Chromosome-scale genomes show rapid diversification and ancient gene flow among bear species

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

Assemblies

The 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)