A chromosome‐anchored genome assembly for Lake Trout (Salvelinus namaycush)

Abstract

Here, we present an annotated, chromosome-anchored, genome assembly for Lake Trout (Salvelinus namaycush) -a highly diverse salmonid species of notable conservation concern and an excellent model for research on adaptation and speciation.We leveraged Pacific Biosciences long-read sequencing, paired-end Illumina sequencing, proximity ligation (Hi-C) sequencing, and a previously published linkage map to produce a highly contiguous assembly composed of 7378 contigs (contig N50 = 1.8 Mb) assigned to 4120 scaffolds (scaffold N50 = 44.975 Mb). Long read sequencing data were generated using DNA from a female double haploid individual.84.7% of the genome was assigned to 42 chromosome-sized scaffolds and 93.2% of Benchmarking Universal Single Copy Orthologues were recovered, putting this assembly on par with the best currently available salmonid genomes. Estimates of genome size based on k-mer frequency analysis were highly similar to the total size of the finished genome, suggesting that the entirety of the genome was recovered. A mitochondrial genome assembly was also produced. Self-versus-self synteny analysis allowed us to identify homeologs resulting from the salmonid specific autotetraploid event (Ss4R) as well as regions exhibiting delayed rediploidization. Alignment with three other salmonid genomes and the Northern Pike (Esox lucius) genome also

Thermal regime during parental sexual maturation, but not during offspring rearing, modulates DNA methylation in brook charr (Salvelinus fontinalis)

“…Data were trimmed using fastp [ 65 ] to remove sequences under 100 bp and with phred scores below 25, and the first and last nucleotides were trimmed. Bwa-meth ( ) was used to align the sequence data to the lake trout ( S. namaycush ) genome (SaNama v. 1.0; NCBI Refseq: GCF_016432855.1) [ 66 ], a closely related sister species of brook charr [ 67 ]. Duplicate reads were removed from the bam files with picard tools v. 1.119 MarkDuplicates ( ).…”

Thermal regime during parental sexual maturation, but not during offspring rearing, modulates DNA methylation in brook charr (Salvelinus fontinalis)

“…Data were trimmed using fastp [60] to remove sequences under 100 bp and with phred scores below 25, and the first and last nucleotides were trimmed. Bwa-meth (https://github.com/brentp/bwa-meth) was used to align the sequence data to the lake trout ( S. namaycush ) genome (SaNama v1.0; NCBI Refseq: GCF_016432855.1) [61], a closely related sister species of brook charr [62]. Duplicate reads were removed from the bam files with picard tools v1.119 MarkDuplicates (https://github.com/broadinstitute/picard).…”

Salmonidae Genome: Features, Evolutionary and Phylogenetic Characteristics

“…Consequently, selection for conservation and loss of duplicated genes is probably multifaceted when delayed rediploidization is involved [ 96 ]. For Ss4R, it is assumed that selection has maintained tetraploidy in SSR regions for tens of millions of years [ 97 ]. It’s also worth wondering why a second round of rediploidization was permitted.…”