Ichthyophis youngorum
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ABSTRACT:
PROVIDER: PRJNA693964 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Ichthyophis bannanicus Genome sequencing and assembly
| PRJNA590807 | ENA
Project description:Ichthyophis bannanicus isolate:Banna01 Genome sequencing and assembly
| PRJNA1020273 | ENA
Project description:Ichthyophis bannanicus strain:wild Transcriptome or Gene expression
| PRJNA590809 | ENA
Project description:Background Banna caecilian (Ichthyophis bannanicus) is the only species of Gymnophiona in China, with unique lifestyles and characteristics. Although there have been some studies on distribution and morphological characteristics in I. bannanicus, little research focused on the molecular level. A comprehensive analysis of gene expression profiling across tissues can provide necessary information for an in-depth understanding of their biological functions. Result To provide new insights into molecular mechanisms of ecological adaptation in I. bannanicus, we performed gene expression analysis across 10 tissues including skin, blood, spleen, liver, kidney, lung, heart, stomach, testis and ovary. By integrating 27 newly generated RNA-seq datasets with 21 publicly available transcriptomes, we performed a systematic gene expression analysis across tissues representing 19 major organ systems, thereby generating a comprehensive and high-resolution transcriptomic atlas for I. bannanicus. We identified 5,092 housekeeping genes (HKGs) and 2,169 tissue-specific genes (TSGs), and conducted weighted gene co-expression network analysis to determine the modules most relevant to each tissue. Functional enrichment indicated that HKGs support basic cellular activities, while TSGs and the module genes are associated with tissue differentiation and specific physiological processes. Our comparative genomic analysis of I. bannanicus and Xenopus tropicalis revealed genes potentially lost in I. bannanicus, including RCVRN.1, GNAT2, SAG, GRK7, SMURF1, NOG, and MAPK14, which may be associated with degeneration of its visual system and limb structures. Notably, cross-species comparison of HKGs, TSGs, and co-expression modules highlighted an enhanced and unique immune capacity in I. bannanicus. Conclusion Our findings demonstrate that HKGs, TSGs, and co-expression module genes offer valuable perspectives on tissue specialization and evolutionary divergence. The comparative transcriptomic analysis across multiple species and diverse tissue types provides valuable clues into the molecular features that may contribute to ecological adaptation in I. bannanicus.
2025-11-04 | GSE268543 | GEO
Project description:A comparative transcriptomic analysis provides new insights into the ecological adaptations in Ichthyophis bannanicus
| PRJNA1117770 | ENA
Project description:Primary objectives: The primary objective is to investigate circulating tumor DNA (ctDNA) via deep sequencing for mutation detection and by whole genome sequencing for copy number analyses before start (baseline) with regorafenib and at defined time points during administration of regorafenib for treatment efficacy in colorectal cancer patients in terms of overall survival (OS).
Primary endpoints: circulating tumor DNA (ctDNA) via deep sequencing for mutation detection and by whole genome sequencing for copy number analyses before start (baseline) with regorafenib and at defined time points during administration of regorafenib for treatment efficacy in colorectal cancer patients in terms of overall survival (OS).
| 2533916 | ecrin-mdr-crc
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