Jinbian carp (
Cyprinus carpio
) is an endemic species in China. The complete mitochondrial genome of Jinbian carp is determined to be 16,581 bp in length and includes 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes, and a control region. Its structural organization and gene order are equivalent to other common carp strains. The phylogenetic analyses will contribute to further insights of the taxonomy and phylogeny in Cyprinidae family.
Colors are important phenotypic traits for fitness under natural conditions in vertebrates. Previous studies have reported several functional genes and genetic variations of pigmentation, but the formation mechanisms of various skin coloration remained ambiguous in fish. Jinbian carp, a common carp variant, displays two colors (yellow and black) in the skin, thus, it is a good model for investigating the genetic basis of pigmentation. In the present study, using the Jinbian carp as model, isobaric tags for relative and absolute quantification (ITRAQ) proteomics analysis was performed for yellow and black skin, respectively. The results showed that 467 differentially expressed proteins (DEPs) were identified between the yellow skin and the black skin. Similar to mammals, the up-regulated DEPs in black skin included UV excision repair protein RAD23 homolog A (Rad23a), melanoregulin (mreg), 5,6-dihydroxyindole-2-carboxylic acid oxidase5 (tyrp1) and melanocyte protein PMEL (PMEL), which were mainly grouped into melanogenesis pathway. However, several up-regulated DEPs in yellow skin were mainly enriched in nucleotide metabolism, such as GTPase IMAP family member 5 (GIMAP5), AMP deaminase 1 (AMPD1), adenosylhomocysteinase b (ahcy-b), and pyruvate kinase (PKM). In summary, several candidate proteins and their enrichment pathways for color variation in Jinbian carp were identified, which may be responsible for the formation of different colorations.
Jinbian carp, a variety of common carp (Cyprinus carpio v. jinbian) with black skin colour and two yellow stripes on both sides of its dorsal fin, has become a popular economic fish species as an edible delicacy and for its unique coloration. However, the genetic background of Jinbian carp is not well documented and the molecular mechanism of the yellow or black colour variation of the skin of this fish is not yet clear. Therefore, it is essential to understand the molecular mechanism of colour variation using advanced technology. In this study, using wild and Jinbian common carp as experimental materials, we performed RNA sequencing transcriptomic analysis with regard to the yellow and black skin colour in these fish. As a result, we identified 162 differentially expressed genes (DEGs) between yellow (Y) and black (B) skin derived from the same Jinbian carp and 2,475 DEGs between yellow skin in Jinbian carp (Y) and black skin in wild common carp (W). Gene functional analysis revealed that most of DEGs were involved in pigmentation‐related and metabolic pathways, among which we mainly focused on the cGMP‐PKG signalling pathway and adrenergic signalling in the cardiomyocyte pathway. In addition, our transcriptome results suggested that genes associated with cysteine metabolism, including scavenger receptor cysteine‐rich type 1 protein M130 (CACNA1E), cysteine N‐palmitoyltransferase HHAT‐like protein (HHATL) and soluble scavenger receptor cysteine‐rich domain‐containing protein (SSC5D) could serve as candidate genes for colour variation in Jinbian carp. In conclusion, our results identify candidate genes and potential pathways involved in colour variation and provide useful genetic information for further breeding of Jinbian carp.
In this study, the complete mitochondrial genome of
Pangasius sanitwongsei
was firstly reported and analyzed. It had a double-stand DNA molecule with 16536 bp in length, consisting of 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes and one control region. The structural organization and gene order was similar to other bony fishes. The complete mitochondrial genome of
P. sanitwongsei
provided in this work would be helpful for further research on phylogenetics and conservation genetics of the Siluriformes and other orders.
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