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We describe an emerging initiative - the 'Functional Annotation of All Salmonid Genomes' (FAASG), which will leverage the extensive trait diversity that has evolved since a whole genome duplication event in the salmonid ancestor, to develop an integrative understanding of the functional genomic basis of phenotypic variation. The outcomes of FAASG will have diverse applications, ranging from improved understanding of genome evolution, to improving the efficiency and sustainability of aquaculture production, supporting the future of fundamental and applied research in an iconic fish lineage of major societal importance.
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5488370 | PMC |
http://dx.doi.org/10.1186/s12864-017-3862-8 | DOI Listing |
Sci Data
August 2025
National and Local Joint Engineering Laboratory for Freshwater Fish Breeding, Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, 150070, China.
Amur pike (Esox reicherti) is endemic to the Heilongjiang River system in Northeast Asia. Serving as a top predator in its ecosystem, Amur pike carries substantial significance in ecological, economic, and cultural dimensions. Molecular studies have firmly established that Esociformes is the sister group of Salmoniformes.
View Article and Find Full Text PDFComp Biochem Physiol Part D Genomics Proteomics
September 2025
Key Laboratory of Plateau Cold-water Fish Culture and Eco-environmental Conservation (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Qinghai University, Xining 810016, PR China; State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining
To investigate the effects of hypoxia on the liver of triploid rainbow trout (Oncorhynchus mykiss), we integrated transcriptomic and bioinformatics analyses to decipher the regulatory roles of miRNAs and their target genes under hypoxic conditions. Comparative analyses identified 45 differentially expressed miRNAs (DEmiRNAs) between the hypoxic (group D) and normoxic (group E) groups, as well as 117 hypoxia-associated miRNA-mRNA pairs that exhibited negative regulatory interactions. A systematic miRNA-mRNA interaction network was subsequently constructed to visualise these relationships.
View Article and Find Full Text PDFG3 (Bethesda)
June 2025
Department of Biology, Concordia University, 3475 West Broadway Street, Montréal, Canada, QC H4B 2A7.
Brook trout (Salvelinus fontinalis) is a socioeconomically important fish species for fisheries, aquaculture, and aquatic conservation. We produced a 2.5-Gb reference assembly by combining Hi-C chromosome conformation capture with high-coverage short- and long-read sequencing of a fully homozygous mitotic gynogenic doubled-haploid fish, which facilitates the assembly of highly complex salmonid genomes.
View Article and Find Full Text PDFHeredity (Edinb)
May 2025
Department of Animal Biosciences, Swedish University of Agricultural Sciences, Uppsala, Sweden.
Differential DNA methylation due to epigenetic phenomena is crucial in regulating gene expression. Understanding the consequences of such differential expression on sperm quality parameters may provide insights into the underlying mechanisms of male reproductive success. Nonetheless, male fertility in fish remains understudied despite its critical importance to overall reproductive success in nature and captivity.
View Article and Find Full Text PDFSci Data
February 2025
Department of Animal and Avian Sciences, University of Maryland, College Park, College Park, MD, USA.
The genome of the Swanson doubled haploid (DH) YY male line of rainbow trout was de novo assembled using the Canu pipeline, high-coverage PacBio long-read sequence data, Bionano optical maps, and Hi-C proximity ligation sequence data, resulting in 29 major scaffolds aligning with the karyotype of the Swanson line (2 N = 58). This assembly, totaling 2.3 Gb with an N50 of 52.
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