:

e.g. YIPF5 or GL831141.1:900186-950186

Assembly

Nile

The Nile tilapia (Oreochromis niloticus) genome produced by the Broad Institute.Illumina technology was used to produced this high quality draft. The whole genome shotgun data was assembled with Allpaths-LG. It is composed of 77578 contigs with an N50 value of 29.5kb and 13517 scaffolds with an N50 value of 2.8Mb.

The genome assembly represented here corresponds to GenBank Assembly ID GCA_000188235.1

Download Tilapia genome sequence (FASTA)

Annotation

The gene set was built using a mixed approach. First the Ensembl pipeline was used to generate 195657 models from orthologous vertebrate proteins from UniprotKB with a protein existence level of 1 or 2. Then, due to the lack of species specific sequences and the availability of RNA-Seq for tilapia, we used 700M paired-end reads sequenced by the Broad Institute. The RNA-Seq data contains 11 tissue types: blood, brain, embryo, eye, heart, kidney, liver, muscle, ovary, skin and testis. We pooled the tissues to avoid creating too many fragmented models. Using the RNA-Seq pipeline, we created 40899 models from the pooled set. By combining the orthologous set, the RNA-Seq set and our ncRNA pipeline we built the final gene set: 21437 protein coding gene models, 22 pseudogenes, 3 retrotransposed and 821 non coding RNA.

RNA-Seq data set. In addition to the main set, we have predicted gene models for each tissue type using the RNA-Seq pipeline. We did a BLASTp of these models against UniProt proteins of protein existence level 1 and 2 in order to confirm the open reading frame (ORF). The best BLAST hit is displayed as a transcript supporting evidence.

The tissue-specific sets of transcript models built using our RNAseq pipeline are as follows:

tissue no. gene models
blood 18777
brain 26171
embryo 27891
eye 26200
heart 25109
kidney 26097
liver 20663
muscle 22738
ovary 28311
skin 24850
testis 33377