Caulophryne jordani
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA74397 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:The ratmouth barbel (Ptychidio jordani) is a critically endangered freshwater fish from the Cyprinidae family, primarily due to overfishing and habitat disruption. To address the challenges of its shrinking wild populations and the difficulties in artificial reproduction, we sequenced, assembled, and annotated a high-quality chromosome-level genome of P. jordani using next-generation short-read sequencing, third-generation long-read sequencing, and Hi-C sequencing. The final genome assembly was 1.14 Gb, consisting of 25 chromosomes with a contig N50 of 25.14 Mb and a scaffold N50 of 42.91 Mb. We identified 25,183 protein-coding genes, 751.75 Mb of repeats, and 19,373 ncRNAs. Methylation loci on most chromosomes ranged from 1,000 to 3,000 per 100 kb window. Gene expression levels across various tissues were analyzed, revealing 12,135 (caudal fin), 11,465 (liver), 14,438 (gill), 12,413 (heart), 8,301 (spleen), and 3,578 (kidney) differentially expressed genes compared to muscle. The comprehensive genomic and transcriptomic resources generated here will aid in understanding the ecology, adaptation, and environmental responses of P. jordani, supporting future research and conservation efforts.
2024-11-26 | GSE282311 | GEO
Project description:The ratmouth barbel (Ptychidio jordani) is a critically endangered freshwater fish from the Cyprinidae family, primarily due to overfishing and habitat disruption. To address the challenges of its shrinking wild populations and the difficulties in artificial reproduction, we sequenced, assembled, and annotated a high-quality chromosome-level genome of P. jordani using next-generation short-read sequencing, third-generation long-read sequencing, and Hi-C sequencing. The final genome assembly was 1.14 Gb, consisting of 25 chromosomes with a contig N50 of 25.14 Mb and a scaffold N50 of 42.91 Mb. We identified 25,183 protein-coding genes, 751.75 Mb of repeats, and 19,373 ncRNAs. Methylation loci on most chromosomes ranged from 1,000 to 3,000 per 100 kb window. Gene expression levels across various tissues were analyzed, revealing 12,135 (caudal fin), 11,465 (liver), 14,438 (gill), 12,413 (heart), 8,301 (spleen), and 3,578 (kidney) differentially expressed genes compared to muscle. The comprehensive genomic and transcriptomic resources generated here will aid in understanding the ecology, adaptation, and environmental responses of P. jordani, supporting future research and conservation efforts.
2024-11-26 | GSE282306 | GEO
Project description:The ratmouth barbel (Ptychidio jordani) is a critically endangered freshwater fish from the Cyprinidae family, primarily due to overfishing and habitat disruption. To address the challenges of its shrinking wild populations and the difficulties in artificial reproduction, we sequenced, assembled, and annotated a high-quality chromosome-level genome of P. jordani using next-generation short-read sequencing, third-generation long-read sequencing, and Hi-C sequencing. The final genome assembly was 1.14 Gb, consisting of 25 chromosomes with a contig N50 of 25.14 Mb and a scaffold N50 of 42.91 Mb. We identified 25,183 protein-coding genes, 751.75 Mb of repeats, and 19,373 ncRNAs. Methylation loci on most chromosomes ranged from 1,000 to 3,000 per 100 kb window. Gene expression levels across various tissues were analyzed, revealing 12,135 (caudal fin), 11,465 (liver), 14,438 (gill), 12,413 (heart), 8,301 (spleen), and 3,578 (kidney) differentially expressed genes compared to muscle. The comprehensive genomic and transcriptomic resources generated here will aid in understanding the ecology, adaptation, and environmental responses of P. jordani, supporting future research and conservation efforts.
| S-EPMC11671578 | biostudies-literature
Project description:In the current study, we evaluate the relationships of Pseudomonas spp. strains with specific biomarkers of exposure to polycyclic aromatic hydrocarbons (PAHs) in wild Chirostoma jordani Woolman, 1894 and assess the capacity of these bacteria to biotransform PAHs
| PRJEB8218 | ENA
Project description:Petrale sole Eopsetta jordani (Pleuronectiformes: Pleuronectidae) is a species of flounder, found in the northeastern Pacific Ocean and the Bering Sea of the United States and Canada. The complete mitochondrial DNA (mtDNA) of E. jordani has 16,483 bp with an overall A + T content of 61% and consists of 2 ribosomal RNA (rRNA) genes, 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, and a non-coding control region. It has incomplete stop codon genes in ND2, COII, ATPase6, COIII, ND3, and ND4. Phylogenetic analysis indicated that E. jordani is not monophyletic with cogeneric Eopsetta grigorjewi and is separated from other species in the same family by a large distance. Present study results provide useful data for further research on genetic diversity and evolution of the Eopsetta and the Pleuronectidae.
| S-EPMC9196804 | biostudies-literature
Project description:BackgroundUnderstanding the processes that influence distribution of organisms is a major goal in evolutionary biology. Speciation in freshwater fishes is mainly associated with the "island-like" model of evolution, in which the formation of land barriers between different hydrographic basins interrupts gene flow and promotes isolation. Freshwater fish therefore provide an excellent model system for macro- and micro-evolutionary studies. The Mesa Silverside, Chirostoma jordani, is one of the most widespread freshwater fish species in the Mexican Plateau, a geologically complex physiographic region with a long history of genesis, destruction and compartmentalization of hydrographic basins that has promoted the dispersal and isolation of freshwater fishes.MethodsWe used mitochondrial (Cytb and D-loop) and nuclear (first intron of the ribosomal protein S7) data and used phylogeographic and coalescent based methods to elucidate the evolutionary history of C. jordani throughout its distributional range on the Mexican Plateau.ResultsThe results obtained in the present study revealed that C. jordani consists of two main genetic groups with geographical correspondence. Clade I occur exclusively in north-western basin and shows population structure. Clade II is widely distributed across the west, central and eastern basins without population structure. The split between these two main clades was estimated at 1.4 Mya. This cladogenetic event may be associated with the allopatric process promoted by the fragmentation and compartmentalization of hydrographic basins induced by the geological and climatic history of the Mexican Plateau.
| S-EPMC11646419 | biostudies-literature