Pattison Richard J, Csukasi Fabiana, Zheng Yi, Fei Zhangjun, van der Knaap Esther, Catalá Carmen
Boyce Thompson Institute for Plant Research, Ithaca, New York 14853 (R.J.P., F.C., Y.Z., Z.F., C.C.);United States Department of Agriculture-Agricultural Research Service, Robert W. Holley Center for Agriculture and Health, Ithaca, New York 14853 (Z.F.);Department of Horticulture and Crop Science, Ohio State University, Wooster, Ohio 44691 (E.v.d.K.); andPlant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, New York 14853 (C.C.).
Boyce Thompson Institute for Plant Research, Ithaca, New York 14853 (R.J.P., F.C., Y.Z., Z.F., C.C.);United States Department of Agriculture-Agricultural Research Service, Robert W. Holley Center for Agriculture and Health, Ithaca, New York 14853 (Z.F.);Department of Horticulture and Crop Science, Ohio State University, Wooster, Ohio 44691 (E.v.d.K.); andPlant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, New York 14853 (C.C.)
Plant Physiol. 2015 Aug;168(4):1684-701. doi: 10.1104/pp.15.00287. Epub 2015 Jun 22.
Fruit formation and early development involve a range of physiological and morphological transformations of the various constituent tissues of the ovary. These developmental changes vary considerably according to tissue type, but molecular analyses at an organ-wide level inevitably obscure many tissue-specific phenomena. We used laser-capture microdissection coupled to high-throughput RNA sequencing to analyze the transcriptome of ovaries and fruit tissues of the wild tomato species Solanum pimpinellifolium. This laser-capture microdissection-high-throughput RNA sequencing approach allowed quantitative global profiling of gene expression at previously unobtainable levels of spatial resolution, revealing numerous contrasting transcriptome profiles and uncovering rare and cell type-specific transcripts. Coexpressed gene clusters linked specific tissues and stages to major transcriptional changes underlying the ovary-to-fruit transition and provided evidence of regulatory modules related to cell division, photosynthesis, and auxin transport in internal fruit tissues, together with parallel specialization of the pericarp transcriptome in stress responses and secondary metabolism. Analysis of transcription factor expression and regulatory motifs indicated putative gene regulatory modules that may regulate the development of different tissues and hormonal processes. Major alterations in the expression of hormone metabolic and signaling components illustrate the complex hormonal control underpinning fruit formation, with intricate spatiotemporal variations suggesting separate regulatory programs.
果实形成和早期发育涉及子房各种组成组织的一系列生理和形态转变。这些发育变化因组织类型而异，但在全器官水平上的分子分析不可避免地掩盖了许多组织特异性现象。我们使用激光捕获显微切割技术结合高通量RNA测序来分析野生番茄物种醋栗番茄的子房和果实组织的转录组。这种激光捕获显微切割-高通量RNA测序方法能够在以前无法达到的空间分辨率水平上对基因表达进行定量全局分析，揭示了众多不同的转录组图谱，并发现了罕见的和细胞类型特异性的转录本。共表达基因簇将特定组织和阶段与子房到果实转变过程中的主要转录变化联系起来，并为内部果实组织中与细胞分裂、光合作用和生长素运输相关的调控模块提供了证据，同时果皮转录组在应激反应和次生代谢方面也存在平行特化。对转录因子表达和调控基序的分析表明了可能调控不同组织发育和激素过程的假定基因调控模块。激素代谢和信号转导成分表达的主要变化说明了支撑果实形成的复杂激素控制，其复杂的时空变化表明存在独立的调控程序。
