Single-cell RNA-seq analysis reveals ploidy-dependent and cell-specific transcriptome changes in Arabidopsis female gametophytes
Single-cell RNA-seq analysis reveals ploidy-dependent and cell-specific transcriptome changes in Arabidopsis female gametophytes
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DOI：
10.1186/s13059-020-02094-0
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发表时间：
2020-07-22
期刊：
影响因子：
12.3
通讯作者：
Chen, Z. Jeffrey
中科院分区：
文献类型：
--
作者：
Song, Qingxin;Ando, Atsumi;Chen, Z. Jeffrey
背景多倍性提供了新的遗传物质，促进了进化的新奇，物种适应性和作物驯化。多倍体通常导致细胞或生物体大小的增加，这可能会影响转录本丰度或转录组大小，但多倍体和转录组变化之间的关系仍然知之甚少。植物细胞经常进行核内复制，混淆了多倍体效应。结果为了减轻这些影响，我们选择了发育稳定且无核内复制的雌性配子细胞。使用单细胞RNA测序（scRNA-seq）在拟南芥四倍体系和等基因二倍体，我们表明，转录组丰度在卵细胞中增加一倍，在中央细胞中增加约1.6倍，与细胞大小的变化一致。在四倍体植物的中央细胞中，DEMETER（DME）表达上调，它可以激活PRC 2家族成员FIS 2和MEA，并可能抑制其他基因的表达。四倍体中细胞大小调节因子（包括TOR和OSR 2）的上调可能会增加生殖细胞的大小。在二倍体中，转录组丰度的顺序是中央细胞、助细胞和卵细胞，这与它们的细胞大小变化一致。值得注意的是，我们发现了新的一套女性配子体细胞特异性转录物与预测的生物学作用;最丰富的转录物编码富含半胱氨酸的肽家族，这意味着在双受精过程中细胞-细胞识别的作用。结论与二倍体相比，四倍体植物中单细胞的转录组加倍，而变化的程度以及与细胞大小的关系取决于细胞类型。这些scRNA-seq资源没有交叉污染，对于推进植物杂交、生殖生物学和多倍体基因组学具有独特的价值。
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) inArabidopsis thalianatetraploid lines and isogenic diploids, we show that transcriptome abundance doubles in the egg cell and increases approximately 1.6-fold in the central cell, consistent with cell size changes. In the central cell of tetraploid plants,DEMETER(DME) is upregulated, which can activatePRC2family membersFIS2andMEA, and may suppress the expression of other genes. Upregulation of cell size regulators in tetraploids, includingTORandOSR2, 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.