Invertebrate metagenome
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA427721 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Metabarcoding of terrestrial arthropod assemblages of grasslands of the southern Kenai Peninsula, Alaska
| PRJNA321553 | ENA
Project description:Direct, untargeted sequencing of environmental samples (metagenomics) and de novo genome assembly enable the study of uncultured and phylogenetically divergent organisms. However, separating individual genomes from a mixed community has often relied on the differential-coverage analysis of multiple, deeply sequenced samples. In the metagenomic investigation of the marine bryozoan Bugula neritina, we uncovered seven bacterial genomes associated with a single B. neritina individual that appeared to be transient associates, two of which were unique to one individual and undetectable using certain "universal" 16S rRNA primers and probes. We recovered high quality genome assemblies for several rare instances of "microbial dark matter," or phylogenetically divergent bacteria lacking genomes in reference databases, from a single tissue sample that was not subjected to any physical or chemical pre-treatment. One of these rare, divergent organisms has a small (593 kbp), poorly annotated genome with low GC content (20.9%) and a 16S rRNA gene with just 65% sequence similarity to the closest reference sequence. Our findings illustrate the importance of sampling strategy and de novo assembly of metagenomic reads to understand the extent and function of bacterial biodiversity.
| S-EPMC5041132 | biostudies-literature
Project description:The microbiome associated with an animal's gut and other organs is considered an integral part of its ecological functions and adaptive capacity. To better understand how microbial communities influence activities and capacities of the host, we need more information on the functions that are encoded in a microbiome. Until now, the information about soil invertebrate microbiomes is mostly based on taxonomic characterization, achieved through culturing and amplicon sequencing. Using shotgun sequencing and various bioinformatics approaches we explored functions in the bacterial metagenome associated with the soil invertebrate Folsomia candida, an established model organism in soil ecology with a fully sequenced, high-quality genome assembly. Our metagenome analysis revealed a remarkable diversity of genes associated with antimicrobial activity and carbohydrate metabolism. The microbiome also contains several homologs to F. candida genes that were previously identified as candidates for horizontal gene transfer (HGT). We suggest that the carbohydrate- and antimicrobial-related functions encoded by Folsomia's metagenome play a role in the digestion of recalcitrant soil-born polysaccharides and the defense against pathogens, thereby significantly contributing to the adaptation of these animals to life in the soil. Furthermore, the transfer of genes from the microbiome may constitute an important source of new functions for the springtail.
| S-EPMC6513849 | biostudies-literature
Project description:Ribosome biogenesis is a major cellular processes involving a large inventory of proteinaceous and RNA cofactors. Recent bioinformatics approaches discovered a large but not complete overlap of the inventory between yeast, mammals and plants. We re-inspected the complexity of ribosome biogenesis factors (RBFs) by assigning co-orthologs to each protein family in the A. thaliana and S. lycopersicum genomes. We realized that about 25% of all analyzed RBFs in the two plant genomes are encoded by more than one gene. The majority is expressed in leaves and anthers of tomato as determined by next generation sequencing (NGS). For the analysis of NGS data we developed a software pipeline M-bM-^@M-^XCRACPipeM-bM-^@M-^Y. This pipeline is designed to be very flexible with respect to genome selection and experimental set up. The NGS analysis revealed the expression of 24.538 genes in tomato leaves and of 22.893 genes in anthers. The observed expression of RBFs was confirmed by qRT-PCR for a randomly chosen sub-set of genes. Further, analysis of the expression profile of selected RBFs during male gametophyte development revealed a differential expression in the different developmental stages for the majority of genes. Based on our analysis we conclude that RBFs described in yeast but not present in plant genomes as concluded from previous orthology analysis are in parts replaced by other RBFs for which multiple genes have been identified in here. In addition, the obtained complexity for some RBFs accounts for a tissue and developmental specific regulation of ribosome biogenesis as well. 2 samples
2014-08-01 | E-GEOD-56610 | biostudies-arrayexpress
Project description:Seed germination of a terrestrial plant constitute dynamic changes in various physiological processes related to growth and development. These physiological processes can be affected by various abiotic and biotic stressors. Here we looked at how the two commonly used nanoparticles, nano-titania (TiO2) and nano-ceria (CeO2) can impact the underlying mechanisms associated with germination at genome level. We used microarrays to detail the global programme of gene expression underlying various physiological processes associated with growth and development, and identified distinct classes of up-regulated genes during this process.
2014-07-29 | GSE59809 | GEO
Project description:Tardigrades are microscopic organisms, famous for their tolerance against extreme environments. The establishment of rearing systems of multiple species has allowed for comparison of tardigrade physiology, in particular in embryogenesis. Interestingly, in-lab cultures of limnic species showed smaller variation in hatching timing than terrestrial species, suggesting a hatching regulation mechanism acquired by adaptation to their habitat. To this end, we screened for coordinated gene expression during the development of two species of tardigrades, Hypsibius exemplaris and Ramazzottius varieornatus, and observed induction of the arthropod molting pathway. Exposure of ecdysteroids and juvenile hormone analog affected egg hatching but not embryonic development in only the limnic H. exemplaris. These observations suggest a hatching regulation mechanism by the molting pathway in H. exemplaris.
2019-10-31 | GSE130111 | GEO
Project description:Pilot study testing next-generation sequencing technology for inventorying terrestrial arthropod biodiversity on Kenai National Wildlife Refuge
| PRJNA302451 | ENA
Project description:Microbial diversity of aquatic invertebrate in eutrophic lake
| PRJNA299090 | ENA