DOI: 10.5281/zenodo.17524230
title: Chromosome-scale genomes show rapid diversification and ancient gene flow among bear species

description: These are the files of the assemblies that were 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

These have also been submitted to NCBI and should be available soon. We are sharing all the information that has been made available to us from NCBI, while the genomes are still being processed, and the NCBI platform is, as of the day of this submission, under the following notice:



Notice: Because of a lapse in government funding, the information on this website may not be up to date, transactions submitted via the website may not be processed, and the agency may not be able to respond to inquiries until appropriations are enacted. The NIH Clinical Center (the research hospital of NIH) is open. For more details about its operating status, please visit cc.nih.gov. Updates regarding government operating status and resumption of normal operations can be found at opm.gov.


The files here are the ones submitted to NCBI. 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)

Locus Tag Prefixes: ACSF8H



mTreOrn2.NCBI.a_ctg.fasta.gz: Alternate haplotype assembly. Scaffold-level.



PRJNA1284974 : Tremarctos ornatus Genome sequencing (TaxID: 9638)

Locus Tag Prefixes: ACSF8G







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