The embryonic transcriptome of Arabidopsis thaliana
Preprint posted on November 27, 2018 https://www.biorxiv.org/content/early/2018/11/27/479584
Article now published in Plant Reproduction at http://dx.doi.org/10.1007/s00497-018-00357-2
Comparison of Arabidopsis embryos to other tissues reveals their distinct and specialized transcriptome
Selected by Chandra Shekhar MisraCategories: bioinformatics, developmental biology, genomics, plant biology
Background
In flowering plants, the fertilization of egg and sperm cell forms the zygote which upon a series of cell divisions produces an embryonic tissue with a characteristic body plan, often referred to as embryonic patterning. This body plan later then lays the foundation of shoot and root meristem, epidermal and ground vascular tissues. Each of these processes is marked by changes at the gene expression level and a significant amount of research has been done to understand how a zygote develops into an embryo [1-2]. However, technical challenges in isolating small embryos have precluded successful transcriptomic analysis of the different stages of development. Embryos are deeply embedded within a seed which also makes RNA extraction prone to contamination from surrounding nourishing tissues of endosperm. A lack of sensitive and low input RNA-seq protocols also hampered the study of this vital tissue.
In this preprint, the authors have compared three different low input RNA-seq protocols to study the transcriptome profile of 8 different stages (Fig. 1) of embryo development. The authors compared the publicly available transcriptome datasets of 27 different tissues from 31 developmental time points to gene expression in embryos. Based on these results, they were able to conclude that the embryo transcriptome is highly distinct and specialized compared to the other tissues.
Fig 1: Different stages of embryonic development in Arabidopsis (Hofmann et al., 2018,
)Significant findings
The authors compared low-input mRNA seq library preparation methods – Ovation PicoSL WTA System V2, SMARTer Ultra Low Input RNA Kit, and the non-commercial Smart-seq2 method. According to this study, in terms of the cost per library, quality, and reproducibility, a Smart-seq2 protocol using off-the-shelf reagent is the clear winner.
The time-series RNA–seq data from the 8 different stages of embryo development were free from contamination by RNAs of the surrounding maternal tissues, a problem associated with most of the publicly available datasets from this development stage [3].
The authors compared the transcriptome of the embryo from this study with 27 different tissues using the publicly available datasets. Using model-based clustering analysis, the authors concluded that Arabidopsis embryonic gene expression dynamics are tightly regulated and undergoes large-scale changes which make it a highly specialized and unique transcriptome.
The authors identified 792 specific marker transcripts during embryonic development (Fig. 2). Other than the already known transcription factor markers such as Wox2, Wox8, and DRN, they also identified new markers which call for further research to understand their function. In addition to transcription factors, the authors also found potential transcriptional co-activators such as putative ubiquitin ligase and ubiquitin-like proteins.
Fig 2: : Identification of different stage-specific marker from different phases of embryo development (Hofmann et al., 2018,
)However, the most interesting aspect of this study was the comparison of somatic and zygotic embryos in terms of their gene expression profile. This is particularly important because somatic embryos are often considered as a suitable model to study zygotic embryogenesis, but this study proves otherwise. In terms of the transcriptome, the study revealed significant differences between the somatic and zygotic embryos. They concluded that the somatic embryos are more similar to germinating tissues than the embryogenesis process of zygotic embryos.
What I liked about this preprint and why I think this work is important
This study presents a high quality, contamination-free dataset using a low input RNA-seq protocol to study the gene expression profiles during embryo development. While previous studies have shown the transcriptome of either early or late embryonic development, the transcriptome profile of the developmental time series from preglobular to mature stage was still lacking. The authors have tried to bridge this gap by studying the gene expression pattern of intermediate stages as well. The dataset from the embryonic development will be useful for the community to explore this nascent tissue, in which the dynamics of development is still not clear.
Future studies
The authors have identified several potential transcripts from different stages. These transcripts might be a regulator of embryonic development and most of these are yet not fully characterized. It would be important to understand the function of some of these regulator genes during embryonic development.
Questions for the author
While I think the experiments were well conducted and all relevant information provided for the readers, given the nature of this pre-print (genomics paper), there are some minor things I would wish authors could have included.
For example, although the differences between different RNA-seq protocols were pointed out clearly, I didn’t find much discussion regarding the possible reasons for such differences given the same kind of starting material. This extra information would be useful for the people interested in trying one of these methods for other low input RNA-seq applications.
The authors have compared the somatic and zygotic embryo and, in a way, tried to bust a myth that somatic embryo can be proxy for studying embryogenesis. They have argued that culturing conditions rich in auxin may influence the transcriptome. Given that some of the recent publication highlights the role of auxin in embryo development, did authors find any possible mechanism to explain how auxin can differentially influence the transcriptome of somatic embryos and the zygotic embryos?
Did the authors studied the function characterization of any of the development marker gene they identified in this pre-print?
References
- Slane, D., Kong, J., Berendzen, K.W., Kilian, J., Henschen, A., Kolb, M., Schmid, M., Harter, K., Mayer, U., De Smet, I. and Bayer, M. (2014). Cell type-specific transcriptome analysis in the early Arabidopsis thaliana embryo. Development, pp.dev-116459.
- Palovaara, J., Saiga, S., Wendrich, J.R., van‘t Wout Hofland, N., van Schayck, J.P., Hater, F., Mutte, S., Sjollema, J., Boekschoten, M., Hooiveld, G.J. and Weijers, D. (2017). Transcriptome dynamics revealed by a gene expression atlas of the early Arabidopsis embryo. Nature plants, 3(11), p.894.
- Schon, M.A. and Nodine, M.D. (2017). Widespread contamination of Arabidopsis embryo and endosperm transcriptome data sets. The Plant Cell, 29(4), pp.608-617.
Note: The article has been accepted and will appear in an upcoming issue of Plant Reproduction.
Posted on: 17th December 2018 , updated on: 19th December 2018
doi: https://doi.org/10.1242/prelights.6352
Read preprintSign up to customise the site to your preferences and to receive alerts
Register hereAlso in the bioinformatics category:
A developmentally programmed splicing failure attenuates the DNA damage response during mammalian zygotic genome activation
Selected by | Ram |
1
Dissecting Mammalian Spermatogenesis Using Spatial Transcriptomics
Selected by | Martin Estermann |
The hourglass model of evolutionary conservation during embryogenesis extends to developmental enhancers with signatures of positive selection
Selected by | Irepan Salvador-Martinez |
1
Also in the developmental biology category:
Lactate Accelerates Mouse ES Cell Differentiation Towards the XEN Lineage
Selected by | Nozomu Takata |
Development of the foregut in Katharina tunicata (Mollusca; Polyplacophora)
Selected by | Paul Gerald L. Sanchez and Stefano Vianello |
H3 acetylation selectively promotes basal progenitor proliferation and neocortex expansion by activating TRNP1 expression
Selected by | Ana Uzquiano |
Also in the genomics category:
Also in the plant biology category:
Antiviral activity of bacterial TIR domains via signaling molecules that trigger cell death
Selected by | Jonny Coates, Connor Rosen |
Creating Clear and Informative Image-based Figures for Scientific Publications
Selected by | Mariana De Niz |
1
Major components in the KARRIKIN INSENSITIVE2-ligand signaling pathway are conserved in the liverwort, Marchantia polymorpha
AND
The Physcomitrium (Physcomitrella) patens PpKAI2L receptors for strigolactones and related compounds highlight MAX2 dependent and independent pathways
Selected by | Facundo Romani |
preListsbioinformatics category:
in theSingle Cell Biology 2020
A list of preprints mentioned at the Wellcome Genome Campus Single Cell Biology 2020 meeting.
List by | Alex Eve |
Antimicrobials: Discovery, clinical use, and development of resistance
Preprints that describe the discovery of new antimicrobials and any improvements made regarding their clinical use. Includes preprints that detail the factors affecting antimicrobial selection and the development of antimicrobial resistance.
List by | Zhang-He Goh |
Also in the developmental biology category:
EMBL Synthetic Morphogenesis: From Gene Circuits to Tissue Architecture (2021)
A list of preprints mentioned at the #EESmorphoG virtual meeting in 2021.
List by | Alex Eve |
EMBL Conference: From functional genomics to systems biology
Preprints presented at the virtual EMBL conference "from functional genomics and systems biology", 16-19 November 2020
List by | Jesus Victorino |
Single Cell Biology 2020
A list of preprints mentioned at the Wellcome Genome Campus Single Cell Biology 2020 meeting.
List by | Alex Eve |
Society for Developmental Biology 79th Annual Meeting
Preprints at SDB 2020
List by | Irepan Salvador-Martinez, Martin Estermann |
FENS 2020
A collection of preprints presented during the virtual meeting of the Federation of European Neuroscience Societies (FENS) in 2020
List by | Ana Dorrego-Rivas |
Planar Cell Polarity – PCP
This preList contains preprints about the latest findings on Planar Cell Polarity (PCP) in various model organisms at the molecular, cellular and tissue levels.
List by | Ana Dorrego-Rivas |
Cell Polarity
Recent research from the field of cell polarity is summarized in this list of preprints. It comprises of studies focusing on various forms of cell polarity ranging from epithelial polarity, planar cell polarity to front-to-rear polarity.
List by | Yamini Ravichandran |
TAGC 2020
Preprints recently presented at the virtual Allied Genetics Conference, April 22-26, 2020. #TAGC20
List by | Maiko Kitaoka, Madhuja Samaddar, Miguel V. Almeida, Sejal Davla, Jennifer Ann Black, Dey Lab |
3D Gastruloids
A curated list of preprints related to Gastruloids (in vitro models of early development obtained by 3D aggregation of embryonic cells). Preprint missing? Don't hesitate to let us know.
List by | Paul Gerald L. Sanchez and Stefano Vianello |
ASCB EMBO Annual Meeting 2019
A collection of preprints presented at the 2019 ASCB EMBO Meeting in Washington, DC (December 7-11)
List by | Madhuja Samaddar, Ramona Jühlen, Amanda Haage, Laura McCormick, Maiko Kitaoka |
EDBC Alicante 2019
Preprints presented at the European Developmental Biology Congress (EDBC) in Alicante, October 23-26 2019.
List by | Sergio Menchero, Jesus Victorino, Teresa Rayon, Irepan Salvador-Martinez |
EMBL Seeing is Believing – Imaging the Molecular Processes of Life
Preprints discussed at the 2019 edition of Seeing is Believing, at EMBL Heidelberg from the 9th-12th October 2019
List by | Dey Lab |
SDB 78th Annual Meeting 2019
A curation of the preprints presented at the SDB meeting in Boston, July 26-30 2019. The preList will be updated throughout the duration of the meeting.
List by | Alex Eve |
Lung Disease and Regeneration
This preprint list compiles highlights from the field of lung biology.
List by | Rob Hynds |
Young Embryologist Network Conference 2019
Preprints presented at the Young Embryologist Network 2019 conference, 13 May, The Francis Crick Institute, London
List by | Alex Eve |
Pattern formation during development
The aim of this preList is to integrate results about the mechanisms that govern patterning during development, from genes implicated in the processes to theoritical models of pattern formation in nature.
List by | Alexa Sadier |
BSCB/BSDB Annual Meeting 2019
Preprints presented at the BSCB/BSDB Annual Meeting 2019
List by | Dey Lab |
Zebrafish immunology
A compilation of cutting-edge research that uses the zebrafish as a model system to elucidate novel immunological mechanisms in health and disease.
List by | Shikha Nayar |
Also in the genomics category:
EMBL Conference: From functional genomics to systems biology
Preprints presented at the virtual EMBL conference "from functional genomics and systems biology", 16-19 November 2020
List by | Jesus Victorino |
TAGC 2020
Preprints recently presented at the virtual Allied Genetics Conference, April 22-26, 2020. #TAGC20
List by | Maiko Kitaoka, Madhuja Samaddar, Miguel V. Almeida, Sejal Davla, Jennifer Ann Black, Dey Lab |