
Mulberry sclerotiniose is a devastating fungal disease of mulberry fruit and has been a limitation for the utility of mulberry fruits and the diversified development of sericulture. In the present study, we presented a workflow for screening candidate sclerotiniose-resistance genes and small secreted peptides (SSPs) based on a genome-wide annotation of SSPs and comparative transcriptome analysis of different mulberry varieties. A total of 1088 SSPs with expression evidence were identified and annotated in mulberry. A comprehensive analysis of the sclerotiniose-related RNA sequencing datasets showed that photosynthesis, plant hormone signaling, and metabolic pathways were the main pathways involved in the response to sclerotiniose. Fifty-two candidate sclerotiniose-response genes (SRGs), including 15 SSPs, were identified based on comparative transcriptome analysis. These SRGs are mainly involved in the hormone signaling pathway and cell wall biogenesis. Transient overexpression in tobacco and the knock-down of five SRGs affected the resistance against Ciboria shiraiana. MaMYB29, MaMES17, and MaSSP15 were primarily determined as negative regulators of plant resistance to C. shiraiana infection. Our results provide a foundation for controlling sclerotiniose in mulberry using genetic engineering and biological approaches such as spraying antifungal peptides.
... The majority of the 11,860 predicted protein-coding genes are shared by S. sclerotiorum and B. cinerea., with an average similarity between these species of 84% for 8609 proteins [53]. Additionally, S. sclerotiorum shares 157,162 genes and 2605 ortholog families with 15 other fungi, including necrotrophs, biotrophs, and saprobes [115]. In the phylogenetic tree created with STRIDE (Species Tree Root Inference from gene Duplication Events) and STAG (Species Tree inference from All Genes) methods, S. sclerotiorum was grouped with the Leotiomycetes; B. cinerea, S. shiraiana, and B. graminis f. sp. ...
... hordei. Exclusively, S. sclerotiorum, S. shiraiana, and B. cinerea share 7402 ortholog families [115]. Although S. sclerotiorum is evolutionally nearer to Scleromitrula shiraiana and B. cinerea, the genome coverage remains at 72.3% [53] and 21.4% [115], respectively. ...
... Exclusively, S. sclerotiorum, S. shiraiana, and B. cinerea share 7402 ortholog families [115]. Although S. sclerotiorum is evolutionally nearer to Scleromitrula shiraiana and B. cinerea, the genome coverage remains at 72.3% [53] and 21.4% [115], respectively. Based on these results, it is plausible that S. sclerotiorum and B. cinerea diverged from their predecessors later in evolutionary time than S. shiraiana did. ...
Sclerotinia sclerotiorum (Lib.) de Bary is a broad host-range fungus that infects an inclusive array of plant species and afflicts significant yield losses globally. Despite being a notorious pathogen, it has an uncomplicated life cycle consisting of either basal infection from myceliogenically germinated sclerotia or aerial infection from ascospores of carpogenically germinated sclerotia. This fungus is unique among necrotrophic pathogens in that it inevitably colonizes aging tissues to initiate an infection, where a saprophytic stage follows the pathogenic phase. The release of cell wall-degrading enzymes, oxalic acid, and effector proteins are considered critical virulence factors necessary for the effective pathogenesis of S. sclerotiorum. Nevertheless, the molecular basis of S. sclerotiorum pathogenesis is still imprecise and remains a topic of continuing research. Previous comprehensive sequencing of the S. sclerotiorum genome has revealed new insights into its genome organization and provided a deeper comprehension of the sophisticated processes involved in its growth, development, and virulence. This review focuses on the genetic and genomic aspects of fungal biology and molecular pathogenicity to summarize current knowledge of the processes utilized by S. sclerotiorum to parasitize its hosts. Understanding the molecular mechanisms regulating the infection process of S. sclerotiorum will contribute to devising strategies for preventing infections caused by this destructive pathogen.
... About 126 plant pathogenic bacterial species have a draft or complete genome sequence available. Genomic information on plant pathogens is important to the scientific community in several fundamental ways: 1) Understanding the underlying molecular mechanisms of host specificity and range (Ailloud et al., 2015;Newman and Derbyshire;Lv et al., 2021); 2) Investigating the potential virulence mechanisms and expression pattern differences between different strains (Garita-Cambronero et al., 2016;Susič et al., 2020;Goettelmann et al., 2022); 3) Capable of discerning the causal agent for plant disease development (Pecman et al., 2017;Saville and Ristaino, 2021;Yang et al., 2022); 4) Study of non-cultured microbes (Parks et al., 2017;Lapidus and Korobeynikov;; 5)Taxonomic classification (Prior et al., 2016;Bansal et al., 2021); 6) Examine genetic similarity and difference within and between populations (Jacques et al., 2016;Shah et al., 2021;Xu et al., 2021); 7) Exploring the mechanisms of bacterial evolution and host-bacteria coevolution (Shapiro et al., 2016;Rocha et al., 2020); 8) Determine the mechanisms of hosts resistance and susceptibility (Dalio et al., 2017;Kankanala et al., 2019). Such rigorous knowledge of the biological phenomenon enhances the management of abiotic and biotic stress and disease control and improves plant health, consequently increasing crop yield and food quality (Haggag et al., 2015;Hamilton et al., 2016). ...
The success of sustainable agricultural practices has now become heavily dependent on the interactions between crop plants and their associated microbiome. Continuous advancement in high throughput sequencing platforms, omics-based approaches, and gene editing technologies has remarkably accelerated this area of research. It has enabled us to characterize the interactions of plants with associated microbial communities more comprehensively and accurately. Furthermore, the genomic and post-genomic era has significantly refined our perspective toward the complex mechanisms involved in those interactions, opening new avenues for efficiently deploying the knowledge in developing sustainable agricultural practices. This review focuses on our fundamental understanding of plant-microbe interactions and the contribution of existing multi-omics approaches, including those under active development and their tremendous success in unraveling different aspects of the complex network between plant hosts and microbes. In addition, we have also discussed the importance of sustainable and eco-friendly agriculture and the associated outstanding challenges ahead.
... For the congeneric fungi, Calcarisporium parasiticum has been observed to parasitize several species of Physalospora and closely related fungi [87]. Scleromitrula shiraiana is a causal agent of mulberry sclerotial disease with a narrow host range but includes some species of genus Morus [88]. ...
... In the genome of E. weberi, a specific parasite of ant cultivated Leucoagaricus spp., the depletion of CAZymes was also found [100]. There were fewer genes encoding cell wall-degrading enzymes and effector proteins in the genome of Sclerotinia shiraiana than those of Sclerotinia sclerotiorum and B. cinerea, which was probably a key factor of the narrow host range of S. shiraiana [88]. ...
Calcarisporium cordycipiticola is the pathogen in the white mildew disease of Cordyceps militaris, one of the popular mushrooms. This disease frequently occurs and there is no effective method for disease prevention and control. In the present study, C. militaris is found to be the only host of C. cordycipiticola, indicating strict host specificity. The infection process was monitored by fluorescent labeling and scanning and transmission electron microscopes. C. cordycipiticola can invade into the gaps among hyphae of the fruiting bodies of the host and fill them gradually. It can degrade the hyphae of the host by both direct contact and noncontact. The parasitism is initially biotrophic, and then necrotrophic as mycoparasitic interaction progresses. The approximate chromosome-level genome assembly of C. cordycipiticola yielded an N50 length of 5.45 Mbp and a total size of 34.51 Mbp, encoding 10,443 proteins. Phylogenomic analysis revealed that C. cordycipiticola is phylogenetically close to its specific host, C. militaris. A comparative genomic analysis showed that the number of CAZymes of C. cordycipiticola was much less than in other mycoparasites, which might be attributed to its host specificity. Secondary metabolite cluster analysis disclosed the great biosynthetic capabilities and potential mycotoxin production capability. This study provides insights into the potential pathogenesis and interaction between mycoparasite and its host.
Background: Soil health is critical for sustaining life, influenced by the complex interactions between soil, microorganisms, and plants; indulging in these interactions is indispensable for sustainable agriculture. This chapter explores how plant–soil–microbe dynamics affect soil ecosystem health, focusing on how microorganisms influence nutrient uptake, stress resilience, and plant development.
Scope: Plant growth-promoting microorganisms are helpful in promoting plant growth by taking part in nutrient recycling, suppressing diseases, and mitigating innumerable types of stresses. Through an extensive review of literature and empirical evidence, this chapter elucidates the intricate interplay between plants and microorganisms within soil ecosystems. This chapter also underscores the role of PGPRs in biofertilization, pathogen bio-control, and abiotic stress mitigation strategies.
Conclusion: This chapter explores various omics-based studies in the area of plant–soil–microbe interactions. By understanding and leveraging the symbiotic relationship between plants and microorganisms, we can advance our efforts toward fostering resilient and productive soil ecosystems. This chapter also tries to provide a way to use these studies in the agriculture field to improve crop production and soil health.
Plant recognition of pathogen-associated molecular patterns (PAMPs) is pivotal in triggering immune responses, highlighting their potential as inducers of plant immunity. However, the number of PAMPs identified and applied in such contexts remains limited. In this study, we characterize a novel PAMP, designated Ss4368, which is derived from Scleromitrula shiraiana. Ss4368 is specifically distributed among a few fungal genera, including Botrytis, Monilinia, and Botryotinia. The transient expression of Ss4368 elicits cell death in a range of plant species. The signaling peptides, three conserved motifs, and cysteine residues (C46, C88, C112, C130, and C148) within Ss4368 are crucial for inducing robust cell death. Additionally, these signaling peptides are essential for the protein’s localization to the apoplast. The cell death induced by Ss4368 and its homologous protein, Bc4368, is independent of the SUPPRESSOR OF BIR1-1 (SOBIR1), BRI1-ASSOCIATED KINASE-1 (BAK1), and salicylic acid (SA) pathways. Furthermore, the immune responses triggered by Ss4368 and Bc4368 significantly enhance the resistance of Nicotiana benthamiana to Phytophthora capsici. Therefore, we propose that Ss4368, as a novel PAMP, holds the potential for developing strategies to enhance plant resistance against P. capsici.
Many gene banks have adopted various genomic tools and have integrated them into their routine genebank operations. In this chapter, we review the actual and potential applications of genomics in advancing seed bank-based ex situ conservation and utilization of plant genetic resources. Genomic tools are supporting germplasm acquisition efforts through conservation gap analysis and enabling the identification of rare, threatened, and novel genetic resources that need to be prioritized for conservation. Analysis of germplasm from different environments using transcriptomic approaches assists in identifying the candidate genes associated with desirable traits and biologically important pathways. Identification of genetic redundancy is enabling collection rationalization thus enhancing cost efficiency in plant genetic resources conservation. Genomics is providing greater capacity on developing core collections and trait-specific subsets thus promoting utilization of plant genetic resource collections. Emerging genomic technologies are providing capacity to support in situ conservation and biodiversity restoration using ex situ conserved diversity. Analysis of genome environment associations is enabling the identification of germplasm that potentially possesses the necessary adaptive capacity and desired traits. The lack of a standardized approach on documenting and sharing big genomic data being generated from ex situ collections however remains a major challenge in enhancing genomics-assisted conservation.
