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第一作者:Qingxin Song
第一单位:德克萨斯大学奥斯汀分校
通讯作者:Z. Jeffrey Chen
Abstract
Background: Polyploidy provides new genetic material that facilitates evolutionary novelty, species adaptation, and crop domestication. Polyploidy often leads to an increase in cell or organism size, which may affect transcript abundance or transcriptome size, but the relationship between polyploidy and transcriptome changes remains poorly understood. Plant cells often undergo endoreduplication, confounding the polyploid effect.
Results: To mitigate these effects, we select female gametic cells that are developmentally stable and void of endoreduplication. Using single-cell RNA sequencing (scRNA-seq) in Arabidopsis thaliana tetraploid lines and isogenic diploids, we show that transcriptome abundance doubles in the egg cell and increases approximately 1.6-foldin the central cell, consistent with cell size changes. In the central cell of tetraploid plants, DEMETER(DME) is upregulated, which can activate PRC2 family members FIS2 and MEA, and may suppress the expression of other genes. Upregulation of cell size regulators in tetraploids, including TOR and OSR2, may increase the size of reproductive cells. In diploids, the order of transcriptome abundance is central cell, synergid cell, and egg cell, consistent with their cell size variation. Remarkably, we uncover new sets of female gametophytic cell-specific transcripts with predicted biological roles; the most abundant transcripts encode families of cysteine-rich peptides, implying roles in cell-cell recognition during double fertilization.
Conclusions: Transcriptome in single cells doubles in tetraploid plants compared to diploid, while the degree of change and relationship to the cell size depends on cell types. These scRNA-seq resources are free of cross-contamination and are uniquely valuable for advancing plant hybridization, reproductive biology, and polyploid genomics.
摘 要
多倍体为加速演化创新、物种适应以及作物驯化提供了新的遗传材料。多倍体常会导致细胞或生物尺寸的增加,可能会影响到转录本丰度或转录组的大小,但是倍性与转录组变化之间的关系一直都不清楚。植物细胞通常会经历核内复制,从而混淆多倍体的效应。为了避免这种影响,作者选择了发育稳定、并且没有核内复制的雌配子细胞作为试验材料。利用单细胞RNA测序技术,作者对拟南芥的四倍体株系与二倍体等基因系进行研究,发现四倍体中卵细胞的转录组丰度加倍,而中央细胞的转录组丰度增加了约1.6倍,这与这两种细胞在四倍体和二倍体之间尺寸上面的变化相一致。在四倍体的中央细胞中,DME基因上调表达,该基因能够激活PRC2家族成员FIS2和MEA基因,可能会抑制其它基因的表达。另外,四倍体中细胞大小调控因子TOR和OSR2等基因的表达上调,可能增加了生殖细胞的大小。在二倍体中,转录组丰度大小排序中央细胞、助细胞、卵细胞,与其细胞大小的变异一致。此外,作者还鉴定了新的雌配子细胞特异性的转录本,并且具有预测的生物学功能。其中,大量的转录本来源于富含半胱氨酸的多肽,暗示其可能在双受精过程中作用于细胞-细胞的识别。与二倍体相比,四倍体单个细胞中的转录组加倍,然而改变的程度以及与细胞大小之间的关系则取决于细胞的类型。本文的单细胞转录组测序结果没有交叉污染,对于有关植物杂交、生殖生物学以及多倍体基因组学的研究具有非常重要的参考价值。
p.s. FIS2和MEA基因属于Polycomb Repressive Complex 2家族的成员,PRC2家族通过组蛋白H3K27me3甲基化来沉默相关基因的表达,拟南芥中的研究显示FIS2和MEA基因均属于来自于母本的印记基因(imprinted gene),通过抑制未受精的中央细胞发生增殖参与种子的发育。
通讯作者
**Z. Jeffrey Chen**
个人简介:
浙江农业大学,学士;
南京农业大学,硕士;
得克萨斯农工大学,博士;
明尼苏达大学、华盛顿大学,博士后。
研究方向:
多倍体和杂种优势的遗传和表观遗传机制及其对作物驯化和改良的影响。
doi: 10.1186/s13059-020-02094-0
Journal: Genome Biology
Published date: July 22, 2020
p.s. 往期植scRNA-seq相关研究链接:
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