Dataset Information

Fungal Mitogenomes: Relevant Features to Planning Plant Disease Management.

ABSTRACT: Mitochondrial genomes (mt-genomes) are characterized by a distinct codon usage and their autonomous replication. Mt-genomes encode highly conserved genes (mt-genes), like proteins involved in electron transport and oxidative phosphorylation but they also carry highly variable regions that are in part responsible for their high plasticity. The degree of conservation of their genes is such that they allow the establishment of phylogenetic relationships even across distantly related species. Here, we describe the mechanisms that generate changes along mt-genomes, which play key roles at enlarging the ability of fungi to adapt to changing environments. Within mt-genomes of fungal pathogens, there are dispensable as well as indispensable genes for survival, virulence and/or pathogenicity. We also describe the different complexes or mechanisms targeted by fungicides, thus addressing a relevant issue regarding disease management. Despite the controversial origin and evolution of fungal mt-genomes, the intrinsic mechanisms and molecular biology involved in their evolution will help to understand, at the molecular level, the strategies for fungal disease management.

SUBMITTER: Medina R

PROVIDER: S-EPMC7272585 | biostudies-literature | 2020

REPOSITORIES: biostudies-literature

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Fungal Mitogenomes: Relevant Features to Planning Plant Disease Management.

Medina Rocio R Franco Mario Emilio Ernesto MEE Bartel Laura Cecilia LC Martinez Alcántara Virginia V Saparrat Mario Carlos Nazareno MCN Balatti Pedro Alberto PA

Frontiers in microbiology 20200529

Mitochondrial genomes (mt-genomes) are characterized by a distinct codon usage and their autonomous replication. Mt-genomes encode highly conserved genes (mt-genes), like proteins involved in electron transport and oxidative phosphorylation but they also carry highly variable regions that are in part responsible for their high plasticity. The degree of conservation of their genes is such that they allow the establishment of phylogenetic relationships even across distantly related species. Here, ...[more]

PMID: 32547508

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Project description:BackgroundThe potentially negative effects of timber harvesting on biodiversity and habitat conservation leads to the consideration of a wide range of restrictions to forest logging in natural areas. In particular, high noise levels produced by forest machinery present a challenge to developing sustainable forest management plans. The Cinereous vulture (Aegypius monachus), the largest bird of prey whose nests are located in mature trees, is considered to be appropriate as an indicator species for environment-friendly forest planning. In this work, we evaluated spatially differences in sound propagation between stands. We hypothesized that differences due to the influence of orography in mountainous forests would allow the relaxation of spatial and temporary restrictions to timber logging, without causing any great disturbance at nesting sites of sensitive species.MethodsOur study was conducted in a Scots pine (Pinus sylvestris) forest of Spain, where an important colony of the Western European population of Cinereous vulture is located. We built 62 noise maps to characterize noise pollution due to tree logging at planning level. We modeled two different scenarios, in order to characterize; (i) the effect of a chainsaw operator during a complete cycle for felling a tree (Scenario 1), and (ii) the effect of the peak level produced by the breaking noise emitted by the trunk of the tree and its impact on the ground (Scenario 2). A strategy of three logical steps was designed; (i) landscape-scale analysis of noise propagation in stands, (ii) hierarchical cluster analysis of stands, (iii) assessment of the potentially significant influence of noise management in timber harvesting.ResultsThe minimum distance (DIST) from chainsaw operator sites to the 40 dB(A) contour lines was the only variable that had a significant influence on the clustering results. On the other hand, mean values of a newly proposed metric called average radius or radial distance (ARD) oscillated between 174 m in cluster #1 (Scenario 1) and 407 m in cluster #2 (Scenario 2).DiscussionOur results highlight the convenience of considering noise modeling tools at a forest planning level in order to address the compatibility of forest logging and the necessity of protecting nature. We found that spatial propagation of noise made by chainsaws at felling sites does not differ between stands even in a mountainous terrain, contrary to what we initially hypothesized. However, temporary logging restrictions could be excluded in about 36% of the current conditioned management areas according to ARD results in Scenario 2 (400 m). This proposal could be based on a sound pressure level (in decibels) criteria instead of conventional buffer protection distance criteria. In addition, it is suggested that the current size of restricted management areas could be generally extended from a 100 m radius to a 200 m one around the Cinereous vulture nest sites.

Project description:The folding and dynamics of three-dimensional (3D) genome organization are fundamental for eukaryotes executing genome functions but have been largely unexplored in nonmodel fungi. Using high-throughput sequencing coupled with chromosome conformation capture (Hi-C) data, we generated two chromosome-level assemblies for Puccinia striiformis f. sp. tritici, a fungus causing stripe rust disease on wheat, for studying 3D genome architectures of plant pathogenic fungi. The chromatin organization of the fungus followed a combination of the fractal globule model and the equilibrium globule model. Surprisingly, chromosome compartmentalization was not detected. Dynamics of 3D genome organization during two developmental stages of P. striiformis f. sp. tritici indicated that regulation of gene activities might be independent of the changes of genome organization. In addition, chromatin conformation conservation was found to be independent of genome sequence synteny conservation among different fungi. These results highlighted the distinct folding principles of fungal 3D genomes. Our findings should be an important step toward a holistic understanding of the principles and functions of genome architecture across different eukaryotic kingdoms. IMPORTANCE Previously, our understanding of 3D genome architecture has mainly come from model mammals, insects, and plants. However, the organization and regulatory functions of 3D genomes in fungi are largely unknown. In this study, we comprehensively investigated P. striiformis f. sp. tritici, a plant fungal pathogen, and revealed distinct features of the 3D genome, comparing it with the universal folding feature of 3D genomes in higher eukaryotic organisms. We further suggested that there might be distinct regulatory mechanisms of gene expression that are independent of chromatin organization changes during the developmental stages of this rust fungus. Moreover, we showed that the evolutionary pattern of 3D genomes in this fungus is also different from the cases in mammalian genomes. In addition, the genome assembly pipeline and the generated two chromosome-level genomes will be valuable resources. These results highlighted the unexplored distinct features of 3D genome organization in fungi. Therefore, our study provided complementary knowledge to holistically understand the organization and functions of 3D genomes across different eukaryotes.

Dataset Information

Fungal Mitogenomes: Relevant Features to Planning Plant Disease Management.

Publications

Fungal Mitogenomes: Relevant Features to Planning Plant Disease Management.

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