After 2.5 years of assembly curation, the GRC presents the new zebrafish reference genome assembly, GRCz11. This latest assembly has been refined by the addition of nearly 1000 finished clone sequences and the resolution of more than 400 genome issues. GRCz11 shows a significant reduction in scaffold numbers and increase in scaffold N50 whilst the overall genome size was not affected. For the first time in a zebrafish assembly, GRCz11 also features alternate loci scaffolds (ALT_REF_LOCI) for representations of variant sequences. The alignments of the alternate loci scaffolds to the primary chromosomal path are also included in the GRCz11 assembly to provide the chromosome context for these alternate sequences.
The Ensembl GRCz11 assembly was annotated using Ensembl's automatic annotation pipeline. Predictions from zebrafish proteins have been given priority over predictions from other non-mammalian vertebrate species. All Uniprot proteins were filtered to remove predictions (PE level 3 and above). Aligned zebrafish cDNAs and zebrafish RNASeq data have been used to add UTRs. RNASeq data from embryonic and olfactory epithelium tissues were also used to produce gene models. Genes are named based on the alignment of their coding regions to known entries in public databases; ZFIN genes have priority in this process.
The Ensembl annotations were then merged with Vega annotations at the transcript level. Transcripts were merged if they shared the same internal exon-intron boundaries (i.e. had identical splicing pattern) with slight differences in the terminal exons allowed. Importantly, all Vega source transcripts (regardless of merge status) were included in the final merged gene set.
General information about this species can be found in Wikipedia.
|Assembly||GRCz11 (Genome Reference Consortium Zebrafish Build 11), INSDC Assembly GCA_000002035.4, May 2017|
|Golden Path Length||1,373,471,384|
|Annotation method||Full genebuild|
|Genebuild started||Aug 2017|
|Genebuild released||Mar 2018|
|Genebuild last updated/patched||Apr 2018|
Gene counts (Primary assembly)
|Coding genes||25,592 (incl 47 ) readthrough|
|Non coding genes||6,599|
|Small non coding genes||3,227|
|Long non coding genes||3,278 (incl 6 ) readthrough|
|Misc non coding genes||94|
Gene counts (Alternative sequence)
|Genscan gene predictions||50,550|