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Pan-Genomics: Applications, Challenges, and Future Prospects Pan-Genomics: Applications, Challenges, and Future Prospects PAN-GENOMICS: APPLICATIONS, CHALLENGES, AND FUTURE PROSPECTS PAN-GENOMICS: APPLICATIONS, CHALLENGES, AND FUTURE PROSPECTS Edited by DEBMALYA BARH, PhD Scientist, Centre for Genomics and Applied Gene Technology, Institute of Integrative Omics and Applied Biotechnology (IIOAB) Nonakuri, India SIOMAR SOARES, PhD Assistant Professor at Department of Immunology, Microbiology and Parasitology, Institute of Biological Sciences and Natural Sciences, Federal University of Triangulo Mineiro (UFTM) Uberaba, Brazil SANDEEP TIWARI, PhD Post-Doctoral Researcher, Laboratory of Cellular and Molecular Genetics, Federal University of Minas Gerais (UFMG) Belo Horizonte, Brazil VASCO AZEVEDO, PhD Senior Professor, Institute of Biological Sciences, Federal University of Minas Gerais (UFMG) Belo Horizonte, Brazil Academic Press is an imprint of Elsevier 125 London Wall, London EC2Y 5AS, United Kingdom 525 B Street, Suite 1650, San Diego, CA 92101, United States 50 Hampshire Street, 5th Floor, Cambridge, MA 02139, United States The Boulevard, Langford Lane, Kidlington, Oxford OX5 1GB, United Kingdom © 2020 Elsevier Inc. All rights reserved. No part of this publication may be reproduced or transmitted in any form or by any means, electronic or mechanical, including photocopying, recording, or any information storage and retrieval system, without permission in writing from the publisher. Details on how to seek permission, further information about the Publisher’s permissions policies and our arrangements with organizations such as the Copyright Clearance Center and the Copyright Licensing Agency, can be found at our website: www.elsevier.com/permissions. This book and the individual contributions contained in it are protected under copyright by the Publisher (other than as may be noted herein). Notices Knowledge and best practice in this field are constantly changing. As new research and experience broaden our understanding, changes in research methods, professional practices, or medical treatment may become necessary. Practitioners and researchers must always rely on their own experience and knowledge in evaluating and using any information, methods, compounds, or experiments described herein. In using such information or methods they should be mindful of their own safety and the safety of others, including parties for whom they have a professional responsibility. To the fullest extent of the law, neither the Publisher nor the authors, contributors, or editors, assume any liability for any injury and/or damage to persons or property as a matter of products liability, negligence or otherwise, or from any use or operation of any methods, products, instructions, or ideas contained in the material herein. Library of Congress Cataloging-in-Publication Data A catalog record for this book is available from the Library of Congress British Library Cataloguing-in-Publication Data A catalogue record for this book is available from the British Library ISBN 978-0-12-817076-2 For information on all Academic Press publications visit our website at https://www.elsevier.com/books-and-journals Publisher: Stacy Masucci Acquisitions Editor: Rafael E. Teixeira Editorial Project Manager: Sara Pianavilla Production Project Manager: Maria Bernard Designer: Greg Harris Typeset by SPi Global, India Dedication I dedicate this book to my mother late Cacilda de Fa´tima Soares, a strong woman who always worked hard to give the best to all her sons. Dr. Siomar de Castro Soares I dedicate this book to my maternal grandfather late Prof. Ramawadh Mishra, a philosopher and guide who had enlightened me to find the meaning of life and shaped my future. Dr. Sandeep Tiwari I dedicate this book to my father-in-law late Anacer Abi-ackel. The Arabic to English translation of his first name and family name says it all. “Anacer” means helps us and “Abi-ackel” is synonyms to father of wisdom. You are the father of wisdom who always helped us. Prof. Vasco Azevedo I dedicate this book to Nityananda Sarkar, signifying the meaning of his name; he is always a happy man whatever the circumstances may be. Dr. Debmalya Barh Contributors Talita Emile Ribeiro Adelino Laborato´rio de Genetica Celular e Molecular, ICB, Universidade Federal de Minas Gerais; Fundac¸a˜o Ezequeil Dias (Funed), Belo Horizonte, Brazil Jamil Ahmad Research Center for Modeling & Simulation (RCMS), National University of Sciences and Technology (NUST), Islamabad, Pakistan Shahbaz Ahmed Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan Luiz Carlos Junior Alcantara PG Program in Bioinformatics, Institute of Biological Sciences, Federal University of Minas Gerais (UFMG), Belo Horizonte; Laborato´rio de Flavivı´rus, Instituto Oswaldo Cruz, Fundac¸a˜o Oswaldo Cruz, Rio de Janeiro; Laborato´rio de Genetica Celular e Molecular, ICB, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil Amjad Ali Department of Plant Biotechnology, Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Islamabad, Pakistan Rabia Amir Department of Plant Biotechnology, Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Islamabad, Pakistan Fabricio Araujo Institute of Biological Sciences, Federal University of Para´ (UFPA), Belem, Brazil Muneeba Arveen Department of Plant Biotechnology, Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Islamabad, Pakistan Vasco Azevedo PG Program in Bioinformatics, Institute of Biological Sciences, Federal University of Minas Gerais (UFMG), Belo Horizonte, Brazil Jahanzaib Azhar Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan Luciana Balbo State University of Londrina, Londrina, Brazil Li Bao National Clinical Research center for Cancer, Tianjin Medical University Cancer Institute and Hospital; Key Laboratory of Cancer Prevention and Therapy, Tianjin, China xv xvi Contributors Debmalya Barh Centre for Genomics and Applied Gene Technology, Institute of Integrative Omics and Applied Biotechnology (IIOAB), Purba Medinipur, India Fernanda Khouri Barreto Laborato´rio de Patologia Experimental, Instituto Gonc¸alo Moniz, Fiocruz Bahia; Instituto Multidisciplinar em Sau´de—IMS, Universidade Federal da Bahia (UFBA), Salvador, Brazil Attya Bhatti Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan Andreas Burkovski Friedrich-Alexander-Universit€at Erlangen-Nurnberg,€ Erlangen, Germany Roberta Torres Chideroli State University of Londrina, Londrina, Brazil Mauricio Corredor GEBIOMIC Group, FCEN, University of Antioquia, Medellin, Colombia Kenny da Costa Pinheiro Institute of Biological Sciences, Federal University of Para´ (UFPA), Belem, Brazil Artur Luiz da Costa Silva Institute of Biological Sciences, Federal University of Para´ (UFPA), Belem, Brazil Hamza Arshad Dar Department of Plant Biotechnology, Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Islamabad, Pakistan Letı´cia de Castro Oliveira Department of Immunology, Microbiology and Parasitology, Institute of Biological Science and Natural Sciences, Federal University of Tri^angulo Mineiro (UFTM), Uberaba, Brazil Siomar de Castro Soares Department of Immunology, Microbiology and Parasitology, Institute of Biological Science and Natural Sciences, Federal University of Tri^angulo Mineiro (UFTM), Uberaba, Brazil Jaqueline Goes de Jesus Laborato´rio de Flavivı´rus, IOC, Fundac¸a˜o Oswaldo Cruz, Rio de Janeiro; Laborato´rio de Patologia Experimental, Instituto Gonc¸alo Moniz, Fiocruz Bahia, Salvador, Brazil Thiago de Jesus Sousa PG Program in Bioinformatics, Institute of Biological Sciences, Federal University of Minas Gerais (UFMG), Belo Horizonte, Brazil Tulio de Oliveira KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa Stephane Fraga de Oliveira Tosta PG Program in Bioinformatics, Institute of Biological Sciences, Federal University of Minas Gerais (UFMG); Laborato´rio de Genetica Celular e Molecular, ICB, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil Ulisses de Pa´dua Pereira State University of Londrina, Londrina, Brazil Contributors xvii Vagner de Souza Fonseca Laborato´rio de Flavivı´rus, IOC, Fundac¸a˜o Oswaldo Cruz, Rio de Janeiro; Laborato´rio de Genetica Celular e Molecular, ICB, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil; KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa Dipali Dhawan Baylor Genetics, Houston, TX, United States Cesar Toshio Facimoto State University of Londrina, Londrina, Brazil Nuno Rodrigues Faria Department of Zoology, University of Oxford, Oxford, United Kingdom Nosheen Fatima Department of Plant Biotechnology, Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Islamabad, Pakistan Henrique Cesar Pereira Figueiredo AQUACEN, National Reference Laboratory for Aquatic Animal Diseases, Ministry of Fisheries and Aquaculture, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil Marta Giovanetti PG Program in Bioinformatics, Institute of Biological Sciences, Federal University of Minas Gerais (UFMG), Belo Horizonte; Laborato´rio de Flavivı´rus, IOC,
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