Fungarium phylogenomics
Ontology highlight
ABSTRACT:
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| CEMC01.dat.gz | Other | |||
| CEMC01.fasta.gz | Fasta.gz | |||
| CEMC01.master.dat | Other | |||
| CEMG01.dat.gz | Other | |||
| CEMG01.fasta.gz | Fasta.gz |
Items per page: 5 1 - 5 of 74 |
Similar Datasets
Project description:Molecular networking and pattern-based genome mining improves discovery of biosynthetic gene clusters and their products from Salinispora
2016-01-27 | MSV000079484 | GNPS
Project description:We investigated genome folding across the eukaryotic tree of life. We find four general manifestations of genome organization at chromosome-scale that each emerge and disappear repeatedly over the course of evolution. The submission represents chromosome-length Hi-C contact maps, architecture type and homolog separation analyses for 26 species across the tree of life, representing all subphyla of chordates, all 7 extant vertebrate classes, and 7 out of 9 major animal phyla, as well as plants and fungi.
2021-04-23 | GSE169088 | GEO
Project description:Deep sequencing of mRNA from Chinese tree shrew; Chinese tree shrew (Tupaia belangeri chinensis) is placed in Order Scandentia and embraces many unique features for a good experimental animal model. Currently, there are many attempts to employ tree shrew to establish model for a variety of human disorders such as social stress, myopia, HCV and HBV infection, and hepatocellular carcinoma .We present here a publicly available annotated genome sequence for Chinese tree shrew. Phylogenomic analysis of tree shrew and other mammalians highly supported its close affinity to primates. Characterization of key factors and signaling pathways of the nervous and immune systems in tree shrews showed that this animal had common and unique features, and had essential genetic basis for being a promising model for biomedical researches. Analysis of ploy(A)+ RNA of different specimens:kidney, pancreas, heart, liver, brain, testis and ovary form Chinese tree shrew
2013-01-14 | E-GEOD-39150 | biostudies-arrayexpress
Project description:We sought to characterize the host response through proteome profiling of nasopharyngeal swab specimens. A mass spectrometer combining trapped ion mobility spectrometry and high-resolution QTOF mass spectrometer with a parallel accumulation-serial fragmentation (PASEF) was deployed for unbiased proteome profiling. First, deep proteome profiling of nasopharyngeal swabs was performed in PASEF-DDA mode, which identified 7,723 proteins and 102,392 peptides that were then used for constructing a spectral library. Subsequently, quantitative proteome profiling was carried out for 90 nasopharyngeal swab samples in diaPASEF mode which resulted in 5,023 protein identifications. Functional analysis revealed two significant features of biological processes of innate immune response and viral life cycle. Overall, we provide the in-depth proteome record from nasopharyngeal swab samples and suggest relevant host response along with proteins playing a pivotal role against viral infection, which would assist for mining promising drug targets in the future.
2021-09-10 | PXD025277 | Pride
Project description:The soft rot pathogen Janthinobacterium agaricidamnosum causes devastating damage to button mushrooms (Agaricus bisporus), one of the most cultivated and commercially relevant mushrooms. We previously discovered that this pathogen releases the membrane-disrupting lipopeptide jagaricin. This bacterial toxin, however, could not solely explain the rapid decay of mushroom fruiting bodies, indicating that J. agaricidamnosum implements a more sophisticated infection strategy. In this study, we show that secretion systems play a crucial role in soft rot disease. By mining the genome of J. agaricidamnosum, we identified gene clusters encoding a type I (T1SS), a type II (T2SS), a type III (T3SS), and two type VI secretion systems (T6SS). Through a combination of knockout studies and bioassays, we found that the T2SS and T3SS of J. agaricidamnosum are required for soft rot disease. Furthermore, comparative secretome analysis and activity-guided fractionation identified a number of secreted lytic enzymes responsible for mushroom damage. Our findings regarding the contribution of secretion systems to the disease process expand the current knowledge of bacterial soft rot pathogens and represent a significant stride towards identifying targets for their disarmament with secretion system inhibitors.
2023-07-02 | PXD040852 | Pride
Project description:Aim of the project: Genome wide gene expression profiles across the cambial zone are analyzed in 35um resolution from wild type hybrid aspen (Populus tremula x tremuloides) and two independent LMX5::AtIPT7 over expressor transgenic Populus tree lines.
2016-07-14 | E-MTAB-4631 | biostudies-arrayexpress
Project description:The evolution of parasitism is a recurring event in the history of life and a core question in evolutionary biology. Trypanosomatids are important parasites including the human pathogens Trypanosoma brucei, T. cruzi and Leishmania spp., which have evolved complex life cycles to exploit a series of defined host environments after diverging from free-living, phagotrophic bodonids. However, the origins of genomic adaptations for transmission, disease and pathogenesis remain obscure because there has been no genomic comparison of parasitic and free-living species. Addressing this absence, we have produced a genome sequence for Bodo saltans, the closest known non-parasitic relative of trypanosomatids. Here we show how genomic reduction and innovation contributed to the character of trypanosomatid genomes. We find that despite a genetic ‘streamlining’ of diverse physiological functions, including macromolecular degradation and cellular homeostasis, the origin of trypanosomatid parasitism did not lead to a substantial reduction in genome function. Instead, we observe dramatic elaboration of gene families that facilitate host-parasite interactions and pathogenesis. We also show how parasite-specific proteins that characterize the enigmatic cell surfaces of Trypanosoma and Leishmania were derived from the same ancestral proteins, still represented in B. saltans. Our new evidence distinguishes adaptive innovations of trypanosomatids that post-date their parasitic origin from essentially kinetoplastid legacies of a free-living past. It shows that when the labile environment of a phagotrophic ancestor was replaced by the defined conditions of their various hosts, trypanosomatid physiology was reoriented towards host interaction, and ancestral structures were radically transformed to provide adaptations for obligate parasitism.
2018-10-24 | PXD002628 | Pride
Project description:Mycorrhiza helper bacteria (MHB) promote the formation of ectomycorrhizae between tree roots and ectomycorrhizal fungi. Despite the high relevance of MHB for forestry and for sustainable tree production in tree nurseries, little is known about the properties of the bacteria that contribute to their helper abilities. The MHB strain Pseudomonas fluorescens BBc6R8 is used as a model to study the mechanisms of the helper effect. We took advantage of new technologies to obtain, for the first time, the whole genome sequence of an MHB. Analyses reveal an important plasticity of the genome with numerous functions acquired by horizontal gene tranfer. Genome mining was combined with transcriptomic and mutagenesis approaches to reveal molecular determinants of the helper effect. The data suggest that the production of helper molecules is likely to be constitutive in vitro. The helper effect appears to be pleiotropic and to rely, for a substantial part, on trophic interactions. Despite its helper abilities, the bacterium is also able in specific conditions to outcompete ectomycorrhizal fungi and inhibit their growth. We conclude that the helper bacterium possess a broad range of properties whose expression depending on the biotic and abiotic conditions can result in either a beneficial, neutral or antagonistic interaction between the plant, the ectomycorrhizal fungus and the bacterium.
2014-06-12 | GSE38243 | GEO
Project description:Temperature preference behavior in Drosophila depends on the level of PKA signaling in the mushroom bodies. To identify new components downstream to PKA, we carried out a genome-wide screen for genes regulated by PKA signaling in the mushroom bodies.
2014-03-25 | GSE28181 | GEO
Project description:Temperature preference behavior in Drosophila depends on the level of PKA signaling in the mushroom bodies. To identify new components downstream to PKA, we carried out a genome-wide screen for genes regulated by PKA signaling in the mushroom bodies. Using the Gal4-UAS system, we increased or decreased PKA activity in the mushroom bodies by expressing dominant-negative (UAS-PKADN) or constitutively active PKA (UAS-PKACA), respectively. Expression of PKA transgenes was targeted to the mushroom bodies using the mushroom body-specific MB247-Gal4 driver. PKA expression was induced for 12-16 hours in three-day-old adults by inactivating the temperature-sensitive Gal80 at the restrictive temperature. We then analyzed gene-expression profiles to identify the genes showing altered expression levels in response to the high or low PKA activity.
2014-03-25 | E-GEOD-28181 | biostudies-arrayexpress