Despite its recent invasion into the marine realm, the sea otter (Enhydra lutris) has evolved a suite of adaptations for life in cold coastal waters, including limb modifications and dense insulating fur. This uniquely dense coat led to the near-extinction of sea otters during the 18th-20th century fur trade and an extreme population bottleneck. We used the de novo genome of the southern sea otter (E. l. nereis) to reconstruct its evolutionary history, identify genes influencing aquatic adaptation, and detect signals of population bottlenecks. We compared the genome of the southern sea otter to the tropical freshwater-living giant otter (Pteronura brasiliensis) to assess common and divergent genomic trends between otter species, and to the closely related northern sea otter (E. l. kenyoni) to uncover population-level trends. We found signals of positive selection in genes related to aquatic adaptations, particularly limb development and polygenic selection on genes related to hair follicle development. We found extensive pseudogenization of olfactory receptor genes in both the sea otter and giant otter lineages, consistent with patterns of sensory gene loss in other aquatic mammals. At the population level, the southern sea otter and the northern sea otter showed extremely low genomic diversity, signals of recent inbreeding, and demographic histories marked by population declines. These declines pre-date the fur trade and appear to have resulted in an increase in putatively deleterious variants that could impact the future recovery of the sea otter.
Southern sea otter genome annotation
This gff file is the annotation of the southern sea otter (Enhydra lutris nereis) genome, generated using MAKER2 based on evidence from RNA-Seq of sea otter whole blood and protein data from domestic ferret, domestic cat and domestic dog. Gene models were predicted by AUGUSTUS after three rounds of training. Protein and domain information from the Swissprot/Uniprot database (accessed in 2016) and Interproscan 5.19-58 are included in the annotations. See details in SI Methods of Beichman et al. (2019).
final_sea_otter_23May2016_bS9RH.round5.AED1.0.blast1e-06.renamed.rmDupScaffs.20171118.gff.gz
Southern sea otter genome annotation protein sequences
This fasta file contains the sequences of proteins from the southern sea otter (Enhydra lutris nereis) genome, generated using MAKER2 and AUGUSTUS. See details in SI Methods of Beichman et al. (2019).
final_sea_otter_23May2016_bS9RH_proteins.round5.AED1.0.blast1e-06.renamed.rmDupScaffs.20171118.fasta.gz
Southern sea otter genome annotation transcript sequences (without UTRs)
This fasta file contains the sequences of transcripts from the southern sea otter (Enhydra lutris nereis) genome, generated using MAKER2 and AUGUSTUS. UTR regions have been removed. See details in SI Methods of Beichman et al. (2019).
sea_otter_23May2016_bS9RH.all.maker.transcripts.round5.AED1.0.renamed.NOUTRS.rmDupScaffs.20171118.fasta.gz
Southern sea otter genotypes
This directory contains the filtered genotypes from southern sea otter (Enhydra lutris nereis) sequencing reads (Project number: PRJNA472597, Acc. SRR8597300) mapped to the domestic ferret reference genome (GCF_000215625.1). The files are in vcf format, and the genome was split into 323 chunks to reduce file sizes. Each of the first 1-224 .vcf files contain a single scaffold, and the remaining 225-323 vcf files each contain groups of 76 smaller scaffolds. The directory ferret_genome_interval_bedfiles.tar.gz contains the bed files that give the scaffold coordinates of each .vcf file (e.g. interval_244.bed gives the coordinates of the scaffolds contained in the vcf file labeled as 244: *.raw_variants.244.*.HQsites.Only.rmDotGenotypes.rmBadVars.vcf.gz).
The reads were mapped, genotypes were called and filtered as described in the README and SI Methods in Beichman et al. 2019.
southern_sea_otter.vcfFiles.tar.gz
Northern sea otter genotypes
These vcf files contain filtered genotypes from the northern sea otter (Enhydra lutris kenyoni) sequencing reads (SRA: SRX2967283, from Jones et al. (2018)) mapped to the domestic ferret reference genome (GCF_000215625.1). When gVCF files were generated, the genome was split into 323 chunks to parallelize processing and reduce filesize. Each of the first 1-224 .vcf files each contain a single scaffold, and the remaining 225-323 .vcf files each contain groups of 76 smaller scaffolds. The directory ferret_genome_interval_bedfiles.tar.gz contains the bed files that give the scaffold coordinates of each .vcf file (e.g. interval_244.bed gives the coordinates of the scaffolds contained in the vcf file labeled as 244: *.raw_variants.244.*.HQsites.Only.rmDotGenotypes.rmBadVars.vcf.gz).
northern_sea_otter.vcfFiles.tar.gz
Ferret genome intervals used to split vcf files
The vcf files of each otter were split into intervals to reduce filesize. This directory (ferret_genome_interval_bedfiles.tar.gz) contains bed files that give the scaffold coordinates of each each interval. For example interval_244.bed gives the coordinates of the scaffolds contained in the vcf file labeled 244: *.raw_variants.244.*.HQsites.Only.rmDotGenotypes.rmBadVars.vcf.gz).
ferret_genome_interval_bedfiles.tar.gz
Giant otter genotypes
These vcf files contain filtered genotypes from the giant otter (Pteronura brasiliensis) sequencing reads (Project number: PRJNA399365) mapped to the domestic ferret reference genome (GCF_000215625.1). When gVCF files were generated, the genome was split into 323 chunks to parallelize processing and reduce filesize. Each of the first 1-224 .vcf files each contain a single scaffold, and the remaining 225-323 .vcf files each contain groups of 76 smaller scaffolds. The directory ferret_genome_interval_bedfiles.tar.gz contains the bed files that give the scaffold coordinates of each .vcf file (e.g. interval_244.bed gives the coordinates of the scaffolds contained in the vcf file labeled as 244: *.raw_variants.244.*.HQsites.Only.rmDotGenotypes.rmBadVars.vcf.gz).
giant_otter.vcfFiles.tar.gz