Proteogenomic Annotation of Chinese Hamsters Reveals Extensive Novel Translation Events and Endogenous Retroviral Elements

A high-quality
genome annotation greatly facilitates successful
cell line engineering. Standard draft genome annotation pipelines
are based largely on de novo gene prediction, homology, and RNA-Seq
data. However, draft annotations can suffer from incorrect predictions
of translated sequence, inaccurate splice isoforms, and missing genes.
Here, we generated a draft annotation for the newly assembled Chinese
hamster genome and used RNA-Seq, proteomics, and Ribo-Seq to experimentally
annotate the genome. We identified 3529 new proteins compared to the
hamster RefSeq protein annotation and 2256 novel translational events
(e.g., alternative splices, mutations, and novel splices). Finally,
we used this pipeline to identify the source of translated retroviruses
contaminating recombinant products from Chinese hamster ovary (CHO)
cell lines, including 119 type-C retroviruses, thus enabling future
efforts to eliminate retroviruses to reduce the costs incurred with
retroviral particle clearance. In summary, the improved annotation
provides a more accurate resource for CHO cell line engineering, by
facilitating the interpretation of omics data, defining of cellular
pathways, and engineering of complex phenotypes.