Project description:Over the last century, rainbow trout (RBT) has been widely used as a biological model in many biological disciplines and has become one of the best-studied fish. For example, RBT is an excellent model to study gene evolution as it is a partially tetraploid organism that underwent a whole-genome duplication (salmonid-specific 4th WGD) followed by a partial re-diploidization and significant genome rearrangements. In the meantime, RBT domestication spread quickly and globally to six continents for aquaculture and recreation. Efforts to sequence a pangenome reference have begun, and genome sequence is available for at least three rainbow trout clonal lines. However, epigenome reference annotations are needed to understand the functional genomic basis of RBT's phenotypic, environmental, and evolutional variations. This study provides a comprehensive catalog and epigenome annotation tracks of the rainbow trout. Gene regulatory elements, including chromatin histone modifications, chromatin accessibility, and DNA methylation, were identified by integrating data from ChIP-seq, ATAC-seq, and Methyl Mini-seq across RBT tissues together with RNA-seq gene expression data sets.
Project description:As an important cold-water economic fish species, rainbow trout (Oncorhynchus mykiss) exhibits several intra-specific variation in skin pigmentation that can give rise to distinctive phenotypes, and wild-type rainbow trout with black skin (WR) and yellow mutant rainbow trout with yellow skin (YR) are the major two types in the farms, whose distinct skin colors make them suitable model for elucidating the skin pigmentation process. Skin color as a key indicator for selection in rainbow trout farming as well as has a strong visual impact on the consumer when rainbow trout are marketed. Previously, extensive studies have been conducted on skin color in rainbow trout, including the observation of skin spots and the expression analysis of some important pigment genes. However, up to date, no studies have systematically examined the molecular regulation mechanism of skin color difference between WR and YR through a high throughput method. Therefore, the aim of this study was to reveal the molecular regulation mechanism of skin color difference between these two strains at the mRNA and miRNA transcriptome level, and candidate genes, miRNAs and miRNA-mRNA pairs that may be responsible for rainbow trout albinism were obtained.
Project description:Rainbow trout (Oncorhynchus mykiss) is an important aquaculture fish species that is farmed worldwide, and it is also the most widely cultivated cold water fish in China. This species, a member of the salmonidae family, is an ideal model organism for studying the immune system in fish. Two phenotypes of rainbow trout are widely cultured; wild-type rainbow trout with black skin (WR_S) and yellow mutant rainbow trout with yellow skin (YR_S). Fish skin is an important immune organ, however, little is known about the differences in skin immunity between WR_S and YR_S in a natural flowing water pond aquaculture environment, and very few studies were conducted to investigate the ceRNA mechanism for fish skin.
