Ontology highlight
ABSTRACT:
PROVIDER: PRJNA816194 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Globisporangium irregulare DAOM BR486 Genome sequencing and assembly
| PRJNA169053 | ENA
Project description:The Zika outbreak, spread by the Aedes aegypti mosquito, highlights the need to create high-quality assemblies of large genomes in a rapid and cost-effective fashion. Here, we combine Hi-C data with existing draft assemblies to generate chromosome-length scaffolds. We validate this method by assembling a human genome, de novo, from short reads alone (67X coverage, Sample GSM1551550). We then combine our method with draft sequences to create genome assemblies of the mosquito disease vectors Aedes aegypti and Culex quinquefasciatus, each consisting of three scaffolds corresponding to the three chromosomes in each species. These assemblies indicate that virtually all genomic rearrangements among these species occur within, rather than between, chromosome arms. The genome assembly procedure we describe is fast, inexpensive, accurate, and can be applied to many species.
2017-03-24 | GSE95797 | GEO
Project description:Parasitism is a major ecological niche for a variety of nematodes. Multiple nematode lineages have specialized as pathogens, including deadly parasites of insects that are used in biological control. We have sequenced and analyzed the draft genomes and transcriptomes of the entomopathogenic nematode Steinernema carpocapsae and four congeners (S. scapterisci, S. monticolum, S. feltiae, S. glaseri) distantly related to Caenorhabditis elegans. We used these genomes to establish phylogenetic relationships, explore gene conservation across species, identify genes uniquely expanded in insect parasites, and to identify conserved non-coding regulatory motifs that influence similar biological processes. Protein domain analysis of these genomes reveals a striking expansion of numerous putative parasitism genes including certain protease and protease inhibitor families as well as fatty acid- and retinol-binding proteins. We identify rapid evolution and expansion of the important developmental Hox gene cluster and identify novel conserved non-coding regulatory motifs associated with orthologous genes in Steinernema and Caenorhabditis. The deep conservation of the network of non-coding DNA motifs between these two genera for a subset of orthologous genes involved in neurogenesis and embryonic development suggests that a kernel of protein-DNA relationships is conserved through nematode evolution. We analyzed the gene expression of a total of 24 RNA-seq samples from 3 nematode species( S. carpocapsae, S. feltiae, and C. elegans) for comparative analysis. We collected the RNA at four developmental time points (mixed embryo, L1, infective juvenile/dauer, young adult) for each species in replicates.
2015-06-05 | E-GEOD-68588 | biostudies-arrayexpress
Project description:Frogs are an ecologically diverse and phylogenetically ancient group of anuran amphibians that include important vertebrate cell and developmental model systems, notably the genus Xenopus. Here we report a high-quality reference genome sequence for the western clawed frog, Xenopus tropicalis, along with draft chromosome-scale sequences of three distantly related emerging model frog species, Eleutherodactylus coqui, Engystomops pustulosus and Hymenochirus boettgeri. Frog chromosomes have remained remarkably stable since the Mesozoic Era, with limited Robertsonian (i.e., centric) translocations and end-to-end fusions found among the smaller chromosomes. Conservation of synteny includes conservation of centromere locations, marked by centromeric tandem repeats associated with Cenp-a binding, surrounded by pericentromeric LINE/L1 elements. We explored chromosome structure across frogs, using a dense meiotic linkage map for X. tropicalis and chromatin conformation capture (Hi-C) data for all species. Abundant satellite repeats occupy the unusually long (~20 megabase) terminal regions of each chromosome that coincide with high rates of recombination. Both embryonic and differentiated cells show reproducible association of centromeric chromatin, and of telomeres, reflecting a Rabl-like configuration. Our comparative analyses reveal 13 conserved ancestral anuran chromosomes from which contemporary frog genomes were constructed.
2022-03-30 | GSE199671 | GEO
Project description:Draft genomes of nine plant pathogenic Botrytis species
| PRJNA401386 | ENA
Project description:Peanut (Arachis hypogaea) has a large (~2.7 Gbp) allotetraploid genome with closely related component genomes making its genome very challenging to assemble. Here we report genome sequences of its diploid ancestors (A. duranensis and A. ipaënsis). We show they are similar to the peanutâs A- and B-genomes and use them use them to identify candidate disease resistance genes, create improved tetraploid transcript assemblies, and show genetic exchange between peanutâs component genomes. Based on remarkably high DNA identity and biogeography, we conclude that A. ipaënsis may be a descendant of the very same population that contributed the B-genome to cultivated peanut. Whole Genome Bisulphite Sequencing of the peanut species Arachis duranensis and Arachis ipaensis.
2016-07-03 | E-GEOD-71357 | biostudies-arrayexpress
Project description:Transcript profiles of Heterobasion irregulare from different tissues and mycelium grown on different substrates were analyzed. The array probes were designed from gene models taken from the Joint Genome Institute (JGI, department of energy) Heterobasidion annosum genome sequence version 1. One aim of this study was to verify the expression of the automatically annotated gene models under various conditions. Another goal was to compare gene expression profiles from different tissues of Heterobasidion irregulare and from mycelium grown on liquid MMN medium, liquid medium amended with lignin or cellulose and on wood. The Heterobasidion annosum custom-exon expression array (4 x 72K) manufactured byRoche NimbleGen Systems Limited (Madison, WI) (http://www.nimblegen.com/products /exp/index.html) contained five independent, nonidentical, 60-mer probes per gene model coding sequence. For 12,199 of the 12,299 annotated protein-coding gene models probes could be designed. For 19 gene models no probes could be generated and 81 gene models shared all five probes with other gene models. Included in the array were 916 random 60-mer control probes and labelling controls. For 2032 randomly chosen gene models, technical duplicates were included on the array. We performed 18 hybridizations (NimbleGen) with samples derived from Heterobasidion irregulare fruiting bodies (four biological replicates) , from necrotic bark of pines inoculated with H. irregulare (21dpi; three biological replicates), from H. irregulare mycelium grown in liquid MMN medium (three biological replicates) as well as from H. irregulare grown on wood shavings from pine (four biological replicates), grown in liquid medium amended with lignin (2 biological replicates) and growth in liquid medium amended with cellulose from Spruce (2 biological replicates). Cultures were harvested after 3 weeks of incubation 22°C in darkness. All samples were labeled with Cy3.
2012-03-15 | E-GEOD-30230 | biostudies-arrayexpress