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
Base Pairs608,029,870
Golden Path Length832,114,588
Annotation methodMixed strategy build
Genebuild startedJan 2010
Genebuild releasedAug 2011
Genebuild last updated/patchedAug 2011
Database version90.1

Gene counts

Coding genes20,095
Pseudogenes518
Gene transcripts24,159

Other

Genscan gene predictions78,431

About this species