Abstract
BackgroundHibernation in an appropriate environment not only is important for the survival of hibernators in winter, but also is crucial for breeding in the following season for many hibernating species. However, the genetic and epigenetic mechanism underlying this process remain unclear. In the current study, we performed an integrative multi-omics analysis of gonads collected from Chinese alligators that overwintered in wild cave and artificial warmroom to explore transcriptomic and epigenomic alternations in these organs.ResultsThe data revealed that in the breeding season, female alligators were more strongly affected in terms of gene expression than males by non-hibernation because of overwintering in a warm room, especially for genes related to oocyte maturation, and this effect commenced in winter with the downregulation of STAR, which is the rate limiting factor of steroid biosynthesis. Further, miRNAs were found to play essential roles in this negative effect of overwintering in the warm room on hibernation. The upregulated miRNAs likely were responsible for the suppression of oocyte maturation in the breeding season. Finally, DNA methylome changes, especially hypomethylation, were found to play an important role in the alterations in ovarian function-related gene expression induced by non-hibernation.ConclusionsOur study revealed the crucial role of hibernation quality for oocyte maturation in the Chinese alligator and the underlying genetic and epigenetic mechanisms, and highlights the importance of habitat, and especially, the overwintering site, in the conservation of not only the Chinese alligator, but also other endangered hibernators.
Highlights
Hibernation in an appropriate environment is important for the survival of hibernators in winter, and is crucial for breeding in the following season for many hibernating species
Data summary We carried out RNA-seq, sRNA-seq, and bisulfte sequencing (BS-seq) analyses of ovary and testis samples collected in winter and summer from individual alligators that overwintered in the wild or in a warm room to gain insights into the molecular mechanisms underlying the effects of hibernation quality on gonadal development (Fig. 1a)
The eight stand-specific mRNA-seq libraries generated a total of 468.72 million reads, 419.72 million (89.55%) of which were uniquely mapped to the Chinese alligator reference genome [29]. mRNA-seq data analysis was based on the mapped reads, using a Chinese alligator gene annotation database containing 27,500 proteincoding genes [4]. sRNA-seq of the eight sRNA-seq libraries generated 100.63 million clean single-end reads, 85.63 million (85.10%) of which were 18–35 nt in length and were uniquely mapped to the Chinese alligator genome. sRNA-seq data analysis was based on the mapped reads and Chinese alligator sRNA annotation data generated in our previous study [4]
Summary
Hibernation in an appropriate environment is important for the survival of hibernators in winter, and is crucial for breeding in the following season for many hibernating species. We performed an integrative multi-omics analysis of gonads collected from Chinese alligators that overwintered in wild cave and artificial warmroom to explore transcriptomic and epigenomic alternations in these organs. The underlying molecular mechanisms vary between endotherms and. Our understanding of the molecular mechanisms underlying the effects of hibernation on reproduction is limited. When Chinese alligators move to a warmer area or overwinter in the discomfort of an artificial environment, they become less fertile [9, 15,16,17]. The Chinese alligator can serve as an ideal model to study the role of hibernation in reproduction, and the underlying molecular mechanisms
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