Transcriptomics of diapause in an isogenic self-fertilizing vertebrate.
Transcriptomics of diapause in an isogenic self-fertilizing vertebrate.
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DOI：
10.1186/s12864-015-2210-0
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发表时间：
2015-11-23
期刊：
影响因子：
4.4
通讯作者：
Avise JC
中科院分区：
文献类型：
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作者：
Mesak F;Tatarenkov A;Avise JC
许多脊椎动物物种有能力经历数周甚至数月的滞育（在早期个体发育期间暂时停止发育）。由于大多数脊椎动物的遗传异质性，滞育基因的鉴定一直具有挑战性。在这里，我们利用的红树林rivulus鱼（Kryptolebias marmoratus或Kmar）-唯一的脊椎动物，是非常近亲繁殖，由于一贯的自我受精-产生转录组解剖的等基因谱系。由于Kmar基因组尚未公开，我们构建了从头基因组（642 Mb）和转录组组装，以作为通过RNA-Seq进行Kmar滞育全球遗传分析的参考。卡马尔滞育特有的转录物被证明只占转录产物总库的极小部分（0.1%）。多数基因在滞育期的表达量低于滞育后。然而，一些基因（特别是dusp 27，klhl 38和sqstm 1）在滞育期间显着上调，而其他基因（col 9a 1，dspp和fmnl 1）大幅下调，无论是滞育前和滞育后。Kmar为了解滞育期间基因表达模式提供了一个强有力的模型。我们的研究强调了使用基因组和转录组组合作为基于NGS的RNA-Seq分析参考的重要性。至于所有已鉴定的滞育基因，在未来的研究中，将不同水平的RNA表达与编码产物的功能作用联系起来将是至关重要的。本文的在线版本（doi：10.1186/s12864-015-2210-0）包含补充材料，可供授权用户使用。
Many 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. Here 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. Kmar 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. The online version of this article (doi:10.1186/s12864-015-2210-0) contains supplementary material, which is available to authorized users.