Transcriptome profiling of male gametophyte development in Nicotiana tabacum.
Transcriptome profiling of male gametophyte development in Nicotiana tabacum.
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DOI：
10.1016/j.gdata.2014.12.002
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发表时间：
2015-03
期刊：
影响因子：
--
通讯作者：
Honys D
中科院分区：
文献类型：
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作者：
Bokvaj P;Hafidh S;Honys D
花粉是显花植物雄性生殖器官中极为简化的二细胞或三细胞结构，是研究植物发育和生理过程的重要模型。花粉发育是植物个体发育的一个脆弱而重要的阶段，花粉是第一个在转录组水平上完全表征的单一植物组织之一（Honys和Twell）。拟南芥花粉发育转录组已经在十多年前发表（Honys和Twell，2004），并且随后发表了其他物种发育花粉的转录组（Rice，Deveshwar等人; Triticeae，Tran et al.;高地棉，Ma等人）。然而，描述烟草花粉，细胞生物学研究的双细胞模型的发展的转录组学数据一直缺失。在这里，我们提供了涵盖三个阶段的转录组学数据（Tuppermet al.，1983）的野生型烟草（Nicotiana tabacum，cv. Samsun）花粉发育：单核小孢子（UNM，第1阶段）、早期双细胞花粉（eBCP，第3阶段）和晚期双细胞花粉（IBCP，第5阶段）作为我们先前研究中提供的成熟花粉（MP）、4 h-花粉管（PT 4）、24 h-花粉管（PT 24）、叶（LF）和根（RT）转录组学数据的补充（Hafidh等，2012 a; Hafidh等人，2012年b）。我们对这些转录组进行了表征，以完善雄配子体富集基因以及在花粉发育的各个阶段优先表达的基因的知识库。除了更新组织特异性基因的列表，我们还研究了早期表达基因的差异表达基因。雌蕊中花粉管的生长和竞争可以看作是一个优胜劣汰的过程。因此，高等植物在花粉成熟过程中存在着明显的物质储备和营养储存的进化趋势。这种供应确保了花粉萌发后，花粉管主要利用其资源在雌蕊中快速伸长。先前来自拟南芥的转录组学数据显示，编码形成两种核糖体亚基的蛋白质的基因大量表达，所述核糖体亚基在发育中的花粉中积累，而它们的表达在生长中的花粉管中检测不到（Honys和Twell，2004）。我们观察到一个类似的现象，在较不发达的双细胞烟草花粉。在这里，我们详细描述了我们如何获得和分析保存在基因表达综合数据库（GSE 62349）中的经验证的微阵列数据集。
Pollen, an extremely reduced bicellular or tricellular male reproductive structure of flowering plants, serves as a model for numerous studies covering wide range of developmental and physiological processes. The pollen development represents a fragile and vital phase of plant ontogenesis and pollen was among the first singular plant tissues thoroughly characterized at the transcriptomic level (Honys and Twell). Arabidopsis pollen developmental transcriptome has been published over a decade ago (Honys and Twell, 2004) and transcriptomes of developing pollen of other species have followed (Rice, Deveshwar et al.; Triticeae, Tran et al.; upland cotton, Ma et al.). However, the transcriptomic data describing the development of tobacco pollen, a bicellular model for cell biology studies, have been missing. Here we provide the transcriptomic data covering three stages (Tupý et al., 1983) of wild type tobacco (Nicotiana tabacum, cv. Samsun) pollen development: uninucleate microspores (UNM, stage 1), early bicellular pollen (eBCP, stage 3) and late bicellular pollen (lBCP, stage 5) as a supplement to the mature pollen (MP), 4 h-pollen tube (PT4), 24 h-pollen tubes (PT24), leaf (LF) and root (RT) transcriptomic data presented in our previous studies (Hafidh et al., 2012a; Hafidh et al., 2012b). We characterized these transcriptomes to refine the knowledge base of male gametophyte-enriched genes as well as genes expressed preferentially at the individual stages of pollen development. Alongside updating the list of tissue-specific genes, we have investigated differentially expressed genes with respect to early expressed genes. Pollen tube growth and competition of pollen tubes in female pistil can be viewed as a race of the fittest. Accordingly, there is an apparent evolutionary trend among higher plants to store significant material reserves and nutrients during pollen maturation. This supply ensures that after pollen germination, the pollen tube utilizes its resource predominantly for its rapid elongation in the female pistil. Previous transcriptomic data from Arabidopsis showed massive expression of genes encoding proteins forming both ribosomal subunits that were accumulated in developing pollen, whereas their expression was not detectable in growing pollen tubes (Honys and Twell, 2004). We observed a similar phenomenon in less advanced bicellular tobacco pollen. Here, we describe in detail how we obtained and analyzed validated microarray dataset deposited in Gene Expression Omnibus (GSE62349).