Title |
De Novo Genome and Transcriptome Assembly of the Canadian Beaver (Castor canadensis)
|
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Published in |
G3: Genes, Genomes, Genetics, February 2017
|
DOI | 10.1534/g3.116.038208 |
Pubmed ID | |
Authors |
Si Lok, Tara A Paton, Zhuozhi Wang, Gaganjot Kaur, Susan Walker, Ryan K C Yuen, Wilson W L Sung, Joseph Whitney, Janet A Buchanan, Brett Trost, Naina Singh, Beverly Apresto, Nan Chen, Matthew Coole, Travis J Dawson, Karen Ho, Zhizhou Hu, Sanjeev Pullenayegum, Kozue Samler, Arun Shipstone, Fiona Tsoi, Ting Wang, Sergio L Pereira, Pirooz Rostami, Carol Ann Ryan, Amy Hin Yan Tong, Karen Ng, Yogi Sundaravadanam, Jared T Simpson, Burton K Lim, Mark D Engstrom, Christopher J Dutton, Kevin C R Kerr, Maria Franke, William Rapley, Richard F Wintle, Stephen W Scherer |
Abstract |
The Canadian beaver (Castor canadensis) is the largest indigenous rodent in North America. We report a draft annotated assembly of the beaver genome, the first for a large rodent and the first mammalian genome assembled directly from uncorrected and moderate coverage (< 30 ×) long-reads generated by single-molecule sequencing. The genome size is 2.7 Gb estimated by k-mer analysis. We assembled the beaver genome using the new Canu assembler optimized for noisy reads. The resulting assembly was refined using Pilon supported by shortreads (80 ×) and checked for accuracy by congruency against an independent short-read assembly. We scaffolded the assembly using the exon-gene models derived from 9805 full-length open reading frames (FL-ORFs) constructed from the beaver leukocyte and muscle transcriptomes. The final assembly comprised 22,515 contigs with an N50 of 278,680 bp and an N50-scaffold of 317,558 bp. Maximum contig and scaffold lengths were 3.3 and 4.2 Mb, respectively, with a combined scaffold length representing 92% of the estimated genome size. The completeness and accuracy of the scaffold assembly was demonstrated by the complete and precise exon placement for 91.1% of the 9,805 assembled FL-ORFs and 83.1% of the BUSCO (Benchmarking Universal Single-Copy Orthologs) gene set used to assess the quality of genome assemblies. Well-represented were genes involved in dentition and enamel deposition, defining characteristics of rodents with which the beaver is well-endowed. The study provides insights for genome assembly and an important genomics resource for Castoridae and rodent evolutionary biology. |
X Demographics
Geographical breakdown
Country | Count | As % |
---|---|---|
United States | 22 | 31% |
Canada | 15 | 21% |
United Kingdom | 5 | 7% |
Switzerland | 2 | 3% |
Comoros | 1 | 1% |
Brazil | 1 | 1% |
India | 1 | 1% |
Germany | 1 | 1% |
France | 1 | 1% |
Other | 0 | 0% |
Unknown | 21 | 30% |
Demographic breakdown
Type | Count | As % |
---|---|---|
Scientists | 36 | 51% |
Members of the public | 28 | 40% |
Science communicators (journalists, bloggers, editors) | 4 | 6% |
Practitioners (doctors, other healthcare professionals) | 2 | 3% |
Mendeley readers
Geographical breakdown
Country | Count | As % |
---|---|---|
Netherlands | 1 | 2% |
United States | 1 | 2% |
Unknown | 63 | 97% |
Demographic breakdown
Readers by professional status | Count | As % |
---|---|---|
Researcher | 12 | 18% |
Student > Bachelor | 11 | 17% |
Student > Ph. D. Student | 10 | 15% |
Student > Master | 9 | 14% |
Professor > Associate Professor | 4 | 6% |
Other | 11 | 17% |
Unknown | 8 | 12% |
Readers by discipline | Count | As % |
---|---|---|
Agricultural and Biological Sciences | 24 | 37% |
Biochemistry, Genetics and Molecular Biology | 13 | 20% |
Computer Science | 4 | 6% |
Medicine and Dentistry | 3 | 5% |
Veterinary Science and Veterinary Medicine | 2 | 3% |
Other | 8 | 12% |
Unknown | 11 | 17% |