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

1. Front Matter

   Pages i-xii

   PDF

2. Expression Analysis and Genome Annotations with RNA Sequencing

   • Masaaki Kobayashi, Hajime Ohyanagi, Kentaro Yano

   Pages 1-12

3. The Application of Next Generation Sequencing Techniques to Plant Epigenomics

   • Manu J. Dubin

   Pages 13-31

4. Whole Genome Sequencing to Identify Genes and QTL in Rice

   • Ryohei Terauchi, Akira Abe, Hiroki Takagi, Muluneh Tamiru, Rym Fekih, Satoshi Natsume et al.

   Pages 33-42

5. Variant Calling Using NGS Data in European Aspen (Populus tremula)

   • Jing Wang, Douglas Scofield, Nathaniel R. Street, Pär K. Ingvarsson

   Pages 43-61

6. Leafy Spurge Genomics: A Model Perennial Weed to Investigate Development, Stress Responses, and Invasiveness

   • David Horvath, James V. Anderson, Wun S. Chao, Michael E. Foley, Münevver Doğramaci

   Pages 63-78

7. Utilization of NGS and Proteomic-Based Approaches to Gain Insights on Cellular Responses to Singlet Oxygen and Improve Energy Yields for Bacterial Stress Adaptation

   • Roger S. Greenwell Jr., Mobashar Hussain Urf Turabe Fazil, H. P. Pandey

   Pages 79-99

8. Experimental Evolution and Next Generation Sequencing Illuminate the Evolutionary Trajectories of Microbes

   • Mario A. Fares

   Pages 101-113

9. Plant Carbohydrate Active Enzyme (CAZyme) Repertoires: A Comparative Study

   • Huansheng Cao, Alex Ekstrom, Yanbin Yin

   Pages 115-134

10. Metagenomics of Plant–Microbe Interactions

    • Riccardo Rosselli, Andrea Squartini

    Pages 135-153

11. Genes and Trans-Factors Underlying Embryogenic Transition in Plant Soma-Cells

    • Dhananjay K. Pandey, Bhupendra Chaudhary

    Pages 155-178

12. Bioinformatics Tools to Analyze Proteome and Genome Data

    • Ritesh Kumar, Shalini Singh, Vikash Kumar Dubey

    Pages 179-194

13. High-Throughput Transcriptome Analysis of Plant Stress Responses

    • Güzin Tombuloğlu, Hüseyin Tombuloğlu

    Pages 195-209

14. CNV and Structural Variation in Plants: Prospects of NGS Approaches

    • Enrico Francia, Nicola Pecchioni, Alberto Policriti, Simone Scalabrin

    Pages 211-232

15. Back Matter

    Pages 233-241

    PDF

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.

• Pathway identification
• deletion mutants
• expressed sequence tags
• genome shuffling
• insertional mutants

• Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy

  Gaurav Sablok

• Institute of Life Sciences, Nalco Square, Bhubaneswar, India

  Sunil Kumar

• Department of Forest Genetics, Forestry and Forest Products Research Institute (FFRI), Tsukuba, Japan

  Saneyoshi Ueno

• Department of Planning and Research, National Museum of Marine Biology and Aquarium, Pingtung, Taiwan

  Jimmy Kuo

• Biodiversity and Molecular Ecology, Fondazione Edmund Mach, San Michele all'Adige, Italy

  Claudio Varotto

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

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