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A chromosome-scale reference genome for Spironucleus salmonicida.

Feifei Xu1,2, Alejandro Jiménez-González3, Zeynep Kurt3

  • 1Department of Cell and Molecular Biology, BMC, Box 596, Uppsala University, SE-751 24, Uppsala, Sweden. feifei.xu@mcb.uu.se.

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We present a highly complete chromosome-level genome assembly for Spironucleus salmonicida, a pathogen of salmon. This improved genome resource enhances our understanding of diplomonad genomics and parasitic infections.

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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.