De novo characterization of placental transcriptome in the Eurasian beaver (Castor fiber L.).

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.