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.

Pan-tissue transcriptome analysis of long noncoding RNAs in the American beaver Castor canadensis

“…Despite having termed the 40 contigs with known orthologs as "known lncRNA" to distinguish them from the 147 contigs with no detectable orthologs, we note that the 40 "known" lncRNAs are also new insofar as they have been identified (and their tissue expression distributions mapped) in beaver for the first time. The sixteen beaver tissues that we profiled constitute a broad transcriptome atlas that extends beyond the three beaver tissues previously profiled [7]. While other beaver tissues (e.g., testis) remain to be profiled in a future study, sequence alignment of a set of 4104 high-confidence pan-vertebrate genes (BUSCO genes) vs. a concatenation of six beaver transcript assemblies that we generated using four assemblers indicates that at least 91% of mammalian BUSCO genes have beaver orthologs.…”

“…One contig (Ccan_OSU1_lncRNA_contig62060.1) had two nonoverlapping alignments within 33 nucleotides of each other on the draft genome, which may indicate excision of an intron. To further validate the 147 novel contigs, we aligned them against a completely independently-generated beaver genome assembly [7] using BLASTn (see Methods); 144 of them (all except contig72949.1, contig80019.1, and contig83657.1) aligned with a bestmatch E-value of less than 10 − 18 . Of the 144 aligned contigs, all of them had greater than 90% sequence mapped and 140 of them had greater than 95% sequence mapped.…”

“…4, left panel, fifth row from bottom); it has no matches in the NCBI non-redundant nucleotide database, lncRNAdb [35], or in RNA Central [36], suggesting that if it is indeed a functional beaver lncRNA, it is not known to be conserved in other rodents. As an independent check on the biological validity of the RNA-seq-based lncRNA gene expression measurements, we compared the log 2 expression in muscle of all 187 known and novel lncRNAs as measured in our study and by the Lok et al study [7], which were obtained using different sequencing technologies and using tissue samples from different beavers. We found that the two sets of lncRNA expression measurements were correlated at R = 0.66 (P < 10 − 15 ), as shown in Additional file 2 Figure S2.…”

“…To validate the 147 high-confidence lncRNA contigs, we aligned them against an independently-generated beaver genome assembly [7] that was generated using a different blood sample, a different sequencing technology (PacBio SMRT DNA sequencing) and a different assembly tool (Canu) than were used to obtain the OSU beaver genome assembly. We obtained the sequence file Castor_canadensis.C.can_genome_ v1.0.dna.nonchromosomal.fa from Ensembl and aligned the 147 contigs against it using BLASTn with default parameters.…”

“…The genome and three tissue transcriptomes of the American beaver Castor canadensis (Order Rodentia, Family Castoridae) have recently been sequenced [7,8], enabling the systematic search for molecular determinants of this semi-aquatic herbivore's unique physiologic, anatomic, and behavioral adaptations. For example, the beaver's ability to hold its breath for up to fifteen minutes [9] suggests adaptations in the brain, heart, liver, and lungs to mitigate hypoxia-associated tissue damage and optimize oxygen uptake [10].…”