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

• DOI: 10.1007/s10142-019-00663-6
• Publication Date: 2019-02-18T17:54:41Z
• Authors: Aleksandra Lipka; Lukasz Paukszto; Marta Majewska; Jan Pawel Jastrze...; Grzegorz Panasiewicz; Bozena Szafranska
• Keywords: Ensembl

Our pioneering data provide the first comprehensive view of placental transcriptome beaver during single and multiple gestation. RNA-Seq a de novo approach allowed global pattern identification C. fiber transcriptome. Non-redundant comprised 211,802,336 nt transcripts, grouped into 128,459 contigs clustered 83,951 unigenes. An Ensembl database search revealed 14,487, 14,994, 15,004, 15,267 15,892 non-redundant homologs for Ictidomys tridecemlineatus, Rattus norvegicus, Mus musculus, Homo sapiens Castor canadensis, respectively. Due to expression levels, identified transcripts were divided two sets: highly expressed (FPKM > 2 in at least three examined samples), analysed simultaneously. Among 17,009 12,147 had BLASTx hits. GO annotations (175,882) found 4301 that assigned biological process (16,386), cellular component (9149) molecular function (8338) categories; 666 unigenes also classified 122 KEGG pathways. Comprehensive analyses performed 411 3078 annotated with list processes linked 'placenta' (31 terms) or 'embryo' (324 terms), entire CDS annotation, 281 (placenta) 34 (embryo) alternative splicing events identified. A total 8499 putative SNVs (~ 6.2 SNV/transcript 1.7 SNV/1 kb) predicted 0.1 minimum frequency maximum variant quality (p value 10e-9). results broad-based characterization Enhancement transcriptomic resources should improve understanding crucial pathways relevant proper placenta development successful reproduction.