Protein genes in repetitive sequence-antifreeze glycoproteins in Atlantic cod genome.

ABSTRACT:

Background

Highly repetitive sequences are the bane of genome sequence assembly, and the short read lengths produced by current next generation sequencing technologies further exacerbates this obstacle. An adopted practice is to exclude repetitive sequences in genome data assembly, as the majority of repeats lack protein-coding genes. However, this could result in the exclusion of important genotypes in newly sequenced non-model species. The absence of the antifreeze glycoproteins (AFGP) gene family in the recently sequenced Atlantic cod genome serves as an example.

Results

The Atlantic cod (Gadus morhua) genome was assembled entirely from Roche 454 short reads, demonstrating the feasibility of this approach. However, a well-known major adaptive trait, the AFGP, essential fo

SUBMITTER: Zhuang X 

PROVIDER: S-EPMC3441883 | biostudies-literature | 2012 Jul

REPOSITORIES: biostudies-literature