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Giant panda assembly and gene annotation

The giant panda (Ailuropoda melanoleuca) is a bear native to south central China. For many decades, the precise taxonomic classification of the giant panda was under debate because it shares characteristics with both bears and raccoons. However, molecular studies indicate the giant panda is a true bear, part of the family Ursidae. These studies show it differentiated early (about 19 million years ago) from the main ursine stock; since it is the most basal member of the group, it is equidistant from all other extant ursids. The giant panda has been referred to as a living fossil.

Assembly

The ASM200744v2 assembly was submitted by Institute of Zoology, Chinese Academy of Sciences on May 2020. The assembly is on chromosome level, consisting of 127,086 contigs assembled into 77,288 scaffolds. From these sequences, 21 chromosomes have been built. 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 127,380 while the scaffold N50 is 129,245,720.

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

AssemblyASM200744v2, INSDC Assembly GCA_002007445.2, Apr 2020
Base Pairs2,444,060,653
Golden Path Length2,444,060,653
Annotation providerEnsembl
Annotation methodFull genebuild
Genebuild startedMay 2020
Genebuild releasedApr 2020
Genebuild last updated/patchedJun 2020
Database version104.2

Gene counts

Coding genes20,857
Non coding genes3,022
Small non coding genes2,233
Long non coding genes774
Misc non coding genes15
Pseudogenes583
Gene transcripts43,348

Other

Genscan gene predictions59,679

About this species

HASH(0x5195e78)