Abstract
BackgroundMany vertebrate species have the ability to undergo weeks or even months of diapause (a temporary arrest of development during early ontogeny). Identification of diapause genes has been challenging due in part to the genetic heterogeneity of most vertebrate animals.ResultsHere we take the advantage of the mangrove rivulus fish (Kryptolebias marmoratus or Kmar)—the only vertebrate that is extremely inbred due to consistent self-fertilization—to generate isogenic lineages for transcriptomic dissection. Because the Kmar genome is not publicly available, we built de novo genomic (642 Mb) and transcriptomic assemblies to serve as references for global genetic profiling of diapause in Kmar, via RNA-Seq. Transcripts unique to diapause in Kmar proved to constitute only a miniscule fraction (0.1 %) of the total pool of transcribed products. Most genes displayed lower expression in diapause than in post-diapause. However, some genes (notably dusp27, klhl38 and sqstm1) were significantly up-regulated during diapause, whereas others (col9a1, dspp and fmnl1) were substantially down-regulated, compared to both pre-diapause and post-diapause.ConclusionKmar offers a strong model for understanding patterns of gene expression during diapause. Our study highlights the importance of using a combination of genome and transcriptome assemblies as references for NGS-based RNA-Seq analyses. As for all identified diapause genes, in future studies it will be critical to link various levels of RNA expression with the functional roles of the coded products.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-2210-0) contains supplementary material, which is available to authorized users.
Highlights
Many vertebrate species have the ability to undergo weeks or even months of diapause
Various terms describe the phenomenon in specific situations in nature: (i) embryonic diapause, in which an embryo’s development is temporarily arrested during early ontogeny [1]; (ii) torpor, when body temperature and metabolic rate in endothermic animals are significantly reduced during certain times of the day [2]; (iii) hibernation or multiday torpor, as utilized by various animals to escape harsh winter conditions [3, 4]; (iv) aestivation, when multiday torpor occurs in hot or dry seasons in warm climates [5]; and (v) cryptobiosis, which entails a temporary absence of measurable metabolic activity [6, 7]
Mapping of Kmar RNA-Seq reads to known reference genomes By using TopHat software [22], we found that less than 10 % of Kmar RNA-Seq reads could be mapped against the annotated genomes of humans, mice, and several fishes (Amazon molly, platyfish, medaka, zebrafish, and fugu) (Table 1)
Summary
Many vertebrate species have the ability to undergo weeks or even months of diapause (a temporary arrest of development during early ontogeny). Various terms describe the phenomenon in specific situations in nature: (i) embryonic diapause, in which an embryo’s development is temporarily arrested during early ontogeny [1]; (ii) torpor, when body temperature and metabolic rate in endothermic animals are significantly reduced during certain times of the day [2]; (iii) hibernation or multiday torpor, as utilized by various animals to escape harsh winter conditions [3, 4]; (iv) aestivation, when multiday torpor occurs in hot or dry seasons in warm climates [5]; and (v) cryptobiosis, which entails a temporary absence of measurable metabolic activity [6, 7]. Mammalian embryonic diapause can last up to 90 % of the total gestational period [11] Another form of diapause is displayed by some egg-laying fishes in which embryonic hatching can be delayed for a year or more. Such fish may display any of three different types of diapause: Diapause I, occurring during the dispersed-cell phase of early ontogeny; Diapause II, occurring midsomite embryogenesis; and Diapause III, occurring just prior to hatching [12, 13]
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