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Common carp huanghe assembly and gene annotation

Assembly

The Hunaghe_carp_2.0 assembly was submitted by Chinese Academy of Fishery Sciences on January 2019. The assembly is on scaffold level, consisting of 184,435 contigs assembled into 143,821 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 59,678 while the scaffold N50 is 1,596,048.

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

AssemblyHunaghe_carp_2.0, INSDC Assembly GCA_004011575.1, Jan 2019
Base Pairs1,423,633,724
Golden Path Length1,423,633,724
Annotation providerEnsembl
Annotation methodFull genebuild
Genebuild startedApr 2019
Genebuild releasedDec 2019
Genebuild last updated/patchedSep 2019
Database version100.20

Gene counts

Coding genes45,202
Non coding genes2,542
Small non coding genes897
Long non coding genes1,626
Misc non coding genes19
Pseudogenes590
Gene transcripts127,057

Other

Genscan gene predictions74,512

About this species

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