Advances in the Understanding of Biological Sciences Using Next Generation Sequencing (NGS) Approaches

This work is a compiled catalogue of such findings, where several NGS technologies ranging from the genomics, transcriptomics, metagenomics, single cell genomics, QTL, patho-genomics and patho-transcriptomics have been applied to delineate the mystery of the associated mutations, biological pathway transitions, transcriptional fluxes and patterns of host associated or adaptations to certain climatic conditions. The aims and scope of this book focuses more on the biological underpinning to initiate the cross-talks across the traits acquired or lost during the course of evolution. The structured framework of the present volume provides the applicative point of view of the NGS technologies and demonstrates the conceptual way of linking the experimentation to the NGS technologies, to aid in researchers to place their biological hypothesis in a larger context.

Auteur

Guarav Sablok, PhD

Research Fellow, Plant Functional Biology and Climate Change Cluster (C3)

University of Technology, Sydney

PO Box 123

Broadway NSW 2007 Australia

T:: 0039-3270484-732

Email: sablokg@gmail.com

Sunil Kumar, M.Sc ,IPR, MCA, Ph.D

Senior Scientist, Department of Bioinformatics

Institute of Life Sciences

Nalco Square, C S Pur

Bhubaneswar, Odisha 275103, India

T: 91-6742301500

F: 91-6742300728

E-mail: skybiotech@gmail.com

Jimmy Kuo, Ph.D

Associate Researcher, National Museum of Marine Biology and Aquarium

Graduate Institute of Marine Biotechnology, National Dong Haw University

2 Houwan Road, Checheng

Pingtung 944, Taiwan

Tel: 886-8-8825001 ext. 1358

Fax: 886-8-8825087

E-mail: jimmy@nmmba.gov.tw

Saneyoshi Ueno, Ph.D

Department of Forest Genetics

1 Matsunosato, Tsukuba

Ibaraki 3058687, Japan

T: +81-29-8733211

F: +81-29-8743720

Email: saueno@ffpri.affrc.go.jp

Claudio Varotto, Msc, Ph.D

Department of Biodiversity and Molecular Ecology, Research and Innovation Center

Fondazione Edmund Mach, Research and Innovation Center

Via E. Mach 1, 38010 San Michele all'Adige (TN), Italy

T: +39 0461 615 108

F: +390461650956

Email: claudio.varotto@fmach.it

Résumé
Provides a global view of the recent advances in the biological sciences and the adaption of the pathogen to the host plants revealed using NGS. Molecular Omic's is now a major driving force to learn the adaption genetics and a great challenge to the scientific community, which can be resolved through the application of the NGS technologies. The availability of complete genome sequences, the respective model species for dicot and monocot plant groups, presents a global opportunity to delineate the identification, function and the expression of the genes, to develop new tools for the identification of the new genes and pathway identification. Genome-wide research tools, resources and approaches such as data mining for structural similarities, gene expression profiling at the DNA and RNA level with rapid increase in available genome sequencing efforts, expressed sequence tags (ESTs), RNA-seq, gene expression profiling, induced deletion mutants and insertional mutants, and gene expression knock-down (gene silencing) studies with RNAi and microRNAs have become integral parts of plant molecular omic's. Molecular diversity and mutational approaches present the first line of approach to unravel the genetic and molecular basis for several traits, QTL related to disease resistance, which includes host approaches to combat the pathogens and to understand the adaptation of the pathogen to the plant host. Using NGS technologies, understanding of adaptation genetics towards stress tolerance has been correlated to the epigenetics. Naturally occurring allelic variations, genome shuffling and variations induced by chemical or radiation mutagenesis are also being used in functional genomics to elucidate the pathway for the pathogen and stress tolerance and is widely illustrated in demonstrating the identification of the genes responsible for tolerance in plants, bacterial and fungal species.

Contenu

Expression analysis and genome annotations with RNA sequencing.- The application of Next Generation Sequencing techniques to Plant Epigenomics.- Whole genome sequencing to identify genes and QTL in rice.- Variant calling using NGS data in European aspen (Populus tremula).- Leafy Spurge Genomics: A Model Perennial Weed To Investigate Development, Stress Responses, And Invasiveness.- Utilization of NGS and proteomic-based approaches to gain insights on cellular responses to singlet oxygen and improve energy yields for bacterial stress adaptation.- Experimental evolution and next generation sequencing illuminate the evolutionary trajectories of microbes.- Plant carbohydrate active enzyme (CAZyme) repertoires: a comparative Study.- Metagenomics of Plant- Microbe Interactions.- Genes and trans-factors underlying embryogenic transition in plant soma-cells.- Bioinformatics tools to analyze the proteome and genome data.- High through-put transcriptome analysis of plant stress responses.- CNV and structural variation in plants: prospects of NGS Approaches.