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Golden-line barbel assembly and gene annotation

Assembly

The SAMN03320097.WGS_v1.1 assembly was submitted by BGI, Shenzhen on January 2016. The assembly is on scaffold level, consisting of 168,074 contigs assembled into 31,277 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 29,353 while the scaffold N50 is 1,156,368.

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

AssemblySAMN03320097.WGS_v1.1, INSDC Assembly GCA_001515645.1, Dec 2015
Base Pairs1,750,287,761
Golden Path Length1,750,287,761
Annotation providerEnsembl
Annotation methodFull genebuild
Genebuild startedOct 2018
Genebuild releasedDec 2019
Genebuild last updated/patchedMar 2020
Database version100.11

Gene counts

Coding genes44,472
Non coding genes5,171
Small non coding genes2,151
Long non coding genes2,983
Misc non coding genes37
Pseudogenes695
Gene transcripts112,633

Other

Genscan gene predictions83,006

About this species

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