A pan-grass transcriptome reveals patterns of cellular divergence in crops
A pan-grass transcriptome reveals patterns of cellular divergence in crops
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DOI：
10.1038/s41586-023-06053-0
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发表时间：
2023-05-10
期刊：
影响因子：
64.8
通讯作者：
Birnbaum, Kenneth D.
中科院分区：
文献类型：
--
作者：
Guillotin, Bruno;Rahni, Ramin;Birnbaum, Kenneth D.
禾本科植物中的不同植物物种是驯化的平行目标，产生了具有不同进化历史和特征的作物（1）。区分这些物种的关键特征是由专门的细胞类型介导的（2）。本文比较了玉米、高粱和狗尾草三种禾本科植物根细胞的转录组。我们表明，单细胞和单核RNA测序提供了互补的读数的细胞身份在双子叶植物和单子叶植物，结合分析。跨物种绘制细胞类型以鉴定稳健的、正交的标记基因。比较细胞分析表明，某些细胞类型的转录组比其他细胞类型的转录组分化得更快，这部分是由于从其他细胞类型招募基因模块。数据还表明，最近的全基因组复制提供了新的，高度本地化的基因表达域，有利于快速进化的细胞类型的丰富来源。总之，逐个细胞的比较分析显示了精细细胞分析如何从泛转录组中提取保守模块，并提供对介导作物关键功能的细胞进化的见解。
Different plant species within the grasses were parallel targets of domestication, giving rise to crops with distinct evolutionary histories and traits(1). Key traits that distinguish these species are mediated by specialized cell types(2). Here we compare the transcriptomes of root cells in three grass species-Zea mays, Sorghum bicolor and Setaria viridis. We show that single-cell and single-nucleus RNA sequencing provide complementary readouts of cell identity in dicots and monocots, warranting a combined analysis. Cell types were mapped across species to identify robust, orthologous marker genes. The comparative cellular analysis shows that the transcriptomes of some cell types diverged more rapidly than those of others-driven, in part, by recruitment of gene modules from other cell types. The data also show that a recent whole-genome duplication provides a rich source of new, highly localized gene expression domains that favour fast-evolving cell types. Together, the cell-by-cell comparative analysis shows how fine-scale cellular profiling can extract conserved modules from a pan transcriptome and provide insight on the evolution of cells that mediate key functions in crops.