NEW YORK (GenomeWeb) – A Toronto-led team has sequenced and started analyzing a draft genome for the Canadian beaver, Castor canadensis, providing a resource that's intended to aid in studies of everything from evolutionary biology to personalized medicine.
"This project was intended to accelerate the transition of genomics into mainstream biology and ultimately precision medicine, both requiring continued improvements in de novo assemblies for rare variant detection at cohort or population scales," senior author Stephen Scherer, a molecular genetics researcher with the University of Toronto and the Hospital for Sick Children, and his co-authors wrote.
Scherer and his colleagues used Pacific Biosciences sequencing and de novo assembly coupled with RNA sequencing on muscle tissue and blood leukocyte cells to characterize genomic features in a captive-bred beaver named Ward that was born in Quebec and currently lives at the Toronto Zoo. Their work was reported in the journal G3: Genes, Genomes, Genetics late last week.
Results from another effort — the Oregon State University-led Beaver Sequencing Project — were presented at the Plant and Animal Genomes meeting in San Diego this weekend. In the abstract for that study, the researchers noted that they combined Illumina sequencing and assembly of a 4 billion base beaver genome, sequencing and assembly of transcriptome data generated for 17 different beaver tissues, and a phylogenetic analysis of the Canadian beaver in relation to 19 other species.
North America's largest rodent, the beaver has long been a source of ecological and economic interest. As Scherer and his colleagues explained, the animal "is an iconic national symbol" in Canada, in part because trade in pelts and other beaver products "was the economic engine that drove early British and French colonial expansion, leading to the founding of Canada."
For its newly published genome study, that team tackled beaver genomic DNA with single-molecule real-time sequencing on the PacBio RSII SMRT, plucking mitochondrial sequences from the mix to put together an almost 17,000 base mitochondrial genome.
En route to the final, 2.7 billion base de novo genome assembly, meanwhile, the researchers incorporated short read genomic sequence data generated with the Illumina HiSeq X instrument. They also compared the genome with transcriptomes produced by sequencing RNA from leukocyte cells in fresh blood samples and from muscle tissues in frozen beaver tissues from the Royal Ontario Museum collection with the Illumina HiSequation 2500 instrument.
Along with analyses of the assembly itself, the team began annotating the genome, identifying repeat sequences and protein-coding genes resembling those implicated in human diseases, rodent dentition, and other processes.
The researchers noted that further studies of the beaver genome may help in untangling the beaver's history in North America and its influence on both the environment and human population movements.