Seasonal differences in the testicular transcriptome profile of free-living European beavers (Castor fiber L.) determined by the RNA-Seq method

Abstract

The European beaver (Castor fiber L.) is an important free-living rodent that inhabits Eurasian temperate forests. Beavers are often referred to as ecosystem engineers because they create or change existing habitats, enhance biodiversity and prepare the environment for diverse plant and animal species. Beavers are protected in most European Union countries, but their genomic background remains unknown. In this study, gene expression patterns in beaver testes and the variations in genetic expression in breeding and non-breeding seasons were determined by high-throughput transcriptome sequencing. Paired-end sequencing in the Illumina HiSeq 2000 sequencer produced a total of 373.06 million of high-quality reads. De novo assembly of contigs yielded 130,741 unigenes with an average length of 1,369.3 nt, N50 value of 1,734, and average GC content of 46.51%. A comprehensive analysis of the testicular transcriptome revealed more than 26,000 highly expressed unigenes which exhibited the highest homology with Rattus norvegicus and Ictidomys tridecemlineatus genomes. More than 8,000 highly expressed genes were found to be involved in fundamental biological processes, cellular components or molecular pathways. The study also revealed 42 genes whose regulation differed between breeding and non-breeding seasons. During the non-breeding period, the expression of 37 genes was up-regulated, and the expression of 5 genes was down-regulated relative to the breeding season. The identified genes encode molecules which are involved in signaling transduction, DNA repair, stress responses, inflammatory processes, metabolism and steroidogenesis. Our results pave the way for further research into season-dependent variations in beaver testes.

Transcriptome‐wide changes in testes reveal molecular differences in photoperiod‐induced seasonal reproductive life‐history states in migratory songbirds

“…In vitro, via GABA‐A receptor activation, GABA increased proliferation of TM3 mouse Leydig cell lines (Geigerseder, Doepner, Thalhammer, Krieger, & Mayerhofer, ). Overall, present RNA‐Seq‐revealed testicular gene expressions in buntings are consistent with those found in European beavers' testes demonstrating seasonal differences in DEGs involved in the signal transduction, DNA repair, steroidogenesis, Wnt signaling, and calcium ion transport pathways (Bogacka et al, ).…”

“…At the molecular level, Maywood et al () identified factors that are possibly involved in the transcriptional, translational, and posttranslational control of testicular functions in the photoperiodic Syrian hamster ( Mesocricetus auratus ). Seasonal differences in testicular gene expressions have also been reported in roe deer, Capreolus capreolus (Weyrich et al, ) and European beavers, Castor fiber (Bogacka et al, ).…”

A functional transcriptomic analysis in the relict marsupial Dromiciops gliroides reveals adaptive regulation of protective functions during hibernation

“…The overall statistics of our assembly (N50, L50, contig length, number of contigs >1k) were similar to the results documented in de novo assembled transcriptomes of other mammals, such as the beaver ( Castor fiber L . ; testis; Bogacka et al., ), and the Nile grass rat ( Arvicanthis ansorgei ; retina; Liu et al., ). However, we had higher values compared with marsupials such as the long‐nosed bandicoot ( Perameles nasuta ; heart, liver, spleen and kidney; Morris et al., ) and the Virginia opossum Didelphis virginiana ; kidney; Eshbach et al., ).…”

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

“…The N50 length (2354 nt), average length (1649 nt) of transcripts, the GC content (46.9%) and number of contigs > 1K nt (69,114) indicate successful library construction and good sequencing quality of the C. fiber placental transcriptome. Analysis of beaver testes transcriptome permitted to de novo assembly 373 million of high-quality reads into 130,741 unigenes with an average length of 1369.3 nt, N50 value of 1734 and GC content of 46.51% (Bogacka et al 2017 ). Our results are very consistent with those obtained in beaver testes, besides the same species was examined, similar methods and parameters were used in both studies that makes the results fully comparable.…”

“…Therefore, only a de novo approach may be efficient for identification of placental spatio-temporal gene expression in the Eurasian beaver. Only a few studies have been performed with some beaver tissues (Bogacka et al 2017 ; Chojnowska et al 2017 ; Czerwinska et al 2017 ; Lipka et al 2017a , b ; Lok et al 2017 ), but none of them concern de novo characterization of the beaver placental transcriptome. Thus, the objective of this study was to identify and characterize the placental transcriptome of the C. fiber .…”