Single-cell RNA-seq analysis reveals ploidy-dependent and cell-specific transcriptome changes in Arabidopsis female gametophytes.

Genome Biology
Qingxin SongZ Jeffrey Chen

Abstract

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. 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-fold in 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. Remarkab...Continue Reading

References

Apr 15, 1997·Proceedings of the National Academy of Sciences of the United States of America·A M ChaudhuryW J Peacock
Mar 9, 1999·The Plant Journal : for Cell and Molecular Biology·S J Clough, A F Bent
Jul 10, 1999·Science·T GalitskiG R Fink
Nov 25, 2003·Science·Tetsu KinoshitaTetsuji Kakutani
Jan 7, 2004·Nature Reviews. Molecular Cell Biology·Zuzana Storchova, David Pellman
Feb 11, 2005·The Plant Journal : for Cell and Molecular Biology·Stefanie SprunckThomas Dresselhaus
Mar 9, 2005·Current Opinion in Plant Biology·Keith L Adams, Jonathan F Wendel
Sep 21, 2005·Genetics·Jianlin WangZ Jeffrey Chen
Nov 24, 2005·Nature Reviews. Genetics·Luca Comai
Jul 11, 2006·The Plant Journal : for Cell and Molecular Biology·Yuxin HuNam-Hai Chua
Jul 11, 2006·Current Biology : CB·Caroline JosefssonLuca Comai
Jun 15, 2007·The Plant Journal : for Cell and Molecular Biology·Joshua G SteffenGary N Drews
Nov 3, 2007·Science·Siobhan M BradyPhilip N Benfey
Apr 26, 2008·Science·A R Leitch, I J Leitch
Jul 25, 2008·Trends in Plant Science·Frédéric BergerTetsuya Higashiyama
Apr 23, 2009·Proceedings of the National Academy of Sciences of the United States of America·Hongqing GuoYanhai Yin
Dec 25, 2009·Current Opinion in Plant Biology·Scott Jackson, Z Jeffrey Chen
Dec 31, 2009·Development·Venkatesan Sundaresan, Monica Alandete-Saez
Mar 3, 2010·Annual Review of Plant Biology·Wei-Cai YangYan-Hong Chen
Sep 30, 2010·Proceedings of the National Academy of Sciences of the United States of America·Zheng YuRamon A Torres-Ruiz
Oct 26, 2010·Current Biology : CB·Jacob ZhurinskyPaul Nurse
Feb 15, 2011·Journal of Experimental Botany·Eleanor MarshallJose Gutierrez-Marcos
Mar 15, 2011·Nature·Nicholas NavinMichael Wigler
Apr 5, 2011·The Plant Journal : for Cell and Molecular Biology·Dávid KoszegiHelmut Bäumlein
Mar 13, 2012·Annual Review of Plant Biology·Claudia KöhlerCharles Spillane
Oct 30, 2012·Cell·Jakob LovénRichard A Young
Oct 30, 2012·Bioinformatics·Alexander DobinThomas R Gingeras
Nov 28, 2012·Science·Stefanie SprunckThomas Dresselhaus
Apr 11, 2013·Molecular Plant·Thomas Dresselhaus, Noni Franklin-Tong
Jun 12, 2013·Nature Reviews. Genetics·Z Jeffrey Chen

❮ Previous
Next ❯

Citations

Nov 6, 2020·Molecular Plant·Rahul ShawJian Xu
Mar 23, 2021·Trends in Plant Science·Sandra Thibivilliers, Marc Libault
Apr 2, 2021·The Plant Cell·Nicholas J ProvartAnn E Loraine
Apr 30, 2021·Current Opinion in Plant Biology·Stefania Giacomello
Apr 27, 2021·Frontiers in Cellular and Infection Microbiology·Marta MachadoMarkus Ganter
Mar 18, 2021·Annual Review of Plant Biology·Carolin SeyfferthBert De Rybel
Aug 24, 2021·Frontiers in Plant Science·Sandra Thibivilliers, Marc Libault
Aug 5, 2021·Journal of Integrative Plant Biology·Hui LiQuanzi Li

❮ Previous
Next ❯

Methods Mentioned

BETA
RNA-seq
scRNA-seq
protein folding
laser
transgenic
PCR

Software Mentioned

R
SciPy
NGS QC Toolkit
STAR
StringTie
HISAT2
UMI

Related Concepts

Related Feeds

Autoimmune Polyendocrine Syndromes

This feed focuses on a rare genetic condition called Autoimmune Polyendocrine Syndromes, which are characterized by autoantibodies against multiple endocrine organs. This can lead to Type I Diabetes.