Full-length transcriptome sequencing analysis reveals differential skin color regulation in snakeheads fish Channa argus

• Published in: Aquaculture and fisheries 2023, Vol.9 (4), p.590-596
• Main Authors: Mao, Leigang, Zhu, Yongan, Yan, Jiaren, Zhang, Longgang, Zhu, Shuren, An, Li, Meng, Qinglei, Zhang, Zhishan, Wang, Xirong
• Format: Article
• Language: English
• Subjects: Albinism; Channa argus; Melanin; Nanopore-based RNA sequencing
• ISSN: 2468-550X; 2468-550X
• DOI: 10.1016/j.aaf.2022.11.008

Albinism is a genetic disorder caused by a series of genetic abnormalities that result in a decrease in melanin. Golden yellow snakehead fish (GCAS) has been discovered while the Channa argus (CAS) breeding, but the genetic mechanism that causes its albinism is not known. Transcriptome sequencing and comparison of CAS and GCAS skin using Oxford Nanopore Technologies (ONT) technology to elucidate the molecular mechanisms of snakehead albinism.27.1 G clean reads and 26,198 full-length non-redundant sequences were generated via ONT sequencing. Overall, 8079 new transcripts and 7231 genes were identified by comparing and analyzing redundant removed transcripts and known reference genome annotations. The results of DEGs analysis showed that a total of 59 transcripts were differentially expressed in the two groups, including 22 up-regulated transcripts and 37 down-regulated transcripts. Five causative genes associated with albinism have been identified, including TYR (Tyrosinase) and SOX10 (SRY-box transcription factor 10) (tyrosinase synthesis and metabolism), S-100 (S100 calcium binding protein A1) (melanin production), NLRC3 (NLR family CARD domain containing 3) (disease immunity) are significantly down-regulated in GCAS, while RhoGEFs expression (melanin synthesis) is up-regulated. Protein interaction analysis revealed that GAPDH (Glyceraldehyde-3-phosphate dehydrogenase) is the top hub gene in the regulation of skin color in C.argus. In addition, the skin of snakehead fish is regulated by metabolic (GAPDH), immune [(Tumor protein p53 (TP53), C-X-C motif chemokine ligand 8 (CXCL8), SRC proto-oncogene, non-receptor tyrosine kinase (SRC), CD274] and neural [(Notch receptor 1 (NOTCH1), C-X-C motif chemokine ligand 12 (CXCL12)] related genes to achieve differences in skin color. These findings in understanding the process by which albinism in fish develops. [Display omitted]