Improved assembly of the Pungitius pungitius reference genome

Area of Science:

• Genomics
• Evolutionary Biology
• Aquatic Ecology

Background:

• The nine-spined stickleback (Pungitius pungitius) is a key model organism for research on local adaptation and sex chromosome evolution.
• Existing reference genome assemblies for P. pungitius are incomplete and lack distinct sex chromosomes, hindering detailed genomic studies.

Purpose of the Study:

• To generate an improved reference genome assembly for the nine-spined stickleback.
• To identify and characterize sex chromosomes within the new assembly.
• To provide a more robust genomic resource for evolutionary and adaptation research.

Main Methods:

• Utilized linked-read mapping technology to improve the genome assembly.
• Performed comparative analysis between the new (v8) and previous (v7) assembly versions.
• Annotated genes and analyzed repetitive elements within the improved genome.

Main Results:

• Generated an improved P. pungitius genome assembly (v8) with 98.3% BUSCO completeness.
• Successfully assigned 4.4 times more contigs to linkage groups, enhancing genome contiguity.
• Identified a ~22.8 Mb Y-linked scaffold (LG22) with near-pure X and Y representation, alongside 26,803 annotated genes.

Conclusions:

• The v8 genome assembly represents a significant advancement over previous versions.
• The identified Y-linked scaffold offers new opportunities for studying sex chromosome evolution.
• This improved assembly will facilitate future genomic research on P. pungitius, particularly in adaptation and evolution.