Transcriptome Analysis and Why It Matters / Sagarika Mishra, editor.

Format:

Book

Contributor:

Mishra, Sagarika, editor.

Series:

Systems biology-theory, techniques, and applications series.

Systems Biology - Theory, Techniques and Applications Series

Language:

English

Subjects (All):

Medical genetics.

Physical Description:

1 online resource (244 pages)

Edition:

First edition.

Place of Publication:

New York : Nova Science Publishers, Inc., [2023]

Summary:

The book is a compilation of broad applications of Transcriptomics in the current field of science and technology and its impact towards the developmental aspects of crop science and clinical applications. The book focuses on the recent advancements in RNA sequencing technologies and the socio-economic impact with generations of huge transcriptome datasets aimed towards crop improvement against biotic and abiotic stress. Nevertheless, it also discusses the impact of transcriptomics in clinical studies focusing on oncology and therapeutics. The book targets mainly the young minds and provides them a basic understanding of how the omics world is contributing towards developmental aspects of science. Again, the book also discusses the various pros and cons of the myriad of datasets generated by the advanced sequencing platforms. Specifically, Chapter 1, 2, and 6 broadly explain the applications of "Transcriptomics" towards studying various abiotic and biotic stress response studies in plants. Chapter 3 focuses on the importance of the transcriptome datasets in extremophiles and studying their adaptive nature for surviving against environmental cues. Similarly, chapter 4 and 5 along with 7 and 8 emphasize on the importance and advancements in legume crops and millets, respectively, some of which are selectively known to display essential traits against various stress conditions affecting their survival. Lastly, chapters 9 and 10 are based on the promising applications of human transcriptomic studies and its profound application in science aimed towards studying various neurological disorders, diseases, and further advancement in therapeutics. Overall, the book is helpful for researchers, students and academicians for getting a better understanding on the wider-range applications of "Transcriptomic Research."

Contents:

Intro

Preface

Plant Transcriptomics Unraveling Potential QTLs (Quantitative Trait Loci) in Crops Responding to Abiotic Stress

Abstract

1.1. Introduction

2.1. The Complexity of Plants Responding to Abiotic Stress

2.2. The QTL Analysis and Molecular Markers

2.3. The Plant Transcriptomics

2.4. The Impact of Gene Cluster Formation on Plants

2.5. Looking for Genes And Potential QTLs of Legume Orphan Species

2.5.1. Stylosanthes scabra Vogel

2.5.2. General Results Identifying Aquaporins

2.5.3. Vigna unguiculata (L.) Walp.

2.5.3.1. The Cowpea Transcriptomics Data - General Information

2.5.3.2. Principles Guiding the Analysis of Cowpea Transcriptomics Data

2.5.3.3. The General Results of the Identified Clusters

2.5.4. The Data-Mining of Cluster Members Based on Previously Published Scientific Articles

2.5.5. The Protein-Protein Interactions with the Members of the Clusters

2.5.6. The Prediction of Transcription Factors Regulating Genes from Clusters

Conclusion

References

The Importance of Transcriptomics in Plant Stress Response Studies

2.1. Introduction

2.2. Transcriptomics and Its Significance in Response to Biotic and Abiotic Stress in Plants

2.3. Transcriptomic Advances and Strategies in the Plant Stress Reponses

2.4. Next-Generation Sequencing, RNA-Library Preparation, and Read Mapping

2.5. Several Strategies for Differential Expression Analysis

2.6. Applications Focusing on Comparative Transcriptomics in the Response to Stresses in Model and Crop Plants

2.7. Single-Cell Technology and Its Emerging Opportunities in Plant Science

2.8. Advances, Opportunities and Challenges in Single-Cell Transcriptomic for Plant Stress Response Studies

Understanding the Facets of Extreme Land Plant Adaptation from Transcriptome Analysis.

Abstract

1. Introduction

2. Expanding Transcriptome Analysis to Extremophiles

2.1. Desert Plants

2.2. Plants from Serpentine Soils

2.3. Mangrove Plants

2.4. Polar and Subpolar Plants

2.5. Mountain Plants

3. Identification of Stress Signaling Mechanisms by Transcriptome Profiling of Extremophiles

3.1. Drought Tolerance Mechanisms in Desert Plants

3.2. Salt Tolerance Mechanisms in Mangrove Plants and Halophytes

3.3. Cold Stress Tolerance Mechanisms

4. Exploring Natural Variation and QTLs for Stress Adaptation from Extremophiles

5. Biotechnological Applications of Extremophiles

6. Conservation of Threatened Extremophiles

Acknowledgment

Transcriptomics in Legume Crops: A Look at How RNA-Seq Has Advanced Research in Legumes

2. Underutilized Legumes and their Importance in Future Food Security

3. Trends in Legume Consumption

4. Orphan Legumes: A Valuable Resource

5. The Need for Genomic Resources in Various Aspects of Improvement in Underutilized Legumes

6. Genomics of Orphan Legumes: The Early Days

7. Next Generation Sequencing Platforms Enabled Transcriptomics in Underutilized Legumes

8. Tools of the Trade: A Brief Overview

9. RNA-Seq has Accelerated the Research in Orphan Legumes

9.1. Marker Identification

9.2. Gene Expression Profiles in Developmental Stages

9.3. Differential Expression during Stress Response

9.4. A Survey of Non-Coding Sequences

10. The Future of RNA-Seq in Legume Transcriptomics

11. Conclusion

Transcriptome Analysis in Peanuts to Decipher Abiotic Stress Responses

2.1. Area, Production, and Productivity

2.2. Constraints to Groundnut Production

2.3. Abiotic Stress Effect on Peanut.

3.1. Transcriptomics: A Closer Look at the Transcripts

3.2. Transcriptome Profiling

3.2.1. Drought

3.2.2. Salinity

3.2.3. Cold

3.2.4. Waterlogging

3.2.5. Nutrient Deficiency

4.1. Genome-Wide Identification and Functional Analysis of Gene Families

4.2. Application of Peanut Transcriptomics

4.2.1. Functional Analysis of Stress-Responsive Genes

4.2.2. Transgenic Plant Generation

Applications of Transcriptomics in Understanding Plant Disease Resistance

2.1. Transcriptome Techniques for Plant-Pathogen Interaction

2.2. Application of RNA Sequencing in Plant-Pathogen Interaction Studies

2.3. RNA Sequencing in Plant-Fungal Interactions

2.3.1. Colletotrichum sublineola

2.3.2. Phytophthora nicotiana

2.3.3. Podosphaera aphanis

2.3.4. Sclerospora graminicola

2.3.5. Puccinia striiformis

2.3.6. Fusarium pseudograminearum

2.3.7. Botrytis cinerea

2.3.8. Magnaporthe oryzae

2.3.9. Fusarium fujikuroi

2.3.10. Verticillium dahliae

2.4. RNA Sequencing in Plant and Phytopathogenic Bacteria Interaction

3.1. Data Base for Transcriptome Information Related to Plant Defense Responses

Pearl Millet Transcriptomics in Response

to Abiotic Stresses: Current Status

and Future Prospects

2. Different Technologies Used for Transcriptomics

3. Pearl Millet Transcriptomics and Responses

to Abiotic Stresses

3.1. Transcriptome Responses of Pearl Millet Genotypes Under Drought Stress

3.2. Transcriptome Responses of Pearl Millet Genotypes Under Salinity Stress

3.3. Transcriptome Responses of Pearl Millet Genotypes Under

Heat Stress

The Role of Transcriptomics Technology

in Understanding Abiotic Stress Tolerance

in Finger Millets.

2. Origin and Phylogeny of Finger Millets

2.1. Finger Millets As Nutritionally Important Underutilized Crop

2.2. Health Benefits of Finger Millet

2.3. Morpho-Physiological and Biochemical Responses of Finger Millet to Abiotic Stress

3. The Essence of Transcriptomics Research to Discern Abiotic Stress Tolerance in Finger Millets

3.1. Transcriptomics Techniques in Enhancing Abiotic Stress Tolerance in Finger Millet

Neurotranscriptomics: A Significant Approach

2. Significance of Transcriptomics in Neurodevelopmental Disorders

2.1. Autism Spectrum Disorder (ASD)

2.2. Attention Deficit Hyperactivity Disorder (ADHD)

2.3. Epilepsy

3. Significance of Transcriptomics in Neurodegenerative Disorders

3.1. Alzheimer's Disease (AD)

3.2. Parkinson's Disease

3.3. Huntington's Disease

Applications of Transcriptomics

in Clinical Studies

2.1. The Alchemy of Central Dogma

2.2. Transcriptome

3.1. The Unfinished Story of Human Transcriptome

3.2. The Applications of Genomics

3.3. The Transcriptome of Healthy Cells

3.4. Annotation of Protein-Coding Genes

4.1. Transcriptome Shotgun Sequencing

4.2. Discovering Transcript Rearrangement

4.3. Analysis of Transcriptomes in Cancer

Pathogenesis and Diagnosis

Index

Blank Page.

Notes:

Includes bibliographical references and index.

Description based on print version record.

Other Format:

Print version: Mishra, Sagarika Transcriptome Analysis and Why It Matters

ISBN:

979-88-911-3098-2