Table 2 Data record details for input and output files.

Step	Archive	Description	Accession/File
1-in	SRA	PacBio SMRT Sequel II long DNA reads	SRR29316387
2-in	SRA	Illumina DNA reads	SRR29316385
3-in	SRA	Illumina Hi-C reads	SRR29316386
5-out	Genome	Assembly with 290 scaffolds	JBEDAC000000000
6-out	DvNO	Assembly after filtering to 262 scaffolds	01a_ccar_genome_v1_262scaffolds_fasta.txt
7-out	DvNO	Soft-masked version of subset genome	01b_ccar_genome_v1_262scaffolds_sm_fasta.txt
8a-out	DvNO	Transfer RNAs	02a_ccar_genome_v1_262scaffolds_trna_gff3.txt
8b-out	DvNO	Ribosomal RNAs	02b_ccar_genome_v1_262scaffolds_rrna_gff3.txt
9-in	SRA	Illumina RNA-seq reads from multiple tissues and individuals	SRR30720712
11-in	SRA	PacBio CCS reads from multiple tissues	SRR31178203
13a-in	DvNO	PacBio IsoSeq HQ isoforms	02c_ccar_isoseq_hq_transcripts_fasta.txt
13c-out	DvNO	Final structural annotation	02d_ccar_annotation_v5_gff3.txt
14-out	DvNO	Protein sequences	03a_ccar_annotation_v5_proteins_fasta.txt
		Transcript sequences	03b_ccar_annotation_v5_transcripts_fasta.txt
15a-out	DvNO	Kegg BlastKOALA output	04a_ccar_annotation_v5_kegg.txt
15b-out	DvNO	Interproscan output	04b_ccar_annotation_v5_interproscan.txt
15c-out	DvNO	Blast + output	04c_ccar_annotation_v5_swissprot_wGO_outfmt6.txt
15c-out	DvNO	Proteins and GO terms	04d_ccar_annotation_v5_swissprot_hits_and_GO_v2.txt
mito	DvNO	Mitochondrial genes	05_ccar_genome_v1_scaffold_107_mito_NCBI.txt

SRA, NCBI Sequence Read Archive; DvNO, DataverseNO; Genome, NCBI Genbank Genome. Data in NCBI SRA and Genome are deposited under BioProject number PRJNA1119394⁵⁸. Data in DataverseNO are deposited under the handle GXMSUH⁶⁰.

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