ArticleScientific reports2021
Global tissue transcriptomic analysis to improve genome annotation and unravel skin pigmentation in goldfish.
Article in Scientific reports, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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10 citing papers in PubMed, 28 citations in OpenAlex.
- An improved transcriptome annotation reveals asymmetric expression and distinct regulation patterns in allotetraploid common carp.Communications biology · 2024Article
- Pax7 is involved in leucophore formation in goldfish and gene knockout improves the transparency of transparent goldfish.Fish physiology and biochemistry · 2024Article
- Unveiling the Role of Dynamic Alternative Splicing Modulation After Infestation with Sea Lice (Caligus rogercresseyi) in Atlantic Salmon.Marine biotechnology (New York, N.Y.) · 2023Article
- Genome assembly and isoform analysis of a highly heterozygous New Zealand fisheries species, the tarakihi (Nemadactylus macropterus).G3 (Bethesda, Md.) · 2023Article
- Article
- Cell Junction and Vesicle Trafficking-Mediated Melanosome/Melanin Transfer Are Involved in the Dynamic Transformation of GoldfishInternational journal of molecular sciences · 2022Article
- Molecular Mechanisms of the Convergent Adaptation of Bathypelagic and Abyssopelagic Fishes.Genome biology and evolution · 2022Article
- Analysis of yellow mutant rainbow trout transcriptomes at different developmental stages reveals dynamic regulation of skin pigmentation genes.Scientific reports · 2022Article
- Global tissue transcriptomic analysis to improve genome annotation and unravel skin pigmentation in goldfish.Scientific reports · 2021Article
- Identification of Potential Blind-Side Hypermelanosis-Related lncRNA-miRNA-mRNA Regulatory Network in a Flatfish Species, Chinese Tongue Sole (Frontiers in genetics · 2021Article
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Authors and funding
10 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Goldfish is an ornamental fish with diverse phenotypes. However, the limited genomic resources of goldfish hamper our understanding of the genetic basis for its phenotypic diversity. To provide enriched genomic resources and infer possible mechanisms underlying skin pigmentation, we performed a large-scale transcriptomic sequencing on 13 adult goldfish tissues, larvae at one- and three-days post hatch, and skin tissues with four different color pigmentation. A total of 25.52 Gb and 149.80 Gb clean data were obtained using the PacBio and Illumina platforms, respectively. Onto the goldfish reference genome, we mapped 137,674 non-redundant transcripts, of which 5.54% was known isoforms and 78.53% was novel isoforms of the reference genes, and the remaining 21,926 isoforms are novel isoforms of additional new genes. Both skin-specific and color-specific transcriptomic analyses showed that several significantly enriched genes were known to be involved in melanogenesis, tyrosine metabolism, PPAR signaling pathway, folate biosynthesis metabolism and so on. Thirteen differentially expressed genes across different color skins were associated with melanogenesis and pteridine synthesis including mitf, ednrb, mc1r, tyr, mlph and gch1, and xanthophore differentiation such as pax7, slc2a11 and slc2a15. These transcriptomic data revealed pathways involved in goldfish pigmentation and improved the gene annotation of the reference genome.
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