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.
| Original language | English |
|---|---|
| Pages (from-to) | 679-694 |
| Number of pages | 16 |
| Journal | Molecular Ecology Resources |
| Volume | 22 |
| Issue number | 2 |
| DOIs | |
| State | Published - Feb 2022 |
Funding
We would like to thank hatchery personnel at Iron River National Fish Hatchery (USFWS), the OMNRF White Lake Fish Culture Station, and Codrington Fish Research Facility for assistance with generating double haploid Lake Trout, sampling fish for Hi-C sequencing, and collecting tissue for RNA sequencing. We would also like the thank the Vertebrate Genomics and Evolution Group (VerGE, Spring 2021) at Michigan State University and the Population Genetics Seminar group (Spring 2021) at the University of Montana for helpful discussion and suggestions. We would also like to thank three anonymous reviewers for their helpful comments and suggestions. SRS, KS, and GL were supported by award 2017_SCR_44067 from the Great Lakes Fisheries Commission. LB and EN were supported by award 2017_BER_44071 from the Great Lakes Fisheries Commission. LB was supported by the Canadian Research Chair in Genomics and Conservation of Aquatic Resources administered by the Canada Research Chair Program. JR was supported by CFI Grant 33408 from the Canada Foundation for Innovation, a Genome Technology Platform Grant from Genome Canada, and the CanSeq150 Sequencing Initiative. KTS was supported through the cooperative agreement Partnership for Ecosystem Research and Management (PERM) between the Department of Fisheries and Wildlife at Michigan State University and the Michigan Department of Natural Resources. We would like to thank hatchery personnel at Iron River National Fish Hatchery (USFWS), the OMNRF White Lake Fish Culture Station, and Codrington Fish Research Facility for assistance with generating double haploid Lake Trout, sampling fish for Hi‐C sequencing, and collecting tissue for RNA sequencing. We would also like the thank the Vertebrate Genomics and Evolution Group (VerGE, Spring 2021) at Michigan State University and the Population Genetics Seminar group (Spring 2021) at the University of Montana for helpful discussion and suggestions. We would also like to thank three anonymous reviewers for their helpful comments and suggestions. SRS, KS, and GL were supported by award 2017_SCR_44067 from the Great Lakes Fisheries Commission. LB and EN were supported by award 2017_BER_44071 from the Great Lakes Fisheries Commission. LB was supported by the Canadian Research Chair in Genomics and Conservation of Aquatic Resources administered by the Canada Research Chair Program. JR was supported by CFI Grant 33408 from the Canada Foundation for Innovation, a Genome Technology Platform Grant from Genome Canada, and the CanSeq150 Sequencing Initiative. KTS was supported through the cooperative agreement Partnership for Ecosystem Research and Management (PERM) between the Department of Fisheries and Wildlife at Michigan State University and the Michigan Department of Natural Resources.
| Funders | Funder number |
|---|---|
| Louisiana Department of Wildlife and Fisheries | |
| 2017_SCR_44067 | |
| Great Lakes Fishery Commission | 2017_BER_44071 |
| Michigan State University | |
| Genome Canada | |
| Canada Foundation for Innovation | 33408 |