Limitations of the Rhesus Macaque Draft Genome Assembly and Annotation

Authors

Xiongfei Zhang, University of Nebraska Medical Center
Joel Goodsell, University of Nebraska Medical CenterFollow
Robert B. Norgren, University of Nebraska Medical CenterFollow

Document Type

Article

Journal Title

BMC Genomics

Publication Date

2012

Volume

13

Abstract

Finished genome sequences and assemblies are available for only a few vertebrates. Thus, investigators studying many species must rely on draft genomes. Using the rhesus macaque as an example, we document the effects of sequencing errors, gaps in sequence and misassemblies on one automated gene model pipeline, Gnomon. The combination of draft genome with automated gene finding software can result in spurious sequences. We estimate that approximately 50% of the rhesus gene models are missing, incomplete or incorrect. The problems identified in this work likely apply to all draft vertebrate genomes annotated with any automated gene model pipeline and thus represent a pervasive challenge to the analysis of draft genomes.

MeSH Headings

Animals, Base Sequence, Chromosomes, Mammalian, Codon, Nonsense, Exons, Frameshift Mutation, Gene Duplication, Genome, Macaca mulatta, Molecular Sequence Annotation, Mutagenesis, Insertional

DOI Link

10.1186/1471-2164-13-206

ISSN

1471-2164

Rights

Creative Commons Attribution License 2.0

Recommended Citation

Zhang, Xiongfei; Goodsell, Joel; and Norgren, Robert B., "Limitations of the Rhesus Macaque Draft Genome Assembly and Annotation" (2012). Journal Articles: Genetics, Cell Biology & Anatomy. 42.
https://digitalcommons.unmc.edu/com_gcba_articles/42