A reference genome for Bluegill (Centrarchidae: Lepomis macrochirus)

Area of Science:

• Genomics
• Evolutionary Biology
• Ichthyology

Background:

• North American sunfishes (Family Centrarchidae) are ecologically important and popular sportfish.
• Limited molecular studies exist on centrarchid evolutionary relationships and species boundaries, despite known hybridization.
• A high-quality genome assembly is needed to address these knowledge gaps.

Purpose of the Study:

• To describe a chromosome-scale genome assembly for Bluegill (Lepomis macrochirus).
• To provide a foundational resource for studying centrarchid evolution and hybridization.
• To enhance genomic resources for spiny-rayed fishes (Acanthomorpha).

Main Methods:

• Utilized long-read Oxford Nanopore sequencing.
• Integrated short-insert whole-genome and Hi-C sequencing data.
• Performed ab initio gene prediction and assessed gene completeness using BUSCO and OrthoDB v10.

Main Results:

• Generated a chromosome-scale assembly (Lm_LA_1.1) of 889 Mb with 1,841 scaffolds (N50 36 Mb).
• Achieved high gene completeness with 99% eukaryotic and 98% actinopterygian BUSCOs.
• Predicted 17,233 genes supported by external data.

Conclusions:

• The Bluegill genome assembly is a significant addition to fish genomic resources.
• This assembly will facilitate future research into centrarchid evolutionary history and species divergence.
• It serves as a valuable tool for understanding the genetics of popular sportfish.