Cod assembly and gene annotation

Assembly

This is the first draft sequence and assembly of the Atlantic cod (Gadus morhua), provided by the cod genome consortium. Whole genome shotgun and paired-end data were generated using the Roche 454 FLX Titanium platform. The 0.9 GB genome was sequenced to 25x coverage and assembled using Newbler, resulting in an assembly with a contig N50 of 2.3 kb and a scaffold N50 of 687.7 kb.

Gene annotation

Owing to the fragmentary nature of the Atlantic cod assembly, it was necessary to combine the standard protein-evidence based annotation approach with a complementary annotation method based on a whole genome alignment to stickleback. Some scaffolds were rearranged into "gene-scaffold" super-structures using our projection method, and 17,920 out of 20,787 protein-coding stickleback genes were mapped onto reorganized scaffolds. In addition, protein-coding genes, pseudogenes and non-coding RNAs were annotated using the standard protein evidenced based Ensembl pipeline. These approaches resulted in a final gene set of 20,095 protein-coding genes, 518 pseudogenes, and 1,541 noncoding RNA genes.

More information

General information about this species can be found in Wikipedia.

Statistics

Summary

AssemblygadMor1, Jan 2010
Database version78.1
Base Pairs608,029,870
Golden Path Length

The golden path is the length of the reference assembly. It consists of the sum of all top-level sequences in the seq_region table, omitting any redundant regions such as haplotypes and PARs (pseudoautosomal regions).

832,114,588
Genebuild byEnsembl
Genebuild methodMixed strategy build
Genebuild startedJan 2010
Genebuild releasedAug 2011
Genebuild last updated/patchedAug 2011

Gene counts

Coding genes

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

20,095
Small non coding genes

Small 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 small non coding genes: miRNA, miscRNA, rRNA, scRNA, snlRNA, snoRNA, snRNA, and also the pseudogenic form of these biotypes. The majority of the small non coding genes in Ensembl are annotated automatically by our ncRNA pipeline. Please note that tRNAs are annotated separately using tRNAscan. tRNAs are included as 'simple fetaures', not genes, because they are not annotated using aligned sequence evidence.

1,541
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.

518
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.24,159

Other

Genscan gene predictions78,431