Shinozaki Yoshihito, Nicolas Philippe, Fernandez-Pozo Noe, Ma Qiyue, Evanich Daniel J, Shi Yanna, Xu Yimin, Zheng Yi, Snyder Stephen I, Martin Laetitia B B, Ruiz-May Eliel, Thannhauser Theodore W, Chen Kunsong, Domozych David S, Catalá Carmen, Fei Zhangjun, Mueller Lukas A, Giovannoni James J, Rose Jocelyn K C
Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA.
Boyce Thompson Institute, Ithaca, NY, 14853, USA.
Nat Commun. 2018 Jan 25;9(1):364. doi: 10.1038/s41467-017-02782-9.
Tomato (Solanum lycopersicum) is an established model for studying fruit biology; however, most studies of tomato fruit growth and ripening are based on homogenized pericarp, and do not consider the internal tissues, or the expression signatures of individual cell and tissue types. We present a spatiotemporally resolved transcriptome analysis of tomato fruit ontogeny, using laser microdissection (LM) or hand dissection coupled with RNA-Seq analysis. Regulatory and structural gene networks, including families of transcription factors and hormone synthesis and signaling pathways, are defined across tissue and developmental spectra. The ripening program is revealed as comprising gradients of gene expression, initiating in internal tissues then radiating outward, and basipetally along a latitudinal axis. We also identify spatial variations in the patterns of epigenetic control superimposed on ripening gradients. Functional studies elucidate previously masked regulatory phenomena and relationships, including those associated with fruit quality traits, such as texture, color, aroma, and metabolite profiles.
番茄（Solanum lycopersicum）是研究果实生物学的成熟模型；然而，大多数关于番茄果实生长和成熟的研究都基于匀浆的果皮，并未考虑内部组织，也未考虑单个细胞和组织类型的表达特征。我们利用激光显微切割（LM）或手工解剖结合RNA测序分析，对番茄果实个体发育进行了时空分辨转录组分析。在整个组织和发育谱中定义了调控和结构基因网络，包括转录因子家族以及激素合成和信号通路。成熟程序显示为由基因表达梯度组成，从内部组织开始，然后向外辐射，并沿纬度轴基部向顶部延伸。我们还确定了叠加在成熟梯度上的表观遗传控制模式的空间变化。功能研究阐明了以前被掩盖的调控现象和关系，包括与果实品质性状相关的现象和关系，如质地、颜色、香气和代谢物谱。
