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ABSTRACT:
PROVIDER: PRJNA1029244 | ENA |
REPOSITORIES: ENA
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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
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-11831 | biostudies-arrayexpress
Project description:16s rRNA sequencing of cecal microbiota of the Brandt's voles
| PRJNA394059 | ENA
Project description:Exposure to high-altitude hypoxic environments may lead to dysfunction in the central nervous system. Research on the hypoxic response mechanisms of hypoxia-tolerant animals can provide insights for animal conservation and the treatment of ischemic brain injury. In this study, we focused on Brandt's voles and simulated oxygen environments at altitudes of 100m, 3000m, 5000m, and 7000m within a hypoxic chamber. After 24 hours of exposure, brain tissue was collected for quantitative proteomic and phosphoproteomic analyses. A total of 3,947 proteins and 8,572 phosphosites were quantified. Proteomic data revealed that more differentially expressed (DE) proteins were downregulated than upregulated, with significant enrichment in pathways that inhibit protein synthesis and leukocyte activation, suggesting a strategy for energy conservation in Brandt's voles under hypoxic conditions. Additionally, approximately 43% of the DE proteins were identified as candidate genes in other hypoxia-tolerant species. Phosphoproteomic analysis found that phosphoproteins in the downregulated cluster were significantly enriched in vascular smooth muscle contraction and adaptive immune system, which contribute to enhancing oxygen transport to the brain tissue and reducing energy consumption. Furthermore, many DE proteins and phosphoproteins were related to endocytosis, cytoskeleton organization, and synaptic regulation, which may be strategies employed by Brandt's voles to protect brain tissue from hypoxic damage and maintain cognitive function. Utilizing the KSEA algorithm, we predicted that 10 kinase activities in Brandt's voles are significantly influenced by hypoxia, four of which belonging to the CAMK kinase family. Immunoblot validated that the changes in CAMK2A activity were consistent with predictions, suggesting that CAMK may play a crucial role in the hypoxic response. In conclusion, our findings indicate that Brandt's voles cope with hypoxia by enhancing oxygen transport, reducing energy consumption, and activating neuroprotective mechanisms.
2024-10-17 | PXD056880 |
Project description:Advances in sequencing and assembly technology has led to the creation of genome assemblies for a wide variety of non-model organisms. The rapid production and proliferation of updated, novel assembly versions can create create vexing problems for researchers when multiple genome as-sembly versions are available at once, requiring researchers to work with more than one reference genome. Multiple genome assemblies are especially problematic for researchers studying the genetic makeup of individual cells as single cell RNA sequencing (scRNAseq) requires sequenced reads to be mapped and aligned to a single reference genome. Using the Astyanax mexicanus this study highlights how the interpretation of a single cell dataset from the same sample changes when aligned to its two different available genome assemblies. We found that the number of cells and expressed genes detected were drastically different when aligning to the different assemblies. When the genome assemblies were used in isolation with their respective annotation, cell type identification was confounded as some classic cell type markers were assembly-specific, whilst other genes showed differential patterns of expression between the two assemblies. To overcome the problems posed by multiple genome assemblies, we propose that researchers align to each available assembly and then integrate the resultant datasets to produce a final dataset in which all genome alignments can be used simultaneously. We found this approach increased the accuracy of cell type identification and maximised the amount of data that could be extracted from our single cell sample by capturing all possible cells and transcripts. As scRNAseq becomes more widely available, it is imperative that the single cell community is aware how genome assembly alignment can alter single cell data and its interpretation, especially when reviewing studies on non-model organisms.
2022-02-10 | GSE194093 | GEO
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.
2022-07-01 | E-MTAB-11850 | biostudies-arrayexpress
Project description:To characterize the site-specific methylation landscape of the Mandarin fish ranavirus (MRV) genome, whole-genome bisulfite sequencing (WGBS) was conducted on an isolated MRV strain.
2024-04-02 | GSE262554 | GEO
Project description:We performed whole genome re-sequencing to reveal the comprehensive genetic variation of the fruit development between kumquat (Fortunella japonica) and Clementine mandarin. Total 5,865,235 single-nucleotide polymorphisms (SNPs) and 414,447 insertion/deletion (InDels) were identified in the two citrus species. Meanwhile, a total of 640,801 SNPs and 20,733 InDels were identified based on integrative analysis of genome and transcriptome of fruit. The variation feature, genomic distribution, functional effect and other characteristics of these genetic variation were explored. Total 1,090 differentially expressed genes (DEGs) were found during fruit development process of kumquat and Clementine mandarin by RNA-sequencing. Gene Ontology revealed that these genes were involved in various molecular functional and biological processes. Meanwhile, the genetic variation of 939 DEGs and 74 multiple fruit development pathway genes from previous reported were also identified. In addition, a global survey of genes splicing events identified 24,237 specific alternative splicing (AS) events in the two citrus species and showed that intron retention is the most prevalent pattern of alternative splicing.
2018-02-01 | GSE107812 | GEO
Project description:We use ChIP-seq targeting histone 3 lysine 27-acetylation (H3K27ac) to identify putative enhancer sites genome-wide in the ventral pallidum cortex of adult prairie voles
2018-01-31 | GSE85826 | GEO