Dynamic transcriptome landscape of Asian domestic honeybee (Apis cerana) embryonic development revealed by high-quality RNA sequencing.
Dynamic transcriptome landscape of Asian domestic honeybee (Apis cerana) embryonic development revealed by high-quality RNA sequencing.
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高质量 RNA 测序揭示亚洲家养蜜蜂 (Apis cerana) 胚胎发育的动态转录组景观
DOI：
10.1186/s12861-018-0169-1
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发表时间：
2018-04-13
影响因子：
--
通讯作者：
Zeng Z
中科院分区：
文献类型：
--
作者：
Hu X;Ke L;Wang Z;Zeng Z
蜜蜂的发育分为胚胎、幼虫、蛹和成虫四个阶段。蜜蜂的胚胎发生是细胞分裂和分化的关键过程，需要3天。然而，在蜜蜂，特别是亚洲蜜蜂（Apis cerana）中，胚胎转录组和胚胎转录的动态调控在很大程度上仍然是未知的。在这里，我们使用高质量的RNA-seq来研究亚洲蜜蜂胚胎在大约24、48和72 h（分别称为Day1、Day2和Day3）三个年龄时的转录组。收集了9个胚胎样本，每个年龄3个，用于rna测序。根据我们观察到的蜜蜂胚胎的分期方案和形态特征，我们的第1天、第2天和第3天的胚胎可能分别对应于第四、第八和第十阶段的发育后期。分层聚类和主成分分析表明，相同年龄的样本聚在一起，Day2样本与Day3样本的关系比Day1样本更密切。最后，在中华蜜蜂胚胎中共检测到18284个基因，包含55,646个转录本，其中44.5%由所有三个年龄的胚胎共享的核心转录组组成。在3个胚龄中共鉴定出4088个上调基因和3046个下调基因，其中第1天至第2天、第1天至第3天和第2天至第3天分别上调2010个、3177个和1528个基因，下调2088个、2294个和303个基因。下调基因主要参与细胞、生物合成和代谢过程、基因表达和蛋白定位以及大分子修饰；上调基因主要参与细胞发育分化、组织、器官和系统发育以及形态发生。有趣的是，一些与光刺激响应和检测相关的生物学过程在蜜蜂胚胎发生的第一天中丰富，而在蜜蜂胚胎发生中则没有，这对进一步的研究有价值。我们的转录组学数据大大扩展了蜜蜂基因组中已知转录元件的数量，并提供了蜜蜂胚胎发育转录组动力学的高质量视图。本文的在线版本（10.1186/s12861-018-0169-1）包含补充材料，可供授权用户使用。
Honeybee development consists of four stages: embryo, larva, pupa and adult. Embryogenesis, a key process of cell division and differentiation, takes 3 days in honeybees. However, the embryonic transcriptome and the dynamic regulation of embryonic transcription are still largely uncharacterized in honeybees, especially in the Asian honeybee (Apis cerana). Here, we employed high-quality RNA-seq to explore the transcriptome of Asian honeybee embryos at three ages, approximately 24, 48 and 72 h (referred to as Day1, Day2 and Day3, respectively). Nine embryo samples, three from each age, were collected for RNA-seq. According to the staging scheme of honeybee embryos and the morphological features we observed, our Day1, Day2 and Day3 embryos likely corresponded to the late stage four, stage eight and stage ten development stages, respectively. Hierarchical clustering and principal component analysis showed that same-age samples were grouped together, and the Day2 samples had a closer relationship with the Day3 samples than the Day1 samples. Finally, a total of 18,284 genes harboring 55,646 transcripts were detected in the A. cerana embryos, of which 44.5% consisted of the core transcriptome shared by all three ages of embryos. A total of 4088 upregulated and 3046 downregulated genes were identified among the three embryo ages, of which 2010, 3177 and 1528 genes were upregulated and 2088, 2294 and 303 genes were downregulated from Day1 to Day2, from Day1 to Day3 and from Day2 to Day3, respectively. The downregulated genes were mostly involved in cellular, biosynthetic and metabolic processes, gene expression and protein localization, and macromolecule modification; the upregulated genes mainly participated in cell development and differentiation, tissue, organ and system development, and morphogenesis. Interestingly, several biological processes related to the response to and detection of light stimuli were enriched in the first-day A. cerana embryogenesis but not in the Apis mellifera embryogenesis, which was valuable for further investigations. Our transcriptomic data substantially expand the number of known transcribed elements in the A. cerana genome and provide a high-quality view of the transcriptome dynamics of A. cerana embryonic development. The online version of this article (10.1186/s12861-018-0169-1) contains supplementary material, which is available to authorized users.
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影响因子：
1.2
作者：
Dearden, Peter K.
通讯作者：
Dearden, Peter K.
影响因子：
2.6
作者：
GASCUEL, J;MASSON, C;BEADLE, DJ
通讯作者：
BEADLE, DJ
DOI：
10.1093/bioinformatics/btp101
发表时间：
2009-04-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Bindea G;Mlecnik B;Hackl H;Charoentong P;Tosolini M;Kirilovsky A;Fridman WH;Pagès F;Trajanoski Z;Galon J
通讯作者：
Galon J
影响因子：
64.8
作者：
Graveley BR;Brooks AN;Carlson JW;Duff MO;Landolin JM;Yang L;Artieri CG;van Baren MJ;Boley N;Booth BW;Brown JB;Cherbas L;Davis CA;Dobin A;Li R;Lin W;Malone JH;Mattiuzzo NR;Miller D;Sturgill D;Tuch BB;Zaleski C;Zhang D;Blanchette M;Dudoit S;Eads B;Green RE;Hammonds A;Jiang L;Kapranov P;Langton L;Perrimon N;Sandler JE;Wan KH;Willingham A;Zhang Y;Zou Y;Andrews J;Bickel PJ;Brenner SE;Brent MR;Cherbas P;Gingeras TR;Hoskins RA;Kaufman TC;Oliver B;Celniker SE
通讯作者：
Celniker SE
影响因子：
2.6
作者：
Chan, M. M. Y.;Choi, S. Y. C.;Foster, L. J.
通讯作者：
Foster, L. J.