RNA-Seq Data Analysis for Studying Abiotic Stress in Horticultural Plants

Миронова, В. В.; Weinholdt, Claus; Große, Ivo

doi:10.1007/978-4-431-55251-2_14

Cited by 10 publications

(3 citation statements)

References 118 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Transcriptome study approaches have progressed from basic DNA microarrays platform to RNA- Seq technology in recent times due to the continual developments in sequencing technology ( Mironova et al., 2015 ). It has several perks including high sensitivity, high throughput, and efficacy, which may be used to analyses a complete transcriptome without a genomic reference sequence.…”

Section: Introductionmentioning

confidence: 99%

Upcoming progress of transcriptomics studies on plants: An overview

Tyagi

Singh²,

Mathur³

et al. 2022

Front. Plant Sci.

View full text Add to dashboard Cite

Transcriptome sequencing or RNA-Sequencing is a high-resolution, sensitive and high-throughput next-generation sequencing (NGS) approach used to study non-model plants and other organisms. In other words, it is an assembly of RNA transcripts from individual or whole samples of functional and developmental stages. RNA-Seq is a significant technique for identifying gene predictions and mining functional analysis that improves gene ontology understanding mechanisms of biological processes, molecular functions, and cellular components, but there is limited information available on this topic. Transcriptomics research on different types of plants can assist researchers to understand functional genes in better ways and regulatory processes to improve breeding selection and cultivation practices. In recent years, several advancements in RNA-Seq technology have been made for the characterization of the transcriptomes of distinct cell types in biological tissues in an efficient manner. RNA-Seq technologies are briefly introduced and examined in terms of their scientific applications. In a nutshell, it introduces all transcriptome sequencing and analysis techniques, as well as their applications in plant biology research. This review will focus on numerous existing and forthcoming strategies for improving transcriptome sequencing technologies for functional gene mining in various plants using RNA- Seq technology, based on the principles, development, and applications.

show abstract

Section: Introductionmentioning

confidence: 99%

Upcoming progress of transcriptomics studies on plants: An overview

Tyagi

Singh²,

Mathur³

et al. 2022

Front. Plant Sci.

View full text Add to dashboard Cite

show abstract

“…These differences are of significant importance to research on functional gene mining in medicinal plants, construction of gene regulatory networks, secondary metabolites, resistance genes, and genetic diversity. In recent years, with the steady advancements in sequencing technology, transcriptome research tools have evolved from the traditional chip hybridization platform to RNA sequencing technology (RNA-Seq) (Mironova et al, 2015). This method can be used to perform whole transcriptome analysis without a genomic reference sequence and offers advantages such as high throughput, digital signals, and high sensitivity.…”

Section: Introductionmentioning

confidence: 99%

Research Progress and Future Development Trends in Medicinal Plant Transcriptomics

Guo

Huang²,

Sun

et al. 2021

Front. Plant Sci.

View full text Add to dashboard Cite

Transcriptomics is one of the most popular topics in biology in recent times. Transcriptome sequencing (RNA-Seq) is a high-throughput, high-sensitivity, and high-resolution technique that can be used to study model and non-model organisms. Transcriptome sequencing is also an important method for studying the genomes of medicinal plants, a topic on which limited information is available. The study of medicinal plants through transcriptomics can help researchers analyze functional genes and regulatory mechanisms of medicinal plants and improve breeding selection and cultivation techniques. This article analyzes and compares the applications of transcriptome sequencing in medicinal plants over the past decade and briefly introduces the methods of transcriptome sequencing and analysis, their applications in medicinal plant research, and potential development trends. We will focus on the research and application progress of transcriptome sequencing in the following four areas: the mining of functional genes in medicinal plants, development of molecular markers, biosynthetic pathways of secondary metabolites, and developmental mechanisms of medicinal plants. Our review will provide ideas for the mining of functional genes of medicinal plants and breeding new varieties.

show abstract

“…However, the precise molecular mechanisms, including the complex gene regulation involved in salinity tolerance pathway, remains unclear. Recently, many researchers have attempted to evaluate the complex regulation of genes responsive to salinity stress in plant species using next‐generation sequencing (NGS) technologies (Mironova et al ). For example, major genes and pathways associated with salinity stress and submergence tolerance, including numerous transcription factor (TF)‐encoding genes of various TF families (MYB, bHLH, AP2‐EREBP, WRKY, bZIP and NAC), were reported after integrated transcriptome analysis of differentially expressed genes (DEGs) identified from RNA‐seq of Porteresia coarctata , a halophytic wild relative of rice, during salinity stress treatments (Garg et al ).…”

Section: Introductionmentioning

confidence: 99%

Molecular dissection of Oryza sativa salt‐induced RING Finger Protein 1 (OsSIRP1): possible involvement in the sensitivity response to salinity stress

Hwang

Kim

Lim

et al. 2016

Physiologia Plantarum

View full text Add to dashboard Cite

Ubiquitination-mediated protein degradation via Really Interesting New Gene (RING) E3 ligase plays an important role in plant responses to abiotic stress conditions. Many plant studies have found that RING proteins regulate the perception of various abiotic stresses and signal transduction. In this study, Oryza sativa salt-induced RING Finger Protein 1 (OsSIRP1) gene was selected randomly from 44 Oryza sativa RING Finger Proteins (OsRFPs) genes highly expressed in rice roots exposed to salinity stress. Transcript levels of OsSIRP1 in rice leaves after various stress treatments, including salt, heat, drought and hormone abscisic acid (ABA), were observed. Poly-ubiquitinated products of OsSIRP1 were investigated via an in vitro ubiquitination assay.35S:OsSIRP1-EYFP was distributed in the cytosol of untreated and salt-treated rice protoplasts. Heterogeneous overexpression of OsSIRP1 in Arabidopsis reduced tolerance for salinity stress during seed germination and root growth. Our findings indicate that OsSIRP1 acts as a negative regulator of salinity stress tolerance mediated by the ubiquitin 26S proteasome system.

show abstract

RNA-Seq Data Analysis for Studying Abiotic Stress in Horticultural Plants

Cited by 10 publications

References 118 publications

Upcoming progress of transcriptomics studies on plants: An overview

Upcoming progress of transcriptomics studies on plants: An overview

Research Progress and Future Development Trends in Medicinal Plant Transcriptomics

Molecular dissection of Oryza sativa salt‐induced RING Finger Protein 1 (OsSIRP1): possible involvement in the sensitivity response to salinity stress

Contact Info

Product

Resources

About