A Mid-Atlantic Brook Trout ( Salvelinus fontinalis ) genome to advance conservation and comparative genomics

Abstract

Brook Trout (Salvelinus fontinalis) are experiencing genomic erosion and demographic declines across the southern portion of their native distribution. A regionally representative reference genome is necessary to support conservation genomic initiatives for this species. While Brook Trout exhibit substantial phylogenetic structure across their range, only a single reference genome from Northeastern Canada (ASM2944872v1) is currently used to guide range-wide analyses. Consequently, reference bias is expected to cause erroneous sequence alignment and spurious variant detection for Brook Trout from divergent lineages. To prevent reference bias and invalid inference when studying Mid-Atlantic Brook Trout, we assembled a de novo, chromosome-level genome using a wild individual from Virginia, USA and produced a gene annotation with publicly available RNA-seq data. The assembly combined three complementary sequencing types (PacBio HiFi, Oxford Nanopore Ultra-Long, and Dovetail Omni-C) and benefited from manual curation using the Pretext software suite. The 2.91 Gb genome, known as mSalvFont1.0, consists of 3,333 contigs (N50 = 3.3 Mb) and 1,299 scaffolds (N50 = 55 Mb), with 81% of the assembly contained within 42 chromosome-scale scaffolds. Indices of accuracy and completeness reveal a quality value of 59 (99.999% accuracy), k-mer completeness of 95%, and 99.3% complete BUSCOs from the Actinopterygii orthologous gene set. Additionally, we identified reference bias (26.94% heterozygosity inflation) when variant detection of a Mid-Atlantic-origin sample relied on alignment to ASM2944872v1, instead of mSalvFont1.0. We anticipate that mSalvFont1.0 will increase the accuracy and precision of regional conservation genomic initiatives and expedite the genesis of a Brook Trout pangenome.