Encyclopedia of Metagenomics

Karen E. Nelson Editor

Genes, Genomes and Metagenomes: Basics, Methods, Databases and Tools

With 216 Figures and 64 Tables Editor Karen E. Nelson J. Craig Venter Institute Rockville, MD, USA

ISBN 978-1-4899-7477-8 ISBN 978-1-4899-7478-5 (eBook) ISBN 978-1-4899-7479-2 (print and electronic bundle) DOI 10.1007/978-1-4899-7478-5 Springer New York Heidelberg Dordrecht London

Library of Congress Control Number: 2014954611

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Springer is part of Springer Science+Business Media (www.springer.com) Preface

Welcome to the Encyclopedia of Metagenomics. It is anticipated that the Encyclopedia will become a resource for tools, tool development and all things metagenomic. Volume 1 encompasses Genes, Genomes and Metagenomes. It covers a range of approaches to conduct metagenomics surveys including descriptions of analysis tools. Several of these approaches, including databases, have been under development from the beginning of the metagenome era and are enabling the analysis and interpretation of large microbial data sets from various environments. “Genes, Genomes and Metagenomes” also covers DNA extraction, various cloning and sequencing approaches, quality control and experimental designs: all essential components of the microbiome and metagenomic sequencing process. These approaches have continued to evolve and be reﬁned, and several improvements have been incorporated over the past few years. This has also been driven by a switch to next-generation sequencing (NGS) platforms including Ion Torrent, 454 and various Illumina technologies. Post-sequencing genome assembly, alignment tools, gene prediction and annotation are also critical to successful data interpretation. Deeper dives in Vol. 1 discuss codon usage, clustering programs and functional gene characterization.

MD, USA Karen E. Nelson September 2014

About the Editor

Dr. Karen E. Nelson is the President of the J. Craig Venter Institute (JCVI). Prior to being appointed President, Dr. Nelson held a number of other positions at the Institute including Director of JCVI’s Rockville Campus and Director of Human Microbiology and Metagenomics in the Department of Human Genomic Medicine at the JCVI. She is also a Professor at JCVI with an active research program in genomics and metagenomics. Dr. Nelson has led several genomic and metagenomic efforts including those of several reference microbial genomes and the ﬁrst human metagenomics study that was published in 2006. Additional ongoing studies in her group include metagenomic approaches to study the ecology of the gastrointestinal tract of humans and animals, studies on the relationship between the microbiome and various human and animal disease conditions, reference genome sequencing and analysis primarily for the human body, and other omics studies. Dr. Nelson also heads the microbiome group at Human Longevity Inc., which was recently formed in La Jolla, California. Dr. Nelson received her undergraduate degree from the University of the West Indies and her Ph.D. from Cornell University. She has authored or coauthored over 100 peer-reviewed publications and edited three books and is currently Editor-in-Chief of the journal Microbial Ecology. She also serves on the Editorial Boards of BMC Genomics, GigaScience, and the Central European Journal of Biology. She is also a standing member of the NRC Committee on Biodefense, a member of the National Academy of Sciences Board of Life Sciences, and a Fellow of the American Academy of Micro- biology. She was recently appointed an Honorary Professor at the University of the West Indies.

vii

Contributors

Takashi Abe Graduate School of Science and Technology, Niigata University, Niigata, Japan Yutaka Akiyama Department of Computer Science, Tokyo Institute of Technology, Meguro-ku Tokyo, Japan Rudolf Amann Molecular Ecology Group, Max Planck Institute for Marine Microbiology, Bremen, Germany Jaime Henrque Amorim Universidade Estadual de Santa Cruz, Laborato´rio de Biotecnologia Microbiana, Ilhe´us, BA, Brazil Luke D. Bainard Semiarid Prairie Agricultural Research Centre, Agriculture and Agri-Food Canada, Swift Current, SK, Canada Annalisa Ballarini Laboratory of Microbial Genomics, Centre for Integrative Biology (CIBIO), University of Trento, Trento, Italy Navneet Batra Department of Biotechnology, GGDSD College, Chandigarh, India Arvind Behal Department of Biotechnology, GGDSD College, Chandigarh, India Robert G. Beiko Faculty of Computer Science, Dalhousie University, Halifax, NS, Canada Terrence H. Bell Department of Natural Resource Sciences, McGill University, Sainte–Anne–de–Bellevue, QC, Canada Johan Bengtsson-Palme Institute of Neuroscience and Physiology, The Sahlgrenska Academy, University of Gothenburg, Go¨teborg, Sweden Nicholas H. Bergman National Biodefense Analysis and Countermeasures Center, Frederick, MD, USA Sonu Bhatia Department of Biotechnology, GGDSD College, Chandigarh, India Kai Blin Interfakult€ares Institut fur€ Mikrobiologie und Infektionsmedizin Tubingen,€ Mikrobiologie/Biotechnologie, Eberhard-Karls Universit€at, Tubingen,€ Germany

ix x Contributors

Herve´ M. Blottie`re INRA, AgroParisTech, Jouy en Josas, France MetaGenoPolis, INRA, Jouy en Josas, France Paul L. E. Bodelier Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, Netherlands Germán Bonilla-Rosso Laboratorio de Evolucioń Molecular y Experimental, Instituto de Ecologıá UNAM, Universidad Nacional Autońoma de Me´xico, Mexico City, Mexico Mark Borodovsky Joint Georgia Tech and Emory Wallace H Coulter Department of Biomedical Engineering, Center for Bioinformatics and Computational Genomics, Atlanta, GA, USA Yan Boucher Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada Jean-Luc Bouchot Department of Mathematics, Drexel University, Philadelphia, PA, USA Rainer Breitling Manchester Institute of Biotechnology, University of Manchester, Manchester, UK Florence Busato Laboratory for Epigenetics and Environment, Centre National de Geńotypage, CEA- Institut de Geńomique, Evry, France Brandi Cantarel Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA Rebecca J. Case Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada Patrick Chain Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, USA Chon-Kit Kenneth Chan Department of Mechanical Engineering, The University of Melbourne, Melbourne, VIC, Australia Trevor C. Charles Department of Biology, University of Waterloo, Waterloo, ON, Canada Chao Chen Dalian University of Technology, Dalian, China Liangyu Chen Dalian University of Technology, Dalian, China Tsute Chen Department of Microbiology, The Forsyth Institute, Cambridge, MA, USA Francis Y. L. Chin Department of Computer Science, The University of Hong Kong, Hong Kong, China Marco Cosentino Lagomarsino Computational and Quantitative Biology, University Pierre et Marie Curie, Paris, France CNRS, Paris, France Contributors xi

Paul Cotter Teagasc Food Research Centre, Moorepark, Fermoy, Co., Cork, Ireland Alimentary Pharmabiotic Centre, University College, Cork, Ireland Pedro Coutinho Centre National de la Recherche Scientiﬁque & Aix- Marseille Universite´, Marseille, France Don Cowan Centre for Microbial Ecology and Genomics (CMEG), Genome Research Institute (GRI), University of Pretoria, Hatﬁeld, Pretoria, South Africa David E. Crowley Enviromental Sciences, University of California, Riverside, Riverside, CA, USA Mulan Dai Semiarid Prairie Agricultural Research Centre, Agriculture and Agri-Food Canada, Swift Current, SK, Canada Rolf Daniel Institute of Microbiology and Genetics, Georg–August– University Go¨ttingen, Go¨ttingen, Germany Colin Davenport Hannover Medical School, Hannover, Germany Tomas de Wouters INRA, AgroParisTech, Jouy en Josas, France UMR Micalis, AgroParisTech, Jouy en Josas, France Ye Deng Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA Chandrika Deshpande Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW, Australia Floyd Dewhirst Department of Molecular Genetics, The Forsyth Institute, Cambridge, MA, USA Greg Ditzler Department of Electrical and Computer Engineering, Drexel University, Philadelphia, PA, USA Jo€el Dore´ INRA, AgroParisTech, Jouy en Josas, France US 1367 MetaGenoPolis, INRA, Jouy en Josas, France UMR Micalis, AgroParisTech, Jouy en Josas, France Inna Dubchak US Department of Energy Joint Genome Institute, Walnut Creek, CA, USA Lisa Durso Agroecosystem Management Research Unit, US Department of Agriculture, University of Nebraska, Lincoln- East Campus, Lincoln, NE, USA Chitra Dutta Structural Biology & Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, Kolkata, West Bengal, India Akihito Endo Department of Food and Cosmetic Science, Faculty of Bioindustry, Tokyo University of Agriculture, Abashiri, Hokkaido, Japan xii Contributors

K. Martin Eriksson Department of Biological and Environmental Sciences, University of Gothenburg, Go¨teborg, Sweden Jean Euze´by Society of Systematic Bacteriology and Veterinary (SBSV) & National Veterinary School de Toulouse (ENVT), Toulouse, France James A. Foster Department of Biological Sciences, Institute for Bioinformatics & Evolutionary Studies (IBEST), University of Idaho, Moscow, ID, USA Iddo Friedberg Department of Microbiology, Miami University, Oxford, OH, USA Limin Fu Center for Research in Biological Systems (CRBS), University of California, San Diego, La Jolla, CA, USA C. G. M. Gahan Department of Microbiology, School of Pharmacy & Alimentary Pharmabiotic Centre, University College Cork, Cork, Ireland Xiang Geng Dalian University of Technology, Dalian, China Jan Gerken Microbial Genomics and Bioinformatics Research Group, Max Planck Institute for Marine Microbiology, Bremen, Germany Wolfgang Gerlach Institute for Genomics and Systems Biology, Argonne National Laboratory, Argonne, IL, USA Tarini Shankar Ghosh Biosciences R & D, TCS Innovation Labs, Tata Research Development & Design Centre, Tata Consultancy Services Limited, Pune, MH, India Jack Gilbert Department of Ecology & Evolution, University of Chicago, Chicago, IL, USA Frank Oliver Glo¨ckner Microbial Genomics and Bioinformatics Group, Max Planck Institute for Marine Microbiology, Bremen, Germany Jacobs University Bremen gGmbH, Bremen, Germany Johannes Goll Informatics, The J. Craig Venter Institute, Rockville, MD, USA Juan M. Gonzalez Instituto de Recursos Naturales y Agrobiologia, IRNAS-CSIC, Seville, Spain Susumu Goto Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto, Japan Luigi Grassi Physics Department, Sapienza University of Rome, Rome, Italy Stefan J. Green University of Illinois at Chicago, Chicago, IL, USA Charles W. Greer National Research Council Canada, Montreal, QC, Canada Contributors xiii

Igor V. Grigoriev US Department of Energy Joint Genome Institute, Walnut Creek, CA, USA Jacopo Grilli Dipartimento di Fisica “G. Galilei”, CNISM and INFN, Università di Padova, Padova, Italy Saman K. Halgamuge Department of Mechanical Engineering, The University of Melbourne, Melbourne, VIC, Australia Chantal Hamel Semiarid Prairie Agricultural Research Centre, Agriculture and Agri-Food Canada, Swift Current, SK, Canada Jun Hang Viral Diseases Branch, WRAIR, Silver Spring, MD, USA Mohammed Monzoorul Haque Biosciences R & D, TCS Innovation Labs, Tata Research Development & Design Centre, Tata Consultancy Services Limited, Pune, MH, India Stephen J. Harrop School of Physics, University of New South Wales, Sydney, NSW, Australia Martin Hartmann Molecular Ecology, Agroscope Reckenholz-T€anikon Research Station ART, Zurich, Switzerland Zhili He Department of Microbiology and Plant Biology, Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA Bernard Henrissat Centre National de la Recherche Scientiﬁque & Aix-Marseille Universite´, Marseille, France Sarah Highlander Genomic Medicine, J. Craig Venter Institute, La Jolla, CA, USA Colin Hill Alimentary Pharmabiotic Centre, Department of Microbiology, University College, Cork, Ireland David Horn School of Physics and Astronomy, Tel Aviv University, Tel Aviv, Israel Arthur L. Hsu Department of Mechanical Engineering, The University of Melbourne, Melbourne, VIC, Australia Gangqing Hu Systems Biology Center, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA Shih-Ting Huang J. Craig Venter Institute, Rockville, MD, USA Daniel H. Huson Center for Bioinformatics, Algorithms in Bioinformatics, University of Tubingen,€ Tubingen,€ Germany Toshimichi Ikemura Nagahama Institute of Bio-Science and Technology, Nagahama, Shiga, Japan Hachiro Inokuchi Nagahama Institute of Bio-Science and Technology, Nagahama, Shiga, Japan xiv Contributors

Yuki Iwasaki Nagahama Institute of Bio-Science and Technology, Nagahama, Shiga, Japan Mukesh Jain Functional and Applied Genomics Laboratory, National Institute of Plant Genome Research (NIPGR), New Delhi, India Diego Javier Jime´nez Department of Microbial Ecology, University of Groningen, Center for Ecological and Evolutionary Studies (CEES), Groningen, The Netherlands Brian V. Jones Center for Biomedical and Health Science Research, University of Brighton, School of Pharmacy and Biomolecular Sciences, Brighton, East Sussex, UK I. King Jordan School of Biology, Georgia Institute of Technology, Atlanta, GA, USA Amit Joshi Department of Biotechnology & Bioinformatics, SGGS College, Chandigarh, India Olivier Jousson Laboratory of Microbial Genomics, Centre for Integrative Biology (CIBIO), University of Trento, Trento, Italy Minoru Kanehisa Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto, Japan Geun-Joong Kim Department of Biological Sciences, College of Natural Sciences, Chonnam National University, Gwangju, Republic of Korea Joel Kostka School of Biology and Earth & Atmospheric Sciences, Georgia Institute of Technology, Atlanta, GA, USA Masaaki Kotera Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto, Japan Renzo Kottmann Max Plank Institute for Marine Microbiology, Bremen, Germany Marcio R. Lambais Luiz de Queiroz College of Agriculture (ESALQ), University of Sa˜o Paulo (USP), Piracicaba, SP, Brazil Ronald F. Lamont Department of Gynecology and Obstetrics, Clinical Institute, University of Southern Denmark, Odense University Hospital, Odense, Denmark Division of Surgery, University College London, Northwick Park Institute of Medical Research Campus, London, UK Yemin Lan School of Biomedical Engineering, Science and Health, Drexel University, Philadelphia, PA, USA Nicolas Lapaque INRA, AgroParisTech, Jouy en Josas, France Contributors xv

Henry C. M. Leung Department of Computer Science, The University of Hong Kong, Hong Kong, China Weizhong Li J. Craig Venter Institute, La Jolla, CA, USA Mark Liles Department of Biological Sciences, Auburn University, Auburn, AL, USA Ho-Dong Lim Department of Biological Sciences, College of Natural Sciences, Chonnam National University, Gwangju, Republic of Korea Chien-Chi Lo Genome Science Group, Los Alamos National Laboratory, Los Alamos, NM, USA Hernan Lorenzi Informatics, J. Craig Venter Institute, Rockville, MD, USA Petra Louis Rowett Institute of Nutrition and Health, Microbiology Group, Gut Health Programme, University of Aberdeen, Aberdeen, UK Connie Lovejoy Department of Biology, Laval University, Que´bec, QC, Canada Vedran Lucic´ Molecular Biology Department, Division of Biology, Faculty of Science, University of Zagreb, Zagreb, Croatia Wolfgang Ludwig Lehrstuhl Fur€ Mikrobiologie, Technische Universit€at Munchen,€ Freising, Germany Haiwei Luo Department of Marine Sciences, University of Georgia, Athens, GA, USA Bridget Mabbutt Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW, Australia Norman J. MacDonald Faculty of Computer Science, Dalhousie University, Halifax, NS, Canada Emmanuelle Maguin INRA, AgroParisTech, Jouy en Josas, France Sharmila Mande Biosciences R & D, TCS Innovation Labs, Tata Research Development & Design Centre, Tata Consultancy Services Limited, Pune, MH, India Alan J. McCarthy Microbiology Research Group, Institute of Integrative Biology, Biosciences Building, University of Liverpool, Liverpool, UK Alice C. McHardy Algorithmic Bioinformatics, Heinrich Heine University Dusseldorf,€ Dusseldorf,€ Germany David Mead Lucigen Corporation, Middleton, WI, USA Marnix H. Medema Microbial Genomics and Bioinformatics Research Group, Max Planck Institute for Marine Microbiology, Bremen, Germany xvi Contributors

Folker Meyer Institute of Genomic and Systems Biology, Argonne National Laboratory, Argonne, IL, USA Kentaro Miyazaki Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Sapporo, Japan Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Sapporo, Japan Yuki Moriya Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto, Japan Mark Morrison Diamantina Institute, The University of Queensland, Woolloongabba, Brisbane QLD, Australia Michael J. Moser Lucigen Corporation, Middleton, WI, USA Raul Munoz Marine Microbiology Group, Department of Ecology and Marine Resources, Institut Mediterrani d’Estudis Avanc¸ats (CSIC-UIB), Illes Balears, Spain Akira Muto Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki, Aomori, Japan Heiko Nacke Institute of Microbiology and Genetics, Georg–August– University of Go¨ttingen, Go¨ttingen, Germany Istvan Nagy Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, Hungary Tania Nasreen Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada Shamima Nasrin Department of Biological Sciences, Auburn University, Auburn, AL, USA Josh D. Neufeld Department of Biology, University of Waterloo, Waterloo, ON, Canada R. Henrik Nilsson Department of Biological and Environmental Sciences, University of Gothenburg, Go¨teborg, Sweden Beifang Niu Center for Research in Biological Systems (CRBS), University of California, San Diego, La Jolla, CA, USA Brian D. Ondov National Biodefense Analysis and Countermeasures Center, Frederick, MD, USA Orla O’Sullivan Teagasc Food Research Centre, Moorepark, Fermoy, Co., Cork, Ireland Alimentary Pharmabiotic Centre, University College, Cork, Ireland Asli Ismihan Ozen The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark Contributors xvii

Stephan Pabinger Division of Bioinformatics, Biocenter, Innsbruck Medical University, Innsbruck, Austria AIT – Austrian Institute of Technology, Health & Environment Department, Molecular Diagnostics, Vienna, Austria Donovan H. Parks Faculty of Computer Science, Dalhousie University, Halifax, NS, Canada Australian Centre for Ecogenomics, University of Queensland, Brisbane QLD, Australia Ravi K. Patel Functional and Applied Genomics Laboratory, National Institute of Plant Genome Research (NIPGR), New Delhi, India Jo¨rg Peplies Ribocon GmbH, Bremen, Germany Adam M. Phillippy National Biodefense Analysis and Countermeasures Center, Frederick, MD, USA Rob Phillips Departments of Applied Physics and Bioengineering California Institute of Technology, California Institute of Technology, Pasadena, CA, USA Rembert Pieper J. Craig Venter Institute, Rockville, MD, USA Om Prakash National Centre for Cell Science, Pune, Maharashtra, India Elmar Pruesse Microbial Genomics and Bioinformatics Research Group, Max Planck Institute for Marine Microbiology, Bremen, Germany Pei-Yuan Qian KAUST Global Collaborative Program, Division of Life Science, Hong Kong University of Science and Technology, Hong Kong, China Christian Quast Microbial Genomics and Bioinformatics Research Group, Max Planck Institute for Marine Microbiology, Bremen, Germany Jean-Baptiste Ramond Centre for Microbial Ecology and Genomics (CMEG), Genome Research Institute (GRI), University of Pretoria, Hatﬁeld, Pretoria, South Africa Rachel Rezende Universidade Estadual de Santa Cruz, Laborato´rio de Biotecnologia Microbiana, Ilhe´us, BA, Brazil Lavanya Rishishwar Bioinformatics, Georgia Institute of Technology, Atlanta, GA, USA Francisco Rodriguez-Valera Microbiologia, Universidad Miguel Hernandez, Campus San Juan, San Juan, Alicante, Spain Masa Roller Bioinformatics Group, Molecular Biology Department, Division of Biology, Faculty of Science, University of Zagreb, Zagreb, Croatia xviii Contributors

Sandra Ronca Centre for Microbial Ecology and Genomics (CMEG), Genome Research Institute (GRI), University of Pretoria, Hatﬁeld, Pretoria, South Africa David J. Rooks Microbiology Research Group, Institute of Integrative Biology, Biosciences Building, University of Liverpool, Liverpool, UK Gail Rosen Department of Electrical and Computer Engineering, Drexel University, Philadelphia, PA, USA Paul Ross Teagasc Food Research Centre, Moorepark, Fermoy, Co., Cork, Ireland Alimentary Pharmabiotic Centre, University College, Cork, Ireland Ramon Rossello´-Mo´ra Marine Microbiology Group, Department of Ecology and Marine Resources, Institut Mediterrani d’Estudis Avanc¸ats (CSIC-UIB), Illes Balears, Spain Isaam Saeed Optimisation and Pattern Recognition Group, Melbourne School of Engineering, The University of Melbourne, Parkville, Australia Munmun Sarkar CSIR-Indian Institute of Chemical Biology, Kolkata, India Tulasi Satyanarayana Department of Microbiology, University of Delhi, New Delhi, India Karl-Heinz Schleifer Lehrstuhl Fur€ Mikrobiologie, Technische Universit€at Munchen,€ Freising, Germany Thomas W. Schoenfeld Lucigen Corporation, Middleton, WI, USA Matthew B. Scholz Genome Science Group, Los Alamos National Laboratory, Los Alamos, NM, USA Timmy Schweer Microbial Genomics and Bioinformatics Research Group, Max Planck Institute for Marine Microbiology, Bremen, Germany Vineet K. Sharma MetaInformatics Laboratory, Metagenomics and Systems Biology Group, Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal, India Martin Sievers Zurich University of Applied Sciences, Institute of Biotechnology, Waedenswil, Switzerland Jagtar Singh Department of Biotechnology, Panjab University, Chandigarh, India Roy Sleator Department of Biological Sciences, Cork Institute of Technology, Cork, Co. Cork, Ireland Jens Stoye Faculty of Technology, Bielefeld University, Bielefeld, Germany Hikaru Suenaga Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Sapporo, Japan Contributors xix

Moo-Jin Suh J. Craig Venter Institute, Rockville, MD, USA Fengzhu Sun Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, Dana and David Dornsife College of Letters, Arts and Sciences, Los Angeles, CA, USA Visaahini Sureshan Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW, Australia Arbel D. Tadmor TRON – Translational Oncology at the University Medical Center of the Johannes Gutenberg University Mainz, Mainz Germany Hideto Takami Microbial Genome Research Group, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan Eriko Takano Manchester Institute of Biotechnology, University of Manchester, Manchester, UK Sen-Lin Tang Bioinformatics Program, Taiwan International Graduate Program, Institute of Information Science, Academia Sinica, Taipei, Taiwan Shiyuyun Tang School of Biology, Biodiversity Research Center, Georgia Institute of Technology, Atlanta, GA, USA Todd D. Taylor Laboratory for Integrated Bioinformatics, Core for Precise Measuring and Modeling, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan Joaõ Carlos Teixeira Dias Universidade Estadual de Santa Cruz, Laborato´rio de Biotecnologia Microbiana, Ilheús, BA, Brazil Torsten Thomas School of Biotechnology and Biomolecular Sciences & Centre for Marine Bio-Innovation, University of New South Wales, Sydney, NSW, Australia Toshiaki Tokimatsu Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto, Japan Jo¨rg Tost Laboratory for Epigenetics and Environment, Centre National de Geńotypage, CEA-Institut de Geńomique, Evry, France Zlatko Trajanoski Division of Bioinformatics, Biocenter, Innsbruck Medical University, Innsbruck, Austria Susannah Tringe US Department of Energy Joint Genome Institute, Walnut Creek, CA, USA Huai-Kuang Tsai Institute of Information Science, Academia Sinica, Taipei, Taiwan Ching-Hung Tseng Bioinformatics Program, Taiwan International Gradu- ate Program, Biodiversity Research Center, Institute of Information Science, Academia Sinica, Taipei, Taiwan David Wayne Ussery Bioscience Division of Oak Ridge National Labora- tory, Oak Ridge National Laboratory, Oak Ridge, TN, USA xx Contributors

Joy D. Van Nostrand Department of Microbiology and Plant Biology, Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA Digvijay Verma Department of Microbiology, University of Delhi, New Delhi, India Kristian Vlahovicˇek Bioinformatics Group, Molecular Biology Department, Division of Biology, Faculty of Science, University of Zagreb, Zagreb, Croatia Jun Wang BGI Shenzhen, Shenzhen, China Lingling Wang Department of Animal Sciences, The Ohio State University, Columbus, OH, USA Tse-Yi Wang Department of Medical Research, Mackay Memorial Hospital, New Taipei City, Taiwan Yi Wang Department of Computer Science, The University of Hong Kong, Hong Kong, China Yong Wang Division of Deep Sea Science, Sanya Institute of Deep Sea Science and Engineering, San Ya, Hainan, China Yumei Wang Dalian University of Technology, Dalian, China Tandy Warnow Institute for Genomic Biology, University of Illinois, IL, USA Tilmann Weber Interfakult€ares Institut fur€ Mikrobiologie und Infektionsmedizin Tubingen,€ Mikrobiologie/Biotechnologie, Eberhard- Karls Universit€at, Tubingen,€ Germany Martin Wu Department of Biology, University of Virginia, Charlottesville, VA, USA Sitao Wu Center for Research in Biological Systems (CRBS), University of California, San Diego, La Jolla, CA, USA Li Charlie Xia Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, Dana and David Dornsife College of Letters, Arts and Sciences, Los Angeles, CA, USA Jianping Xu Department of Biology, McMaster University, Hamilton, ON, Canada Yuko Yamada Nagahama Institute of Bio-Science and Technology, Nagahama, Shiga, Japan Jian Yang MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College (CAMS&PUMC), Beijing, People’s Republic of China Pablo Yarza Ribocon GmbH., Bremen, Germany Contributors xxi

Yuzhen Ye Indiana University, School of Informatics and Computing, Bloomington, IN, USA Etienne Yergeau National Research Council Canada, Montreal, QC, Canada Pelin Yilmaz Microbial Genomics and Bioinformatics Research Group, Max Planck Institute for Marine Microbiology, Bremen, Germany S. M. Yiu Department of Computer Science, The University of Hong Kong, Hong Kong, China Zhongtang Yu Department of Animal Sciences, Environmental Science Graduate Program, The Ohio State University, Columbus, OH, USA Marı´a Mercedes Zambrano Molecular Genetics and Microbial Ecology, Corporacio´n CorpoGen, Bogotá, DC, Colombia Xinqing Zhao School of Life Science and Biotechnology, Dalian University of Technology, Dalian, People’s Republic of China Jizhong (Joe) Zhou Department of Microbiology and Plant Biology, Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA Department of Environmental Science and Engineering, Tsinghua University, Beijing, China Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA Huaiqiu Zhu Department of Biomedical Engineering, and Center for Theoretical Biology, Peking University, Beijing, China Zhengwei Zhu Center for Research in Biological Systems (CRBS), University of California, San Diego, La Jolla, CA, USA