Advances in the Understanding of Biological Sciences Using Next Generation Sequencing (NGS) Approaches PDF
Preview Advances in the Understanding of Biological Sciences Using Next Generation Sequencing (NGS) Approaches
Gaurav Sablok · Sunil Kumar Saneyoshi Ueno · Jimmy Kuo Claudio Varotto Editors Advances in the Understanding of Biological Sciences Using Next Generation Sequencing (NGS) Approaches Advances in the Understanding of Biological Sciences Using Next Generation Sequencing (NGS) Approaches Gaurav Sablok (cid:129) Sunil Kumar Saneyoshi Ueno (cid:129) Jimmy Kuo (cid:129) Claudio Varotto Editors Advances in the Understanding of Biological Sciences Using Next Generation Sequencing (NGS) Approaches Editors Gaurav Sablok Sunil Kumar Biodiversity and Molecular Ecology Institute of Life Sciences Research and Innovation Centre Nalco Square Fondazione Edmund Mach Bhubaneswar , India San Michele all'Adige , Italy and and ICAR-NBAIM Plant Functional Biology and Climate Kushmaur, Mau (UP) India Change Cluster, C3 University of Technology Sydney Jimmy Kuo Broadway, NSW , Australia Department of Planning and Research National Museum of Marine Saneyoshi Ueno Biology and Aquarium Department of Forest Genetics Pingtung , Taiwan Forestry and Forest Products Research Institute (FFPRI) Tsukuba , Ibaraki , Japan Claudio Varotto Biodiversity and Molecular Ecology Fondazione Edmund Mach San Michele all’Adige, Italy ISBN 978-3-319-17156-2 ISBN 978-3-319-17157-9 (eBook) DOI 10.1007/978-3-319-17157-9 Library of Congress Control Number: 2015942694 Springer Cham Heidelberg New York Dordrecht London © Springer International Publishing Switzerland 2015 T his work is subject to copyright. All rights are reserved by the Publisher, whether the whole or part of the material is concerned, specifi cally the rights of translation, reprinting, reuse of illustrations, recitation, broadcasting, reproduction on microfi lms or in any other physical way, and transmission or information storage and retrieval, electronic adaptation, computer software, or by similar or dissimilar methodology now known or hereafter developed. T he use of general descriptive names, registered names, trademarks, service marks, etc. in this publication does not imply, even in the absence of a specifi c statement, that such names are exempt from the relevant protective laws and regulations and therefore free for general use. T he publisher, the authors and the editors are safe to assume that the advice and information in this book are believed to be true and accurate at the date of publication. Neither the publisher nor the authors or the editors give a warranty, express or implied, with respect to the material contained herein or for any errors or omissions that may have been made. Printed on acid-free paper S pringer International Publishing AG Switzerland is part of Springer Science+Business Media (www.springer.com) Pref ace Next Generation Sequencing has been leveraged primarily in the current era as a de facto for linking the biological hypothesis with the elucidation of the genes, biologi- cal pathways, and mechanistic evolution of certain traits and lineage specifi c evolu- tionary adaptations. Keeping in pace with the recent developments in the NGS technologies, several tools and techniques have been developed widely addressing questions of critical importance across the bacterial, fungal, and plant communities. Advances in the Understanding of the Biological Sciences using the Next Generation Sequencing is a compiled catalogue of such fi ndings, where several NGS technolo- gies ranging from the genomics, transcriptomics, metagenomics, single cell genom- ics, QTL, patho-genomics, and patho-transcriptomics have been applied to delineate the mystery of the associated mutations, biological pathway transitions, transcrip- tional fl uxes, and patterns of host associated or adaptations to certain climatic con- ditions. The aims and scope of this book focus more on the biological underpinning to initiate the cross talks across the traits acquired or lost during the course of evolu- tion. The structured framework of this volume provides the applicative point of view of the NGS technologies and demonstrates the conceptual way of linking the experi- mentation with the NGS technologies, to aid in researchers to place their biological hypothesis in a larger context. This book would have not been accomplished without the support of my numer- ous colleagues, who have helped in editing the volume of the book, contributors, and motivational and organizational support of Prof. Peter Ralph, Executive Director, Plant Functional Biology and Climate Change Cluster, C3, University of Technology Sydney, Australia. This book would have not been possible without the encouragement and support of my wife Mrs. Namrata Sablok. Last but not least, thanks to Daniel, Jessica, and Ken (Springer Publishing) for making this volume fi nally published. Broadway, NSW, Australia Gaurav Sablok, Ph.D. v Contents 1 Expression Analysis and Genome Annotations with RNA Sequencing ............................................................................. 1 Masaaki Kobayashi , Hajime Ohyanagi , and Kentaro Yano 2 The Application of Next Generation Sequencing Techniques to Plant Epigenomics .............................................................................. 13 Manu J. Dubin 3 Whole Genome Sequencing to Identify Genes and QTL in Rice ...................................................................................... 33 Ryohei Terauchi , Akira Abe , Hiroki Takagi , Muluneh Tamiru , Rym Fekih , Satoshi Natsume , Hiroki Yaegashi , Shunichi Kosugi , Hiroyuki Kanzaki , Hideo Matsumura , Hiromasa Saitoh , Kentaro Yoshida , Liliana Cano , and Sophien Kamoun 4 Variant Calling Using NGS Data in European Aspen (Populus tremula) ..................................................................................... 43 Jing Wang , Douglas Scofi eld , Nathaniel R. Street , and Pär K. Ingvarsson 5 Leafy Spurge Genomics: A Model Perennial Weed to Investigate Development, Stress Responses, and Invasiveness ....... 63 David Horvath , James V. Anderson , Wun S. Chao , Michael E. Foley , and Münevver Doğramaci 6 Utilization of NGS and Proteomic-Based Approaches to Gain Insights on Cellular Responses to Singlet Oxygen and Improve Energy Yields for Bacterial Stress Adaptation .............. 79 Roger S. G reenwell Jr. , Mobashar Hussain Urf Turabe Fazil , and H. P. Pandey vii viii Contents 7 Experimental Evolution and Next Generation Sequencing Illuminate the Evolutionary Trajectories of Microbes ........................ 101 Mario A. Fares 8 Plant Carbohydrate Active Enzyme (CAZyme) Repertoires: A Comparative Study ............................................................................. 115 Huansheng Cao , Alex Ekstrom , and Yanbin Yin 9 Metagenomics of Plant–Microbe Interactions ..................................... 135 Riccardo Rosselli and Andrea Squartini 10 Genes and Trans-Factors Underlying Embryogenic Transition in Plant Soma-Cells ................................................................................. 155 Dhananjay K. Pandey and Bhupendra Chaudhary 11 Bioinformatics Tools to Analyze Proteome and Genome Data ........... 179 Ritesh Kumar , Shalini Singh , and Vikash Kumar Dubey 12 High-Throughput Transcriptome Analysis of Plant Stress Responses ....................................................................... 195 Güzin Tombuloğlu and Hüseyin Tombuloğlu 13 CNV and Structural Variation in Plants: Prospects of NGS Approaches ............................................................... 211 Enrico Francia , Nicola Pecchioni , Alberto Policriti , and Simone Scalabrin Index ................................................................................................................. 233 Contributors Akira Abe , Ph.D. D ivision of Genomics and Breeding, I wate Biotechnology Research Center , Kitakami , Iwate , Japan J ames V . A nderson, P h.D. S unfl ower and Plant Biology Research Unit , U SDA-ARS Red River Valley Agricultural Research Center, Bioscience Research Lab, F argo, N D, U SA Liliana Cano , Ph.D. The Sainsbury Laboratory, Norwich Research Park , Norwich , Norfork , UK Huansheng Cao , Ph.D. Department of Biological Sciences , Northern Illinois University , DeKalb , IL , USA Wun S. Chao , Ph.D. Sunfl ower and Plant Biology Research Unit , USDA-ARS Red River Valley Agricultural Research Center, Bioscience Research Lab , Fargo , ND , USA Bhupendra Chaudhary , Ph.D. School of Biotechnology, Gautam Buddha University , Greater Noida , Uttar Pradesh , India Münevver Doğramaci , Ph.D. Sunfl ower and Plant Biology Research Unit, USDA-ARS Red River Valley Agricultural Research Center, Bioscience Research Lab , Fargo , ND , USA Vikash Kumar Dubey , Ph.D. D epartment of Biosciences and Bioengineering, Indian Institute of Technology Guwahati , Assam , India Manu J. Dubin , Ph.D. Gergor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences , Vienna , Austria Alex Ekstrom Department of Computer Science , Northern Illinois University , DeKalb , IL , USA ix
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