IdXylSylv2
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB42874 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Xylota sylvarum (golden-tailed hoverfly) genome assembly, idXylSylv2, alternate haplotype
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Project description:Xylota sylvarum (golden-tailed hoverfly), genomic and transcriptomic data
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Project description:Macaque species share over 93% genome homology with humans and develop many disease phenotypes similar to those of humans, making them valuable animal models for the study of human diseases (e.g.,HIV and neurodegenerative diseases). However, the quality of genome assembly and annotation for several macaque species lags behind the human genome effort. To close this gap and enhance functional genomics approaches, we employed a combination of de novo linked-read assembly and scaffolding using proximity ligation assay (HiC) to assemble the pig-tailed macaque (Macaca nemestrina) genome. This combinatorial method yielded large scaffolds at chromosome-level with a scaffold N50 of 127.5 Mb; the 23 largest scaffolds covered 90% of the entire genome. This assembly revealed large-scale rearrangements between pig-tailed macaque chromosomes 7, 12, and 13 and human chromosomes 2, 14, and 15. We subsequently annotated the genome using transcriptome and proteomics data from personalized induced pluripotent stem cells (iPSCs) derived from the same animal. Reconstruction of the evolutionary tree using whole genome annotation and orthologous comparisons among three macaque species, human and mouse genomes revealed extensive homology between human and pig-tailed macaques with regards to both pluripotent stem cell genes and innate immune gene pathways. Our results confirm that rhesus and cynomolgus macaques exhibit a closer evolutionary distance to each other than either species exhibits to humans or pig-tailed macaques. These findings demonstrate that pig-tailed macaques can serve as an excellent animal model for the study of many human diseases particularly with regards to pluripotency and innate immune pathways.
2020-05-04 | PXD018943 | Pride
Project description:Xylota segnis genome assembly, idXylSegn2, alternate haplotype
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Project description:Golden Jackal Genome Assembly
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Project description:In the ribosome-associated quality control acting on nuclear-encoded mitochondrial proteins (mitoRQC), Vms1 protects mitochondria from toxic effects of Rqc2-generated C-terminal alanyl and threonyl (CAT) tailed proteins that escaped proteosomal degradation facilitated by E3 ubiquitin ligase Ltn1. Here, we performed a genome-wide screen in yeast to identify novel proteins involved in mitoRQC. We found that Pth2, a peptidyl-tRNA hydrolase in the outer mitochondrial membrane, influences aggregation of mitochondrial-targeted CAT-tailed proteins without majorly affecting the CAT-tailing process itself. Peptidyl-tRNA hydrolase activity is essential during this process, however, the activity of Pth2 can be substituted by another peptidyl-tRNA hydrolase, upon proper localization. Our data suggest that Pth2 acts through modulating protein import into mitochondria, enabling CAT-tailed proteins to get access to the cytosolic chaperones and thus relieving the mitochondrial proteostasis network. Other hits obtained in the screen show that, in general, slowing down protein translocation protects mitochondria against toxic CAT-tailed proteins.
2025-11-13 | PXD057575 | Pride