title: De NovoGenome and Transcriptome Assembly of the Canadian Beaver (Castor canadensis).
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 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.
authors.affiliation: The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada si.lok@sickkids.ca stephen.scherer@sickkids.ca.|Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada.
authors.forename: Si
authors.initials: S
authors.lastname: Lok
authors.affiliation: The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada.|Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada.
authors.forename: Tara A
authors.initials: TA
authors.lastname: Paton
authors.affiliation: The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada.|Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada.
authors.forename: Zhuozhi
authors.initials: Z
authors.lastname: Wang
authors.affiliation: The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada.|Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada.
authors.forename: Gaganjot
authors.initials: G
authors.lastname: Kaur
authors.affiliation: The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada.|Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada.
authors.forename: Susan
authors.initials: S
authors.lastname: Walker
authors.affiliation: The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada.|Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada.
authors.forename: Ryan K C
authors.initials: RK
authors.lastname: Yuen
authors.affiliation: The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada.|Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada.
authors.forename: Wilson W L
authors.initials: WW
authors.lastname: Sung
authors.affiliation: The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada.|Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada.
authors.forename: Joseph
authors.initials: J
authors.lastname: Whitney
authors.affiliation: The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada.|Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada.
authors.forename: Janet A
authors.initials: JA
authors.lastname: Buchanan
authors.affiliation: The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada.|Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada.
authors.forename: Brett
authors.initials: B
authors.lastname: Trost
authors.affiliation: The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada.|Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada.
authors.forename: Naina
authors.initials: N
authors.lastname: Singh
authors.affiliation: The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada.|Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada.
authors.forename: Beverly
authors.initials: B
authors.lastname: Apresto
authors.affiliation: The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada.|Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada.
authors.forename: Nan
authors.initials: N
authors.lastname: Chen
authors.affiliation: The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada.|Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada.
authors.forename: Matthew
authors.initials: M
authors.lastname: Coole
authors.affiliation: The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada.|Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada.
authors.forename: Travis J
authors.initials: TJ
authors.lastname: Dawson
authors.affiliation: The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada.|Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada.
authors.forename: Karen
authors.initials: K
authors.lastname: Ho
authors.affiliation: The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada.|Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada.
authors.forename: Zhizhou
authors.initials: Z
authors.lastname: Hu
authors.affiliation: The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada.|Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada.
authors.forename: Sanjeev
authors.initials: S
authors.lastname: Pullenayegum
authors.affiliation: The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada.|Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada.
authors.forename: Kozue
authors.initials: K
authors.lastname: Samler
authors.affiliation: The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada.|Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada.
authors.forename: Arun
authors.initials: A
authors.lastname: Shipstone
authors.affiliation: The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada.|Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada.
authors.forename: Fiona
authors.initials: F
authors.lastname: Tsoi
authors.affiliation: The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada.|Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada.
authors.forename: Ting
authors.initials: T
authors.lastname: Wang
authors.affiliation: The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada.|Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada.
authors.forename: Sergio L
authors.initials: SL
authors.lastname: Pereira
authors.affiliation: The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada.|Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada.
authors.forename: Pirooz
authors.initials: P
authors.lastname: Rostami
authors.affiliation: The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada.|Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada.
authors.forename: Carol Ann
authors.initials: CA
authors.lastname: Ryan
authors.affiliation: Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Ontario M5S 3E1, Canada.
authors.forename: Amy Hin Yan
authors.initials: AH
authors.lastname: Tong
authors.affiliation: Ontario Institute for Cancer Research, MaRS Centre, Toronto, Ontario M5G 0A3, Canada.
authors.forename: Karen
authors.initials: K
authors.lastname: Ng
authors.affiliation: Ontario Institute for Cancer Research, MaRS Centre, Toronto, Ontario M5G 0A3, Canada.
authors.forename: Yogi
authors.initials: Y
authors.lastname: Sundaravadanam
authors.affiliation: Ontario Institute for Cancer Research, MaRS Centre, Toronto, Ontario M5G 0A3, Canada.|Department of Computer Science, University of Toronto, Ontario M5S 3G4, Canada.
authors.forename: Jared T
authors.initials: JT
authors.lastname: Simpson
authors.affiliation: Department of Natural History, Royal Ontario Museum, Toronto, Ontario M5S 2C6, Canada.
authors.forename: Burton K
authors.initials: BK
authors.lastname: Lim
authors.affiliation: Department of Natural History, Royal Ontario Museum, Toronto, Ontario M5S 2C6, Canada.
authors.forename: Mark D
authors.initials: MD
authors.lastname: Engstrom
authors.affiliation: Toronto Zoo, Ontario M1B 5K7, Canada.
authors.forename: Christopher J
authors.initials: CJ
authors.lastname: Dutton
authors.affiliation: Toronto Zoo, Ontario M1B 5K7, Canada.
authors.forename: Kevin C R
authors.initials: KC
authors.lastname: Kerr
authors.affiliation: Toronto Zoo, Ontario M1B 5K7, Canada.
authors.forename: Maria
authors.initials: M
authors.lastname: Franke
authors.affiliation: Toronto Zoo, Ontario M1B 5K7, Canada.
authors.forename: William
authors.initials: W
authors.lastname: Rapley
authors.affiliation: The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada.|Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada.
authors.forename: Richard F
authors.initials: RF
authors.lastname: Wintle
authors.affiliation: The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada si.lok@sickkids.ca stephen.scherer@sickkids.ca.|Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada.|McLaughlin Centre, University of Toronto, Ontario M5S 0A4, Canada.|Department of Molecular Genetics, Faculty of Medicine, University of Toronto, Ontario M5S 1A8, Canada.
authors.forename: Stephen W
authors.initials: SW
authors.lastname: Scherer
mesh_terms: D000818:Animals; D016678:Genome; D023281:Genomics; D058977:Molecular Sequence Annotation; D016366:Open Reading Frames / Q000235:genetics; D012377:Rodentia / Q000235:genetics*; D059467:Transcriptome / Q000235:genetics*
keywords: Canadian beaver; genome annotation; genome assembly; rodent; whole-genome sequencing