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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 allowed us to identify homologous chromosomes in related taxa. We also generated multiple resources useful for future genomic research on Lake Trout, including a repeat library and a sex-averaged recombination map. A novel RNA sequencing data set for liver tissue was also generated in order to produce a publicly available set of annotations for 49,668 genes and pseudogenes. Potential applications of these resources to population genetics and the conservation of native populations are discussed.

SUBMITTER: Smith SR

PROVIDER: S-EPMC9291852 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:Abstract Kinship‐based methods of population assessment such as close‐kin mark‐recapture require accurate and efficient genotyping methods capable of resolving complex relationships among kin. Inference of such relationships can be difficult using biallelic loci due to the large number of markers required to obtain the necessary power. Sequencing‐based microsatellite panels offer an efficient alternative, combining high polymorphism with efficient next‐generation methods. Here we construct, optimize, and test one such panel for lake trout (Salvelinus namaycush) using a combination of previously‐published loci adapted for sequencing and de novo loci mined from a genome assembly. We performed three rounds of primer optimization, yielding a final panel of 131 loci, followed by testing with two different levels of PCR multiplexing (all primers in one or two groups) and two different reaction volumes (5 and 10 μL). Our results showed that the use of the largest multiplex and smallest reaction volume did not substantially change results, allowing significant cost and time savings. To test panel accuracy, we used both a set of 153 known‐origin samples from origins of management interest and a series of hatchery crosses representing nine families with parent‐offspring, half‐sibling, and largely‐unrelated pairs. Our results indicate that sequencing‐based microsatellite panels can efficiently and accurately provide the information required for a population genetics analyses including population assignment, calculation of between‐population FST, and kinship‐based population estimation techniques. Such techniques are seeing increasing applications for a wide range of taxa; our findings should provide insight and guidance for the development of the necessary molecular resources. Kinship‐based methods of population assessment such as close‐kin mark‐recapture require accurate and efficient genotyping methods capable of resolving complex relationships among kin, but inference of such relationships can be difficult using biallelic loci. Sequencing‐based microsatellite panels offer an efficient alternative, combining high polymorphism with efficient next‐generation methods. Here we construct, optimize, and test one such panel for lake trout (Salvelinus namaycush) using a combination of historical loci adapted for sequencing and de novo loci mined from a genome assembly.

Dataset Information

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

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