This dataset contains supporting data for the manuscript: Skern-Mauritzen et al. The salmon louse genome: copepod features and parasitic adaptations. Arthropods show an astonishing diversity and comprise the most populous groups of animals. Aquatic arthropods belonging to the sub-class Copepoda encompass a rich ecological diversity from pestering parasites to pivotal grazers that link primary producers to higher trophic levels. Among the copepod parasites we find Lepeophtheirus salmonis, an important ectoparasite that represents a threat to wild salmonid stocks and causes large annual losses to the salmon farming industry. Despite the important role of copepods in central ecosystem services and their impact as parasites, representative genomic data and genome assemblies are scarce. This limits our opportunity to understand both the specific biology of individual species and unifying copepod genomic features that may govern their capacities to adapt to a changing environment. Here we present the salmon louse genome - the first genome of a parasitic copepod that is fully sequenced and annotated. The 695.4 Mbp assembly was validated by a genetic linkage map and comprises 13 autosomes that recombine almost exclusively in males, one autosome that is shielded from recombination in both sexes and a ZZ-ZW style sex chromosome system. The genome assembly contains approximate 60% repetitive regions and comprise 13081 annotated predicted protein-coding genes. The predicted gene set appears to be quite complete as 92.4% of the expected Arthropod genes were found by BUSCO analysis. The gene annotations were validated by transcriptome sequencing that corresponds to the expected function of selected tissues. Transcriptome sequencing further revealed a marked shift in the gene expression pattern at the transition from the planktonic dispersal phase to the parasitic lifestyle after host attachment. Among other features, genes related to circadian rhythm are down-regulated upon attaching to a host - probably reflecting abandoning a planktonic life with diurnal migration. The genome shows several evolutionary signatures including a large expansion of FNII domains, commonly considered vertebrate specific, and an incomplete heme homeostasis pathway suggesting that heme proteins are obtained from the host. Furthermore, despite a demonstrated large capacity to develop resistance against chemical treatments, the salmon louse has very low numbers of cytochrome P450, ATP-Binding Cassette type transporters, and Glutathione S-transferases genes considering that these genes are commonly involved in detoxification. Interestingly, only one gene family with a putative detoxification role was expanded: the major vault protein. Finally, the salmon louse has lost peroxisomes, a trait that appears shared among Caligida but not in copepods in general. Supplementary data is explained in detail and referenced in the manuscript and the file Supplementary Material 11032021.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

The project was funded by The Ministry of Trade and Fisheries, The Norwegian Seafood Research Fund (project 900400). This research was funded by the Research Council Norway, SFI-Sea Lice Research Centre, grant number 203513/O30.