Full-Length RNA Sequencing Provides Insights into Goldfish Evolution under Artificial Selection.

Area of Science:

• Evolutionary biology
• Genomics
• Developmental biology

Background:

• Goldfish (Carassius auratus) are valuable models for studying fish morphology evolution.
• While genes for ornamental traits are known, the impact of artificial selection on embryonic gene expression remains largely unexplored.

Purpose of the Study:

• To investigate the effects of artificial selection on gene expression profiles in goldfish embryos.
• To compare transcriptomic differences between Celestial-Eye (CE) and Ryukin (RK) goldfish breeds.

Main Methods:

• Hybrid transcriptome sequencing using the PacBio platform.
• Identification and validation of alternative splicing (AS) and alternative polyadenylation (APA) events.
• Detection of long non-coding RNAs and fusion genes.
• RNA-sequencing (RNA-seq) for differential gene expression analysis.
• KEGG enrichment analysis of differentially expressed genes (DEGs).

Main Results:

• Sequencing identified over 54,000 transcript isoforms in both CE and RK goldfish.
• Thousands of inter-breed specific alternative splicing and polyadenylation events were discovered.
• Abundant long non-coding RNAs and fusion genes, mostly breed-specific, were detected.
• Thousands of differentially expressed genes were identified between CE and RK embryos across developmental stages.
• KEGG analysis revealed significant differences in gene expression pathways between the two breeds.

Conclusions:

• Artificial selection has exerted extensive influence on goldfish embryonic gene expression.
• These molecular changes likely form the genetic foundation for the diverse morphological variations observed in goldfish breeds.