Brown trout (fSalTru1.1)

Brown trout assembly and gene annotation

Assembly

The fSalTru1.1 assembly was submitted by SC on June 2019. The assembly is on chromosome level, consisting of 5,378 contigs assembled into 1,441 scaffolds. From these sequences, 40 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 1,703,178 while the scaffold N50 is 52,209,666.

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

AssemblyfSalTru1.1, INSDC Assembly GCA_901001165.1, Jun 2019
Base Pairs2,371,880,186
Golden Path Length2,371,880,186
Annotation providerEnsembl
Annotation methodFull genebuild
Genebuild startedJul 2019
Genebuild releasedDec 2019
Genebuild last updated/patchedDec 2019
Database version111.11

Gene counts

Coding genes43,935
Non coding genes4,441
Small non coding genes2,768
Long non coding genes1,624
Misc non coding genes49
Pseudogenes581
Gene transcripts122,381

Other

Genscan gene predictions64,498