FSprSpr1
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB66150 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Sprattus sprattus (European sprat) genome assembly, fSprSpr1, alternate haplotype
| PRJEB66149 | ENA
Project description:Sprattus sprattus (European sprat), genomic and transcriptomic data
| PRJEB65262 | ENA
Project description:European Lobster (Homarus gammarus) Genome Assembly
| PRJEB63315 | ENA
Project description:In Europe, ticks are the most important vectors of diseases threatening humans, livestock, wildlife and companion animals. Nevertheless, genomic sequence information and functional annotation of proteins of the most important European tick, Ixodes ricinus, is limited. Here we present the first analysis of the I. ricinus genome and of the transcriptome of the unfed I. ricinus midgut. We combined and integrated data from genome, transcriptome and proteome. The de novo assembly of 1 billion paired-end sequences identified 6,415 putative genes providing an unprecedented insight into the I. ricinus genome. Mapping of our midgut mRNA reads to the assembled contigs let us estimate to cover around two third of the unique genomic sequences. In addition, more than 10,000 transcripts from naïve midgut were annotated functionally and/or locally. By combining the alignment-based with a motif-search based annotation approach, we could double the number of annotations throughout all groups without shifting the dataset. Moreover, 1,175 proteins expressed in the naïve midgut were identified by mass spectrometry confirming the high completeness of our transcriptome database, and 608 were significantly annotated for function and/or localization. This multiple-omics study vastly extends the publicly available DNA, RNA and protein databases for I. ricinus and ticks in general.
2015-11-04 | PXD001796 | Pride
Project description:The naked mole-rat (NMR; Heterocephalus glaber) has recently gained considerable attention in the scientific community for its unique potential to unveil novel insights in the fields of medicine, biochemistry, and evolution. NMRs exhibit unique adaptations that include protracted fertility, cancer resistance, eusociality, and anoxia. This suite of adaptations is not found in other rodent species, suggesting that interrogating conserved and accelerated regions in the NMR genome will find regions of the NMR genome fundamental to their unique adaptations. However, the current NMR genome assembly has limits that make studying structural variations, heterozygosity, and non-coding adaptations challenging. We present a complete diploid naked-mole rat genome assembly by integrating long-read and 10X-linked read genome sequencing of a male NMR and its parents, and Hi-C sequencing in the NMR hypothalamus (N=2). Reads were identified as maternal, paternal or ambiguous (TrioCanu). We then polished genomes with Flye, Racon and Medaka. Assemblies were then scaffolded using the following tools in order: Scaff10X, Salsa2, 3d-DNA, Minimap2-alignment between assemblies, and the Juicebox Assembly Tools. We then subjected the assemblies to another round of polishing, including short-read polishing with Freebayes. We assembled the NMR mitochondrial genome with mitoVGP. Y chromosome contigs were identified by aligning male and female 10X linked reads to the paternal genome and finding male-biased contigs not present in the maternal genome. Contigs were assembled with publicly available male NMR Fibroblast Hi-C-seq data (SRR820318). Both assemblies have their sex chromosome haplotypes merged so that both assemblies have a high-quality X and Y chromosome. Finally, assemblies were evaluated with Quast, BUSCO, and Merqury, which all reported the base-pair quality and contiguity of both assemblies as high-quality. The assembly will next be annotated by Ensembl using public RNA-seq data from multiple tissues (SRP061363). Together, this assembly will provide a high-quality resource to the NMR and comparative genomics communities.
2022-06-27 | E-MTAB-11830 | biostudies-arrayexpress