Biological significance of RNA-seq and single-cell genomic research in woody plants

Tang, Wei; Tang, Ao

doi:10.1007/s11676-019-00933-w

Cited by 10 publications

(5 citation statements)

References 113 publications

(109 reference statements)

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“…The information content of an organism is recorded in its genomic DNA and expressed through transcription (Martin et al 2013;Tang and Tang 2019). In this study, publicly available transcriptome data for different tissues of ve Orchidaceae species were used to compare the expression levels of ARF genes in different tissues and developmental stages.…”

Section: Analysis Of Transcriptome Data For Orchid Arf Familymentioning

confidence: 99%

Identification and transcriptome data analysis of ARF family genes in five Orchidaceae species

Bai

Chang

et al. 2023

Plant Mol Biol

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The Orchidaceae is a large family of perennial herbs especially noted for the exceptional diversity of specialized owers adapted for insect pollination. Elucidating the genetic regulation of owering and seed development of orchids is an important research goal with potential utility in orchid breeding programs. Auxin Response Factor (ARF) genes encode auxin-responsive transcription factors, which are involved in the regulation of diverse morphogenetic processes, including owering and seed development. However, limited information on the ARF gene family in the Orchidaceae is available. In this study, 112 ARF genes were identi ed in the genomes of ve orchid species (Phalaenopsis aphrodite, Phalaenopsis equestris, Vanilla planifolia, Apostasia shenzhenica, and Dendrobium catenatum). These genes were grouped into seven subfamilies based on their phylogenetic relationships. Compared with the ARF family in model plants, such as Arabidopsis thaliana and Oryza sativa, one subfamily of ARF genes involved in pollen wall synthesis has been lost during evolution of the Orchidaceae. This loss corresponds with absence of the exine in the pollinia. Transcriptome analysis indicated that the ARF genes of subfamily 4 may play an important role in ower formation and plant growth, whereas those of subfamily 3 are potentially involved in pollen wall development. Through mining of the published genomic and transcriptomic data for the ve species, the present results provide novel insights into the genetic regulation of unique morphogenetic phenomena of orchids. This study lays a foundation for further analysis of the regulatory mechanisms and functions of sexual reproduction-related genes in orchids. Key MessageGenome wide analysis and expression pattern analysis of ARF genes in ve 20 Orchidaceae species highlight their Evolutionary characteristics and roles in IAA response.

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Section: Analysis Of Transcriptome Data For Orchid Arf Familymentioning

confidence: 99%

Identification and transcriptome data analysis of ARF family genes in five Orchidaceae species

Bai

Chang

et al. 2023

Plant Mol Biol

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“…Several studies showed that different plant cell types have unique molecular signatures that determine their differentiated functions (Ryu et al., 2019; Tang & Tang, 2019; Yuan et al., 2018). Advancement in proteomics analysis of small numbers of cells enabled the identification of cell type‐specific proteins with important roles in plant biological processes (Dembinsky et al., 2007; Petricka et al., 2012; Zhu et al., 2016).…”

Section: Commentarymentioning

confidence: 99%

“…However, to improve our understanding of plant cells as a system, there is a critical need to move toward studies focusing on individual plant cell types (Libault, Pingault, Zogli, & Schiefelbein, 2017). Recently, single‐cell RNA sequencing and genomics technologies have led to the discovery and classification of previously unknown cell states in plants (Ryu, Huang, Kang, & Schiefelbein, 2019; Tang & Tang, 2019; Yuan, Lee, Hu, Scheben, & Edwards, 2018). Yet, studies on proteins, as the major structural and functional determinants of cells, are often limited to whole tissue analyses, primarily due to the lack of a reliable and accurate cell‐type‐specific proteomics platform.…”

Section: Introductionmentioning

confidence: 99%

Cell‐Type‐Specific Proteomics Analysis of a Small Number of Plant Cells by Integrating Laser Capture Microdissection with a Nanodroplet Sample Processing Platform

et al. 2021

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Plant organs and tissues contain multiple cell types, which are well organized in 3-dimensional structure to efficiently perform physiological functions such as homeostasis and response to environmental perturbation and pathogen infection. It is critically important to perform molecular measurements at the cell-type-specific level to discover mechanisms and unique features of cell populations that govern differentiation and respond to external perturbations. Although mass spectrometry−based proteomics has been demonstrated as an enabling discovery tool for studying plant physiology, conventional approaches require millions of cells to generate robust biological conclusions. Such requirements mask the cell-to-cell heterogeneities and limit the comprehensive profiling of plant proteins at spatially resolved and cell-type-specific resolutions. This article describes a recently developed proteomics workflow for studying a small number of plant cells by integrating laser capture microdissection, microfluidic nanodroplet−based sample preparation, and ultrasensitive liquid chromatography−mass spectrometry. Using poplar as a model tree species, we provide detailed protocols, including plant leaf and root tissue harvest, sample preparation, cryosectioning, laser microdissection, protein digestion, mass spectrometry measurement, and data analysis. We show that the workflow enables the precise identification and quantification of thousands of proteins from hundreds of isolated plant root and leaf cells.

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“…Transcriptomic data from thousands of single cells provide significant information that can be tapped using computational tools to understand molecular mechanisms of disease processes, host–pathogen interactions and mechanisms involved in cell differentiation, to understand the function of a single cell in various plant species. In future, the single‐cell DNA and RNA sequencing information will significantly help to explore rare transcripts in specific types of cells, facilitate rapid gene discovery and identification of novel biomarkers (Tang & Tang 2019).…”

Section: Future Directionsmentioning

confidence: 99%

Genome‐wide identification studies – A primer to explore new genes in plant species

et al. 2021

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Genome data have accumulated rapidly in recent years, doubling roughly after every 6 months due to the influx of next-generation sequencing technologies. A plethora of plant genomes are available in comprehensive public databases. This easy access to data provides an opportunity to explore genome datasets and recruit new genes in various plant species not possible a decade ago. In the past few years, many gene families have been published using these public datasets. These genome-wide studies identify and characterize gene members, gene structures, evolutionary relationships, expression patterns, protein interactions and gene ontologies, and predict putative gene functions using various computational tools. Such studies provide meaningful information and an initial framework for further functional elucidation. This review provides a concise layout of approaches used in these gene family studies and demonstrates an outline for employing various plant genome datasets in future studies.

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Biological significance of RNA-seq and single-cell genomic research in woody plants

Cited by 10 publications

References 113 publications

Identification and transcriptome data analysis of ARF family genes in five Orchidaceae species

Identification and transcriptome data analysis of ARF family genes in five Orchidaceae species

Cell‐Type‐Specific Proteomics Analysis of a Small Number of Plant Cells by Integrating Laser Capture Microdissection with a Nanodroplet Sample Processing Platform

Genome‐wide identification studies – A primer to explore new genes in plant species

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