Integrating Iso-seq and RNA-seq data for the reannotation of the killifish telencephalon transcriptome

Area of Science:

• Biogerontology
• Comparative Genomics
• Transcriptomics

Background:

• The African turquoise killifish (Nothobranchius furzeri) is a valuable vertebrate aging model.
• Existing genomic and transcriptomic data lack comprehensive gene annotations, hindering research.
• Accurate gene models are crucial for understanding aging mechanisms.

Purpose of the Study:

• To reannotate the transcriptome of the Nothobranchius furzeri telencephalon.
• To generate a more accurate and detailed gene catalog for this aging model.
• To identify novel coding and non-coding sequences and analyze age-related transcriptomic changes.

Main Methods:

• Combined long-read (Smrt-Isoseq) and short-read transcriptome sequencing.
• Integrated long-read and RNA-seq data for comprehensive transcriptome construction.
• Performed alternative splicing analysis to identify age-dependent events.

Main Results:

• Generated 17,008 full-length isoforms, including 6,763 novel ones.
• Identified novel coding and non-coding sequences in young and aged telencephali.
• Discovered 29 age-altered alternative splicing events impacting ribosome function, gap junctions, and mRNA surveillance.

Conclusions:

• Developed a high-quality, comprehensive killifish telencephalon transcriptome resource.
• The new gene models offer greater accuracy and detail compared to existing databases.
• These findings provide essential genomic resources for future functional studies in vertebrate aging research.