Date Published: July 5, 2017
Publisher: Public Library of Science
Author(s): Iwona Bogacka, Łukasz Paukszto, Jan P. Jastrzębski, Joanna Czerwińska, Katarzyna Chojnowska, Barbara Kamińska, Aleksandra Kurzyńska, Nina Smolińska, Zygmunt Giżejewski, Tadeusz Kamiński, Maoteng Li.
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.
The European beaver (Castor fiber L.) is the largest rodent in Eurasia and the world’s second largest rodent after the capybara. In the past, the species was widely distributed across Eurasian forests, between western Europe and eastern Siberia, but it was nearly driven to extinction after centuries of hunting for its fur and castoreum, the exudate from the beaver scent gland. By the end of the 19th century, hunting pressure combined with the decline in beaver habitats reduced the Eurasian beaver population to 1,200 individuals in several remote regions . Fortunately, the introduction of a hunting ban and other conservation measures enabled the beaver population to survive and spread to other regions through natural and artificial recolonization.
To the best of our knowledge, this is the first study providing a comprehensive analysis of transcriptome profiles of European beaver testes with the use of the RNA-Seq technique. It is also the first study to describe variations in transcriptome profiles between breeding and non-breading seasons. The RNA-Seq technique is a powerful tool for generating large-scale transcriptome data that were useful for presenting differentially expressed genes in various species, tissues or cell types. According to some studies, Illumina sequencing data are replicable with relatively little technical variation [35, 36].