Supplementary Data for The salmon louse genome: copepod features and parasitic adaptations.

This dataset contains supporting data for the manuscript: Skern-Mauritzen et al. The salmon louse genome: copepod features and parasitic adaptations.

Copepods encompass a range of ecological roles from parasites to phytoplankton grazers linking primary producers to higher trophic levels. Despite these important roles, copepod genome assemblies are scarce. Lepeophtheirus salmonis is an economically and ecologically important ectoparasitic copepod found on salmonid fish. We present the 695.4 Mbp L. salmonis genome assembly containing ≈60% repetitive regions and 13081 annotated protein-coding genes. The genome comprises 14 autosomes and a ZZ-ZW sex chromosome system. Assembly assessment identified 92.4% of the expected arthropod genes. Transcriptomics supported annotation and indicated a marked shift in gene expression after host attachment, including down-regulation of genes related to circadian rhythm coinciding with abandoning diurnal migration. The genome shows evolutionary signatures including loss of genes needed for peroxisome biogenesis, presence of numerous FNII domains, and an incomplete heme homeostasis pathway suggesting heme proteins to be obtained from the host. Despite large capacity to develop resistance against chemical treatments L. salmonis exhibits low numbers of many genes involved in detoxification.

• Supplementary data is explained in detail and referenced in the manuscript and the file Supplementary Material 30062021 REVISED.pdf
• BUSCO-V5-results-species-comparison.tar.gz contains the raw output and results of all BUSCO  V 5.0.0 runs on the genomes in Table 1 of the manuscript and Supplementary_Table_GenomeStats.xlsx 
• GCA_000181255.2_ASM18125v2_genomic.fna.RepMasker.o ...,  GCA_001005205.1_lsal_atl_canada_female_v1_genomic. ..., GCA_001005235.1_lsal_atl_canada_male_v1_genomic.fn ... and  TableS4-1-LSalAtl2s.fasta.RepMasker.out.gz contain original output from RepeatMasker
• Lsalmonis-RepeatModeler-families.fa.gz and Lsalmonis-RepeatModeler-families.stk.gz contain all repeat families as original output from RepeatModeler