July 7, 2019  |  

De novo genome and transcriptome assembly of the Canadian beaver (Castor canadensis).

Authors: Lok, Si and Paton, Tara A and Wang, Zhuozhi and Kaur, Gaganjot and Walker, Susan and Yuen, Ryan K C and Sung, Wilson W L and Whitney, Joseph and Buchanan, Janet A and Trost, Brett and Singh, Naina and Apresto, Beverly and Chen, Nan and Coole, Matthew and Dawson, Travis J and Ho, Karen and Hu, Zhizhou and Pullenayegum, Sanjeev and Samler, Kozue and Shipstone, Arun and Tsoi, Fiona and Wang, Ting and Pereira, Sergio L and Rostami, Pirooz and Ryan, Carol Ann and Tong, Amy Hin Yan and Ng, Karen and Sundaravadanam, Yogi and Simpson, Jared T and Lim, Burton K and Engstrom, Mark D and Dutton, Christopher J and Kerr, Kevin C R and Franke, Maria and Rapley, William and Wintle, Richard F and Scherer, Stephen W

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 short reads (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 precise exon placement for 91.1% of the 9805 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. Copyright © 2017 Lok et al.

Journal: G3
DOI: 10.1534/g3.116.038208
Year: 2017

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