Genome assembly, structural annotation, functional annotation, quantification, and long-read transcriptome data for the salp Pegea sp. Files: RAD2-039_final_filtered_genome.fasta --> Genome assembly file RAD2-039_genome_mRNAs.fasta --> mRNAs derived from the genome using FINDER RAD2-039_genome_proteins.fasta --> proteins derived from the genomeRAD2-039_FINDER_BRAKER_PROT.gtf --> annotation file RAD2-039_iproscan.tsv --> functional annotation (interproscan) of the proteins RAD2-039_expressionMatrix_cpms.csv --> gene expression data in counts per million from two replicate samples of the same animalRAD2-039_ISOseq_clustered.hq.fasta --> long read mRNA data (PacBio IsoSeq)