Abstract
Our pioneering data provide the first comprehensive view of placental transcriptome of the beaver during single and multiple gestation. RNA-Seq and a de novo approach allowed global pattern identification of C. fiber placental transcriptome. Non-redundant beaver transcriptome comprised 211,802,336 nt of placental transcripts, grouped into 128,459 contigs and clustered into 83,951 unigenes. An Ensembl database search revealed 14,487, 14,994, 15,004, 15,267 and 15,892 non-redundant homologs for Ictidomys tridecemlineatus, Rattus norvegicus, Mus musculus, Homo sapiens and Castor canadensis, respectively. Due to expression levels, the identified transcripts were divided into two sets: non-redundant and highly expressed (FPKM > 2 in at least three examined samples), analysed simultaneously. Among 17,009 highly expressed transcripts, 12,147 had BLASTx hits. GO annotations (175,882) were found for 4301 transcripts that were assigned to biological process (16,386), cellular component (9149) and molecular function (8338) categories; 666 unigenes were also classified into 122 KEGG pathways. Comprehensive analyses were performed for 411 and 3078 highly expressed transcripts annotated with a list of processes linked to ‘placenta’ (31 GO terms) or ‘embryo’ (324 GO terms), respectively. Among transcripts with entire CDS annotation, 281 (placenta) and 34 (embryo) alternative splicing events were identified. A total of 8499 putative SNVs (~ 6.2 SNV/transcript and 1.7 SNV/1 kb) were predicted with 0.1 minimum frequency and maximum variant quality (p value 10e−9). Our results provide a broad-based characterization of the global expression pattern of the beaver placental transcriptome. Enhancement of transcriptomic resources for C. fiber should improve understanding of crucial pathways relevant to proper placenta development and successful reproduction.
Highlights
Within the Rodentia order, the Castoridae family is represented by only two still extant species, Castor canadensis in North America and Castor fiber in Eurasia
All reads were deposited in the Short Read Archive (SRA; http://www.ncbi.nlm.nih.gov/ Traces/sra/sra.cgi) of the National Center for Biotechnology Information (NCBI) under the BioProject Accession number PRJNA313146
Specific characteristics of each cDNA library are provided with quality statistics (Table 1)
Summary
Within the Rodentia order, the Castoridae family is represented by only two still extant species, Castor canadensis in North America and Castor fiber in Eurasia. Both species are the world’s second largest rodents after the capybara, and can be distinguished only by cytogenetic analyses (Lavrov and Orlov 1973). Molecular data strongly support the placement of Castor genus within a ‘mouse-related clade’, including various families: Pedetidae, Anomaluridae, Muridae, Dipodidae, Geomyidae and Heteromyidae and suggest Geomyoidea to be the closest relatives of the beavers (Montgelard et al 2008; Blanga-Kanfi et al 2009). Mitochondrial DNA analyses revealed Anomalurus to be the most closely related to the beavers (Horn et al 2011). At the beginning of the twentieth century, over-hunting had
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