Use of Annotated Chinese Hamster Reference Genome and Transcriptome to Investigate Regulatory Mechanisms and Mutation Rates

Authors: 
Jacob, N. M., University of Minnesota
Yap, M. G. S., Agency for Science and Technology Research (A*STAR)
Karypis, G., University of Minnesota
Lee, D. Y., Bioprocessing Technology institute, A*STAR
Le, H., University of Minnesota
Johnson, K. C., University of Minnesota
Yusufi, F., Bioprocessing Technology Institute A-STAR

We have assembled the Chinese hamster genome as well as comprehensive transcriptomes of hamster tissues and CHO cells. The diploid genome will serve as a reference for the genomic study of CHO cells, which are known to be aneuploid and have a propensity for chromosomal rearrangement. The annotation of the hamster genome was facilitated by our EST repertoire, which was collected from transcriptionally active liver, brain and spleen tissues as well as a wide range of CHO cell lines under different culture conditions to enhance transcript diversity. Over 95% of ESTs aligned to the assembled Chinese hamster genome, indicating excellent coverage of gene-rich regions. Ab initio gene prediction was performed and regions with homology to mouse, rat and human protein coding sequences were identified. Genome annotation facilitated investigation of synteny with mouse to estimate the degree to which gene order is maintained; mouse orthologs were identified for 85% of the hamster genes.