A chromosome-scale reference genome for Spironucleus salmonicida.

Area of Science:

• Genomics
• Parasitology
• Protistology

Background:

• Spironucleus salmonicida is a significant pathogen causing systemic infections in salmon.
• The initial genome assembly (2014) was fragmented, hindering detailed genomic analysis.
• Chromosomal organization and gene structure remained largely uncharacterized.

Purpose of the Study:

• To generate a high-quality, chromosome-level genome assembly for Spironucleus salmonicida.
• To improve the annotation and characterization of the S. salmonicida genome.
• To provide a robust genomic resource for comparative genomics and protist research.

Main Methods:

• Utilized PacBio long-read sequencing technology for extensive genome coverage.
• Integrated optical mapping to aid in chromosome assembly and scaffolding.
• Applied advanced bioinformatic pipelines for genome assembly and annotation.

Main Results:

• Successfully assembled the Spironucleus salmonicida genome into nine near-complete chromosomes.
• The new assembly features significantly improved sequence completeness with only three internal gaps.
• Enhanced annotation provides detailed insights into gene families, organization, and chromosomal structure.

Conclusions:

• The chromosome-level genome assembly represents a major advancement for Spironucleus salmonicida research.
• This resource will facilitate high-resolution comparative genomics within diplomonads.
• The improved genome will be invaluable for understanding salmonid diseases and protist evolution.