Tilapia assembly and gene annotation

Assembly

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

Gene 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.

RNASeq 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:

TissueNumber of gene models
Blood18777
Brain26171
Embryo27891
Eye26200
Heart25109
Kidney26097
Liver20663
Muscle22738
Ovary28311
Skin24850
Testis33377

More information

General information about this species can be found in Wikipedia.

Statistics

Summary

AssemblyOrenil1.0, INSDC Assembly GCA_000188235.1, Jan 2011
Database version75.1
Base Pairs815,725,529
Golden Path Length927,383,394
Genebuild byEnsembl
Genebuild methodMixed strategy build
Genebuild startedMay 2011
Genebuild releasedMar 2012
Genebuild last updated/patchedMar 2012

Gene counts

Coding genes

Genes and/or transcript that contains an open reading frame (ORF).

21,437
Short non coding genes

Short non coding genes are usually fewer than 200 bases long. They may be transcribed but are not translated. In Ensembl, genes with the following biotypes are classed as short non coding genes: miRNA, miscRNA, rRNA, tRNA, ncRNA, scRNA, snlRNA, snoRNA, snRNA, tRNA, and also the pseudogenic form of these biotypes. The majority of the short non coding genes in Ensembl are annotated automatically by our ncRNA pipeline.

821
Pseudogenes

A pseudogene shares an evolutionary history with a functional protein-coding gene but it has been mutated through evolution to contain frameshift and/or stop codon(s) that disrupt the open reading frame.

25
Gene transcriptsNucleotide sequence resulting from the transcription of the genomic DNA to mRNA. One gene can have different transcripts or splice variants resulting from the alternative splicing of different exons in genes.27,609

Other

Genscan gene predictions51,668

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