These are the files generated for the manuscript: T. B. Wooldridge, M. Escalona, B. W. Perry, A. N. Enstrom, D. Salih, W. E. Seligmann, S. Sacco, K. L. Moon, R. Sahasrabudhe, N. Chumchim, O. Nguyen, J. L. Kelley, R. D. E. MacPhee, B. Shapiro, Chromosome-scale genomes show rapid diversification and ancient gene flow among bear species. Genome Biol. Evol., evaf188 (2025). DOI: 10.1093/gbe/evaf188 This is a complementary resource for the manuscript. Additional code corresponding to the analyses in the manuscript can be found here: https://github.com/twooldridge/BearComparativeGenomics AssembliesThe genome assemblies have been submitted to NCBI and should be available soon. The sequences are named: SCAF_X, where X is a number, and they are ordered based on sequence length. For the assemblies tagged as chromosome-level assemblies, we are sharing a table that specifies the relationship between the names. Please follow the prefix of the assemblies to get the CSV file corresponding to the chromosome-assignment table. Files shared: Assemblies: mHalMal1.NCBI.p_ctg.fasta.gz mHalMal1.NCBI.a_ctg.fasta.gz mTreOrn2.NCBI.p_ctg.fasta.gz mTreOrn2.NCBI.a_ctg.fasta.gz mMelUrs1.NCBI.p_ctg.fasta.gz mMelUrs1.NCBI.a_ctg.fasta.gz Chromosome-assignment: mHelMal1.NCBI.p_ctg.chrs.csv mMelUrs1.NCBI.p_ctg.chrs.csv mTreOrn2.NCBI.p_ctg.chrs.csv More information about the assemblies shared: Helarctos malayanus: BioSample: SAMN49720842 Assemblies: mHalMal1.NCBI.p_ctg.fasta.gz: Primary haplotype assembly. Chromosome-level. PRJNA1284979 : Helarctos malayanus Genome sequencing primary haplotype (TaxID: 9634) Locus Tag Prefixes: ACSF8I WGS Accession: JBREYN000000000 mHalMal1.NCBI.a_ctg.fasta.gz: Alternate haplotype assembly. Scaffold-level. PRJNA1284979 : Helarctos malayanus Genome sequencing alternate haplotype (TaxID: 9634) Locus Tag Prefixes: ACSF8J WGS Accession: JBREYO000000000 Tremartctos onrnatus: BioSample: SAMN49720843 Assemblies: mTreOrn2.NCBI.p_ctg.fasta.gz: Primary haplotype assembly. Chromosome-level. PRJNA1284975 : Tremarctos ornatus Genome sequencing (TaxID: 9638) Assembly Accession GCA_054642835.1 Locus Tag Prefixes: ACSF8H WGS Accession: JBTVSB000000000 mTreOrn2.NCBI.a_ctg.fasta.gz: Alternate haplotype assembly. Scaffold-level. PRJNA1284974 : Tremarctos ornatus Genome sequencing (TaxID: 9638) Assembly Accession GCA_054642835.1 Locus Tag Prefixes: ACSF8G WGS Accession: JBTVSC000000000 Melursus ursinus: BioSample: SAMN49720841 Assemblies: mMelUrs1.NCBI.p_ctg.fasta.gz: Primary haplotype assembly. Chromosome-level. PRJNA1284966 : Melursus ursinus Genome sequencing principal haplotype (TaxID: 9636) Locus Tag Prefixes: ACSF8E WGS Accession: JBQCBQ000000000 mMelUrs1.NCBI.a_ctg.fasta.gz: Alternate haplotype assembly. Scaffold-level. PRJNA1284968 : Melursus ursinus Genome sequencing alternate haplotype (TaxID: 9636) Locus Tag Prefixes: ACSF8F WGS Accession: JBQCBR000000000 Annotations Please note that these annotations were used for the analyses in our manuscript. Genes For each of the Brown, Black, Asiatic Black, Polar, Giant Panda, Sun, Sloth, and Andean bears, the following EGAPx genome annotation files are provided. See publication for details of EGAPx methods Files: ${SPECIES}.egapx.genomic.gff.gz - GFF formatted output from EGAPx (gzipped) ${SPECIES}.egapx.genomic.gtf.gz - GTF formatted output from EGAPx (gzipped) ${SPECIES}.egapx.cds.fna.gz - fasta file of coding sequences annotated with EGAPx (gzipped) ${SPECIES}.egapx.proteins.faa.gz - fasta file of protein sequences annotated with EGAPx (gzipped) ${SPECIES}.egapx.transcripts.fna.gz - fasta file of transcripts sequences annotated with EGAPx (gzipped) Repeats For each of the Brown, Black, Asiatic Black, Polar, Giant Panda, Sun, Sloth, and Andean bears, the following RepeatMasker files are provided. See the publication for the details of RepeatModeling + RepeatMasking methods. Files: ${SPECIES}.fasta.out.gff.gz - GFF-formatted output from RepeatMasker (gzipped) ${SPECIES}.fasta.out.html - HTML Repeat Masker report ${SPECIES}.fasta.tbl - Repeat Masker summary table ${SPECIES}.fasta.masked.gz- Soft-masked (A->a) reference genome (gzipped)