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Swan goose assembly and gene annotation

Assembly

The GooseV1.0 assembly was submitted by Poultry Science Institute on June 2017. The assembly is on scaffold level, consisting of 64,862 contigs assembled into 1,801 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 35,039 while the scaffold N50 is 5,027,881.

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

AssemblyGooseV1.0, INSDC Assembly GCA_002166845.1, Jun 2017
Base Pairs1,130,276,682
Golden Path Length1,130,276,682
Annotation providerEnsembl
Annotation methodFull genebuild
Genebuild startedFeb 2019
Genebuild releasedSep 2019
Genebuild last updated/patchedMar 2020
Database version100.1

Gene counts

Coding genes15,439
Non coding genes3,943
Small non coding genes389
Long non coding genes3,551
Misc non coding genes3
Pseudogenes66
Gene transcripts32,080

Other

Genscan gene predictions42,160

About this species

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