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Barramundi perch assembly and gene annotation

Assembly

The ASB_HGAPassembly_v1 assembly was submitted by Temasek Life Sciences Laboratory on December 2017. The assembly is on scaffold level, consisting of 3,917 contigs assembled into 3,807 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 1,066,117 while the scaffold N50 is 1,191,366.

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

AssemblyASB_HGAPassembly_v1, INSDC Assembly GCA_900066035.1, Mar 2017
Base Pairs668,464,831
Golden Path Length668,464,831
Annotation providerEnsembl
Annotation methodFull genebuild
Genebuild startedNov 2018
Genebuild releasedJun 2019
Genebuild last updated/patchedMar 2020
Database version100.1

Gene counts

Coding genes25,109
Non coding genes1,306
Small non coding genes1,281
Long non coding genes3
Misc non coding genes22
Pseudogenes346
Gene transcripts59,868

Other

Genscan gene predictions36,260

About this species

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