Fundulus Rathbuni Killifish Gill Transcriptome Annotation for Salinity Response

A GFF3 annotation file for a de novo transcriptome assembly from the killifish Fundulus rathbuni. It was created using the dammit pipeline with Pfam, Rfam, OrthoDB, and Fundulus heteroclitus amino acid databases. The data originates from gill epithelium tissue of fish acclimated to brackish or fresh water and exposed to an acute salinity challenge, produced by Lisa K. Johnson at UC Davis.

Use Cases

• Analyzing transcriptional responses to salinity challenge based on the described experimental design.
• Identifying annotated gene features for comparative genomics based on the use of multiple reference databases.
• Studying osmoregulation in gill epithelium based on the specified tissue source and environmental acclimation.

Strengths

• Annotation leverages multiple established databases (Pfam, Rfam, OrthoDB, RefSeq).
• Data is derived from a controlled experiment with defined salinity acclimation and challenge conditions.
• The dataset is associated with a specific, peer-reviewed research context from a university lab.

Limitations

• Column-level documentation is absent; field semantics must be inferred after download.
• Row count is unknown, which may limit suitability assessment.
• Last update date is unknown; freshness unverified.

Provenance

Source

University of California, Davis

Collection Method

De novo transcriptome assembly from RNA-seq data of gill epithelium, annotated with the dammit pipeline.