Genome assembly has a major impact on gene content: a comparison of annotation in two Bos taurus assemblies.

ABSTRACT: Gene and SNP annotation are among the first and most important steps in analyzing a genome. As the number of sequenced genomes continues to grow, a key question is: how does the quality of the assembled sequence affect the annotations? We compared the gene and SNP annotations for two different Bos taurus genome assemblies built from the same data but with significant improvements in the later assembly. The same annotation software was used for annotating both sequences. While some annotation differences are expected even between high-quality assemblies such as these, we found that a staggering 40% of the genes (>9,500) varied significantly between assemblies, due in part to the availability of new gene evidence but primarily to genome mis-assembly events and local sequence variations. For

SUBMITTER: Florea L 

PROVIDER: S-EPMC3120881 | biostudies-literature | 2011

REPOSITORIES: biostudies-literature