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Further understanding of the M. phaseolina genome-based plant-pathogen interactions will be instrumental in designing rational strategies for disease control, essential to ensuring global agricultural crop production and security. (biomedcentral.com)
Magnaporthe oryzae , Magnaporthe grisea ), a member of the order Magnaporthales in the class Sordariomycetes, is an important plant pathogen and a model species for studying pathogen infection and plant-fungal interaction. (nature.com)
Furthermore, genome data from non-pathogen lineages are necessary to provide a more robust comparative genomic framework to help place the rice blast fungus in an evolutionary context and to understand the evolution of pathogenesis and other characters of these important organisms. (nature.com)
Signatures of host specialization and a recent transposable element burst in the dynamic one-speed genome of the fungal barley powdery mildew pathogen. (mpg.de)
Mosaic genome structure of the barley powdery mildew pathogen and conservation of transcriptional programs in divergent hosts. (mpg.de)
A major focus is to use genome-wide association studies (GWAS) to directly identify the genes in pathogen genomes linked to the breakdown of host resistance. (unibas.ch)
Three-dimensional chromatin organization promotes genome evolution in a fungal plant pathogen. (uni-koeln.de)
An ancient antimicrobial protein co-opted by a fungal plant pathogen for in planta mycobiome manipulation. (uni-koeln.de)
Transposable elements contribute to genome dynamics and gene expression variation in the fungal plant pathogen Verticillium dahliae . (uni-koeln.de)
To further test the effects of transposon-aided gene amplifications on genome evolution and architecture, the repetitive fraction of the significantly expanded genome of the banana pathogen, Pseudocercospora fijiensis , was analyzed in greater detail. (biomedcentral.com)
a property which associates better with genome size than pathogen lifestyle. (edu.au)
Here, we address this by assembling a global thousand-genome panel of Zymoseptoria tritici, a major fungal pathogen of wheat reported in all production areas worldwide. (bvsalud.org)
Emphasis on cereal-infecting fungal pathogen systems: Structural & Functional Genomic and Proteomic analyses to discover the molecular basis of the wheat leaf rust fungus, Puccinia triticina, and the barley smut, Ustilago hordei, pathogenic and virulence capabilities. (ubc.ca)

Macrophomina phaseolina is one of the most destructive necrotrophic fungal pathogens that infect more than 500 plant species throughout the world. (biomedcentral.com)
The order Magnaporthales in the fungal class Sordariomycetes (Ascomycota) contains economically important pathogens of cereals and grasses, such as the rice blast fungus Pyricularia oryzae (syn. (nature.com)
The best studied species in Magnaporthales is the rice blast fungus, which was ranked number one on the "Top 10 fungal plant pathogens" list based on scientific and economic importance in a survey of 495 votes from the international plant mycology community 1 . (nature.com)
To this end, we recently sequenced the genomes of five species and generated transcriptomes from 21 species of Magnaporthales, including saprobes and plant pathogens 9 . (nature.com)
Most plants face attacks by fungal pathogens. (unibas.ch)
In fungal and oomycete plant pathogens, besides modulating genome size (e.g. (biomedcentral.com)
Genomics on major agricultural fungal pathogens: the basidiomycete wheat leaf rust fungus, Puccinia triticina , and the barley covered smut fungus, Ustilago hordei . (ubc.ca)

For example, Alu elements, at more than a million copies comprising 11% of the human genome, are a major contributor to primate genome evolution and the standing genetic diversity in human populations [ 3 ]. (biomedcentral.com)
To prevent companies and governments from stealing genes, invading genetic privacy and undermining human rights and dignity, we urgently need a Genetic Bill of Rights and a Global Ethics Council, Mae-Wan Ho warns of the fall-outs from the human genome project. (i-sis.org.uk)
These are some of the fall-outs from the Human Genome Project (see Human Genome: The Biggest Sellout in Human History, this issue). (i-sis.org.uk)
See how the University of Washington used HiFi sequencing to uncover a key finding about ALS and the human genome. (pacb.com)
Broad Genomics Platform sequences a whole human genome every four minutes. (broadinstitute.org)
In November 2022, Broad's Genomics Platform sequenced its 500,000th whole human genome, a mere four years after sequencing its 100,000th. (broadinstitute.org)
Engineering the human genome: reflections on the beginning. (chop.edu)

These data are substantiated by other examples in the literature showing that fungi tend to have a "two-speed" genome, in which a plastic compartment enriched in TE host genes is involved in pathogenicity and adaptation to host. (pasteur.fr)
These rapid adaptations in fungi provide excellent models for studying general processes of eukaryotic genome evolution, including the functional and ecological impact of horizontal gene transfer 1 and changes in metabolism 2 . (nature.com)
In this study, we generated genome sequence data from five additional Magnaporthales fungi including non-pathogenic species, and performed comparative genome analysis of a total of 13 fungal species in the class Sordariomycetes to understand the evolutionary history of the Magnaporthales and of fungal pathogenesis. (nature.com)
Finally, analysis of transposable elements (TE) showed differing proportions of TE classes among Magnaporthales genomes, suggesting that species-specific patterns may hold clues to the history of host/environmental adaptation in these fungi. (nature.com)
Supercharging SIP in the Fungal Hyphosphere Applying high-throughput stable isotope probing to the study of a particular fungi, researchers identified novel interactions between bacteria and the fungi. (doe.gov)
Fungi, with their multifaceted phenotypic diversity and relatively small genome size, are ideal models to study the role of TEs in genome evolution and their impact on the host's ecological and life history traits. (inrae.fr)
In clonally reproducing dikaryotic rust fungi, non-sexual processes such as somatic nuclear exchange are postulated to play a role in diversity but have been difficult to detect due to the lack of genome resolution between the two haploid nuclei. (bvsalud.org)
A random mutagenesis tool for filamentous fungi based on a transposable elements has been developed, which will be highly useful to generate knock-out mutants on a large scale. (marinefungi.eu)
Until recently, however, functional analysis of the DED fungi was hampered by the lack of protocols for efficient gene knockout and by the unavailability of a full genome sequence. (sisef.it)
The small genomes of the DED fungi also facilitate genomic analyses. (sisef.it)
We have sequenced the genomes of 18 isolates of the closely related human pathogenic fungi Coccidioides immitis and Coccidioides posadasii to more clearly elucidate population genomic structure, bringing the total number of sequenced genomes for each species to 10. (broadinstitute.org)
are the Mucorales fungi that most commonly cause mucormycosis ( 1 , 2 , 4 ) and are the most common non- Aspergillus cause of invasive filamentous fungal infections ( 5 ). (cdc.gov)
DNA methylation is an important epigenetic control mechanism that in many fungi is restricted to genomic regions containing transposable elements (TEs). (biomedcentral.com)
Compared to animal and plant genomes, fungi typically have smaller and less complex genomes, and they serve as important eukaryote models for various cellular processes including DNA methylation [ 9 ]. (biomedcentral.com)

Furthermore, 36 (28.6%) out of 126 isolates had a transposable element (TE) insertion in AVR-Pib , which resulted in altered virulence. (researchsquare.com)

The laboratory also was involved in analysis and annotation of fungal genome sequences. (marinefungi.eu)
The ongoing annotation of these genomes should spark a new wave of interest in the DED pathosystem, as it should lead to the formal identification of genes modulating parasitic fitness. (sisef.it)
The JGI Annotation Pipeline was used to add functional annotation to this genome. (doe.gov)
Generation of whole genome sequences and annotation efforts, bioinformatic database mining and comparative analyses among rusts. (ubc.ca)
2021) Aethionema arabicum genome annotation using PacBio full-length transcripts provides a valuable resource for seed dormancy and Brassicaceae evolution research. (oeaw.ac.at)

In 2013, the genome sequences of O. ulmi and O. novo-ulmi were publicly released. (sisef.it)
Interestingly, only 20 percent of the genome was made up of transposable elements, one of the natural pathways through which genetic sequences change," said Guiltinan "They do this by moving around the chromosomes, changing the order of the genetic material. (phys.org)
Results: Here, we present a high-quality chromosome-level genome assembly of the Hong Kong oyster, Magallana hongkongensis (2n = 20), for which 93.2% of the genomic sequences are contained on 10 pseudomolecules (~758Mb, scaffold N50 = 72.3Mb). (st-andrews.ac.uk)

Beyond recent advances in genomic and phenomic methods, bioinformatics tools and modeling approaches enable researchers to test hypothesis and expand our knowledge of fungal biodiversity. (frontiersin.org)
Looking to the future, the pairing of integrative taxonomy approaches with multi-locus genomic sequencing and phenomic techniques, such as transcriptomics and proteomics, holds great potential to resolve many unknowns in fungal taxonomic classification. (frontiersin.org)
TE-rich genomic islands in expanded fungal ( P. fijiensis , L. maculans ) and oomycete ( Phytophthora infestans ) genomes carry genes that code for lineage-specific, putative small, secreted proteins. (biomedcentral.com)
We find that the global expansion was accompanied by increased activity of transposable elements and weakened genomic defenses. (bvsalud.org)
In animals, some homeobox genes are clustered together in the genome, either as remnants from ancestral genomic arrangements, or due to coordinated gene regulation. (st-andrews.ac.uk)

Compared to other species of the species complex, the species best adapted to oilseed rape, L. maculans "brassicae", causing important losses in the crop, has a genome that was submitted to a recent and massive burst of transposition by a few families of transposable elements (TEs). (pasteur.fr)
Whether the genome invasion contributed to speciation is still unclear to-date but there is a coincidence between this burst of TEs and divergence between two species. (pasteur.fr)
Nonphagotrophic mechanisms have been seen in the transmission of transposable elements, plastid-derived endosymbiotic gene transfer, prokaryote-derived gene transfer, Agrobacterium tumefaciens-mediated DNA transfer, cross-species hybridization events, and gene transfer between mitochondrial genes. (wikipedia.org)
These features include: inconsistency between phylogeny across genetic elements, high DNA or amino acid similarity from phylogenetically distant organisms, irregular distribution of genetic elements in a variety of species, similar genes shared among species within a specific habitat or geography independent of their phylogenetic relationship, and gene characteristics inconsistent with the resident genome such as high guanine and cytosine content, codon usage, and introns. (wikipedia.org)
Species concepts criteria for fungal delimitation. (frontiersin.org)
The blast clade genomes contain more secretome and avirulence effector genes, which likely play key roles in the interaction between Pyricularia species and their plant hosts. (nature.com)
The genomes of several other phytopathogenic species in the Magnaporthales have thereafter been sequenced 8 . (nature.com)
Transposable elements (TEs) are mobile genetic elements that can profoundly impact the evolution of genomes and species. (stenci.la)
Here we present an account of all TEs found in a high-quality reference genome of the lichen-forming fungus Umbilicaria pustulata, a macrolichen species comprising two climatic ecotypes: Mediterranean and cold temperate. (inrae.fr)
In the case of DED, three fungal species are known to induce the disease. (sisef.it)
How many DNA markers are needed to reveal cryptic fungal species? (google.com.ec)
Smaller amounts of transposons than found in other plant species could lead to slower evolution of the chocolate plant, which was shown to have a relatively simple evolutionary history in terms of genome structure. (phys.org)
Conclusions: The analyses performed in this study and the accompanying genome sequence provide important genetic resources for this economically and culturally valuable oyster species, and offer a platform to improve understanding of animal biology and evolution more generally. (st-andrews.ac.uk)
Transposable element content is comparable to that found in other mollusc species, contrary to the conclusion of another recent analysis. (st-andrews.ac.uk)

We also assemble complete genomes to analyze mechanisms that generate high degrees of sequence polymorphism. (unibas.ch)
Genome evolution in P teres is characterized by genome fissuring through the insertion and expansion of transposable elements (TEs), a process that isolates blocks of genic sequence. (edu.au)
The genome sequence of Barbarea vulgaris facilitates the study of ecological biochemistry. (pacb.com)
Here we report a draft genome sequence of the G-type, and re-sequencing of the P-type for comparison. (pacb.com)
Draft genome sequence of Micromonospora sp. (pacb.com)
Complete genome sequence of Kosakonia oryzae type strain Ola 51(T). (pacb.com)
Here we summarize the features of the strain Ola 51(T) and describe its complete genome sequence. (pacb.com)
We find notable heterogeneity in repetitive sequence composition among the sequenced genomes and present the first detailed genome-wide profile of a repeat-induced point mutation (RIP) process distinctly different from what has been observed in Neurospora. (broadinstitute.org)
The Geosiphon pyriformis genome sequence and gene models were not determined by the Joint Genome Institute (JGI), but were provided by Nicolas Corradi and Mathu Malar C at the University of Ottawa. (doe.gov)

In this paper, we evaluate the link between genome plasticity and adaptive potential using genomics and comparative genomics approaches. (pasteur.fr)
Silver Age of GOLD Introduces New Features The Genomes OnLine Database makes curated microbiome metadata that follows community standards freely available and enables large-scale comparative genomics analysis initiatives. (doe.gov)
Bioinformatics Plant genomics and genome evolution, transposable elements, and regulatory gene evolution. (uga.edu)
Plant Biology Genome bioinformatics, ecological and evolutionary genomics of yeast. (uga.edu)
Plant Biology Crop genetics, comparative genomics and genome evolution. (uga.edu)
The team suggests that a functional genomics approach, one that looks at what the genes do, is needed to confirm potential disease resistant genes in the Criollo genome. (phys.org)

Evidence is found in the unusual features of genetic elements. (wikipedia.org)
In this review we discuss these major challenges and describe methodological approaches that show promise for resolving ambiguity in fungal taxonomy by improving discrimination of genetic and functional traits. (frontiersin.org)
Transposable elements (TEs) or mobile genetic elements are nucleic acid entities that can move in a genome. (biomedcentral.com)
Comprehensive genome assemblies were constructed from long DNA reads, optical and genetic maps. (edu.au)
Genome sequencing of multiple R. solanacearum strains has identified both unique and shared genetic traits influencing their evolution and ability to colonize plant hosts. (pacb.com)
Molecular genetic and cell biological understanding of plant-microbial interactions including attributes that make microbes pathogenic such as pathogenicity and virulence factors including fungal mating systems. (ubc.ca)
Our analysis of the Criollo genome has uncovered the genetic basis of pathways leading to the most important quality traits of chocolate -- oil, flavonoid and terpene biosynthesis," said Siela Maximova, associate professor of horticulture, Penn State, and a member of the research team. (phys.org)

As repeat masking in fungal genomes influences the final gene annotations, an accurate and reproducible pipeline was developed to ensure comparability between isolates. (edu.au)
Assembled genomes of most isolates were ≈25 Mbp, and multiple isolates had substantially larger assembled genomes (43-51 Mbp), indicative of infections with strain types that underwent genome expansion. (cdc.gov)

Tracing the Evolution of Shiitake Mushrooms Understanding Lentinula genomes and their evolution could provide strategies for converting plant waste into sugars for biofuel production. (doe.gov)
We are particularly interested in the action of transposable elements (selfish elements in the genome) and the evolution of gene regulation. (unibas.ch)
Genome Biology & Evolution 13: evab135. (uni-koeln.de)
Transposable elements (TEs) can be key drivers of evolution, but the mechanisms and scope of how they impact gene and genome function are largely unknown. (biomedcentral.com)
These results indicate that the interplay of TEs and RIP can result in different and unpredictable fates of amplified genes, with variable effects on gene and genome evolution. (biomedcentral.com)
TEs have been detected in the genomes of both prokaryotic and eukaryotic organisms [ 1 ], and have been rightly labeled as 'drivers of genome evolution' [ 2 ] due to their direct and indirect impacts on genes and genomes. (biomedcentral.com)
Background: Homeobox-containing genes encode crucial transcription factors involved in animal, plant and fungal development, and changes to homeobox genes have been linked to the evolution of novel body plans and morphologies. (st-andrews.ac.uk)
Consequently, analyses of homeobox gene organization across animal phylogeny provide important insights into the evolution of genome organization and developmental gene control, and their interaction. (st-andrews.ac.uk)

G3-Genes Genomes Genetics , 5 (12), 2539-2545. (ncsu.edu)
Fungal Genetics and Biology is a journal indexed in SJR in Genetics and Microbiology with an H index of 119. (countryofpapers.com)
What is the impact factor of Fungal Genetics and Biology? (countryofpapers.com)
Since then it is involved in different aspects of fungal molecular genetics. (marinefungi.eu)

Fungal dual-domain LysM effectors undergo chitin-induced intermolecular, and not intramolecular, dimerization. (uni-koeln.de)
Gene differences between P. teres forms are mainly associated with gene-sparse regions near or within TE-rich regions, with many genes possessing characteristics of fungal effectors. (edu.au)
The Ustilago hordei-barley interaction is a versatile system to characterize fungal effectors. (ubc.ca)

Previous analyses revealed that TE-mediated gene amplifications can have variable effects on fungal genomes, from inactivation of function to production of multiple active copies. (biomedcentral.com)
Comparative analyses revealed that a similar event occurred in five additional genomes representing the fungal genera Cercospora , Pseudocercospora and Sphaerulina . (biomedcentral.com)
In order to allow comparative analyses with other fungal genomes sequenced by the JGI, a copy of this genome is incorporated into MycoCosm. (doe.gov)

In N. crassa , DNA methylation is restricted to transposable elements (TEs) and is dependent on a single DNMT, Deficient In Methylation-2 (Dim2), an ortholog of Human Dnmt1 that performs de novo as well as maintenance methylation [ 10 ]. (biomedcentral.com)

To determine the likelihood of a common source of the cluster, we performed whole-genome sequencing on samples collected during 2006-2014. (cdc.gov)
Whole-genome sequencing has become an essential tool for studying epidemiology of fungal infections. (cdc.gov)

2021) A genome-wide association study unravels cytokinin as a major component in the root defense responses against Ralstonia solanacearum. (oeaw.ac.at)
2021) 1,135 ionomes reveals the global pattern of leaf and seed mineral nutrient and trace element diversity in Arabidopsis thaliana. (oeaw.ac.at)
Déléris A, Berger F, Duharcourt S (2021) Role of Polycomb in the control of transposable elements. (oeaw.ac.at)

The phenomenon is particularly pronounced in PTT, which has a larger, more repetitive genome than PTM and more recent transposon activity measured by the frequency and size of genome fissures. (edu.au)

Transposable elements (TEs) are an important source of genome plasticity across the tree of life. (inrae.fr)

The researchers assembled 84 percent of the genome identifying 28,798 genes that code for proteins. (phys.org)
Hidden in the genome the researchers also found genes that code for the production of cocoa butter, a substance highly prized in chocolate making, confectionary, pharmaceuticals and cosmetics. (phys.org)

In addition, the location of effector genes within genome regions enriched in TEs has direct consequences on adaptation to plant resistance and favours a multiplicity of mutation events allowing "breakdown" of resistance. (pasteur.fr)

The M. phaseolina genome provides a framework of the infection process at the cytological and molecular level which uses a diverse arsenal of enzymatic and toxin tools to destroy the host plants. (biomedcentral.com)
Analysis of fungal and host transcriptomes (gene expression patterns) and proteomes during P. triticina - wheat and U. hordei - barley interactions and infection. (ubc.ca)

Microbiota manipulation through the secretion of effector proteins is fundamental to the wealth of lifestyles in the fungal kingdom. (uni-koeln.de)
Here, we reported the first Oceanospirillum phage, vB_OliS_GJ44, which was assembled into a 33,786 bp linear dsDNA genome, which includes abundant tail-related and recombinant proteins. (biomedcentral.com)

A phylogeny was constructed from 1689 identified genes and all homologs available from the rice genome (3177 gene families). (wikipedia.org)

Our genome assembly was scaffolded using Hi-C reads, facilitating a larger scaffold size compared to the recently published M. hongkongensis genome of Peng et al (2020), which was scaffolded using the Crassostrea gigas assembly. (st-andrews.ac.uk)

The B. vulgaris genome will promote the study of mechanisms in ecological biochemistry to benefit crop resistance breeding. (pacb.com)

We examined three nuclear-phased genome assemblies of Puccinia triticina, which causes wheat leaf rust disease. (bvsalud.org)

construction of a shuttle vector for heterologous expression of a novel fungal α-amylase gene in aspergillus oryzae. (liverpool.ac.uk)

We established genome-wide patterns of H3K27me3 and H3K9me3 modifications, and found these marks mutually exclusive within gene-rich regions but not within repeats. (biomedcentral.com)

Overall, there is growing recognition that a single set of criteria do not sufficiently describe the diversity seen among fungal lineages. (frontiersin.org)
Haplotype-specific phylogenetic analysis reveals that repeated somatic exchange events have shuffled haploid nuclei between long-term clonal lineages, leading to a global P. triticina population representing different combinations of a limited number of haploid genomes. (bvsalud.org)

Gene silencing induced by small RNAs (sRNAs) is an important mechanism responsible for many crucial physiological responses in plants, such as genome integrity, defense against virus, adaptation to biotic and abiotic stresses and regulation of development. (edu.au)

Similar mechanisms of epigenetic silencing in the fungal kingdom have remained elusive. (edu.au)

Plant shikimate pathway enzymes share similarities to prokaryote homologs and could have ancestry from a plastid progenitor genome. (wikipedia.org)

The interspecific fungal hybrid Verticillium longisporum displays subgenome-specific gene expression. (uni-koeln.de)
Some major effects of Alu -element amplifications include alterations of gene expression from insertions near gene promotors, insertional mutagenesis and repeat-mediated non-homologous recombination that can lead to disease, and 'exonization' of Alu elements yielding alternative splicing of transcripts. (biomedcentral.com)

The genome of Geosiphon pyriformis reveals ancestral traits linked to the emergence of the arbuscular mycorrhizal symbiosis. (doe.gov)

Transfers of a single gene, a complete metabolic pathway 10 , whole chromosomes 11 or even cases of the integration of almost complete genomes from bacterial endosymbionts into their eukaryotic hosts 12 have been described. (nature.com)

A highly polymorphic effector protein promotes fungal virulence through suppression of plant-associated Actinobacteria. (uni-koeln.de)

The team's work identified a variety of gene families that may have future impact on improving cacao trees and fruit either by enhancing their attributes or providing protection from fungal diseases and insects that effect cacao trees. (phys.org)

Genome Insider: Methane Makers in Yosemite's Lakes Meet researchers who sampled the microbial communities living in the mountaintop lakes of the Sierra Nevada mountains to see how climate change affects freshwater ecosystems, and how those ecosystems work. (doe.gov)
But with two projects, communities are forming to generate high quality genomes to benefit researchers. (doe.gov)
The researchers identified two types of disease resistance genes in the Criollo genome. (phys.org)

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