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American black bear assembly and gene annotation

The American black bear (Ursus americanus) is a medium-sized bear native to North America, but is more closely related to the Asian black bear than to other American ursids such as the brown bear and polar bear.

Assembly

The ASM334442v1 assembly was submitted by Jackson Laboratory on July 2018. The assembly is on scaffold level, consisting of 231,673 contigs assembled into 111,495 scaffolds. The N50 size is the length such that 50% of the assembled genome lies in blocks of the N50 size or longer. The N50 length for the contigs is 27,247 while the scaffold N50 is 189,900.

Gene annotation

The gene annotation process was carried out using a combination of protein-to-genome alignments, annotation mapping from a suitable reference species and RNA-seq alignments (where RNA-seq data with appropriate meta data were publicly available). For each candidate gene region, a selection process was applied to choose the most appropriate set of transcripts based on evolutionary distance, experimental evidence for the source data and quality of the alignments.
Small ncRNAs were obtained using a combination of BLAST and Infernal/RNAfold.
Pseudogenes were calculated by looking at genes with a large percentage of non-biological introns (introns of <10bp), where the gene was covered in repeats, or where the gene was single exon and evidence of a functional multi-exon paralog was found elsewhere in the genome.
lincRNAs were generated via RNA-seq data where no evidence of protein homology or protein domains could be found in the transcript.

In accordance with the Fort Lauderdale Agreement, please check the publication status of the genome/assembly before publishing any genome-wide analyses using these data.

More information

General information about this species can be found in Wikipedia.

Statistics

Summary

AssemblyASM334442v1, INSDC Assembly GCA_003344425.1, Jul 2018
Base Pairs2,588,393,916
Golden Path Length2,588,393,916
Annotation providerEnsembl
Annotation methodFull genebuild
Genebuild startedSep 2018
Genebuild releasedDec 2018
Genebuild last updated/patchedMar 2020
Database version100.1

Gene counts

Coding genes20,568
Non coding genes3,730
Small non coding genes2,371
Long non coding genes774
Misc non coding genes585
Pseudogenes349
Gene transcripts37,445

Other

Genscan gene predictions74,554

About this species

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