Bioinformatics in Aquaculture: Principles and Methods

Bioinformatics derives knowledge from computer analysis of biological data. In particular, genomic and transcriptomic datasets are processed, analysed and, whenever possible, associated with experimental results from various sources, to draw structural, organizational, and functional information relevant to biology. Research in bioinformatics includes method development for storage, retrieval, and analysis of the data. Bioinformatics in Aquaculture provides the most up to date reviews of next generation sequencing technologies, their applications in aquaculture, and principles and methodologies for the analysis of genomic and transcriptomic large datasets using bioinformatic methods, algorithm, and databases. The book is unique in providing guidance for the best software packages suitable for various analysis, providing detailed examples of using bioinformatic software and command lines in the context of real world experiments. This book is a vital tool for all those working in genomics, molecular biology, biochemistry and genetics related to aquaculture, and computational and biological sciences.

Table of Contents:
About the Editor xxiii List of Contributors xxv Preface xxxi Part I Bioinformatics Analysis of Genomic Sequences 1 1 Introduction to Linux and Command Line Tools for Bioinformatics 3 Shikai Liu and Zhanjiang Liu 2 Determining Sequence Identities: BLAST, Phylogenetic Analysis, and Syntenic Analyses 30 Sen Gao, Zihao Yuan, Ning Li, Jiaren Zhang and Zhanjiang Liu 3 Next-Generation Sequencing Technologies and the Assembly of Short Reads into Reference Genome Sequences 43 Ning Li, Xiaozhu Wang and Zhanjiang Liu 4 Genome Annotation: Determination of the Coding Potential of the Genome 74 Ruijia Wang, Lisui Bao, Shikai Liu and Zhanjiang Liu 5 Analysis of Repetitive Elements in the Genome 86 Lisui Bao and Zhanjiang Liu 6 Analysis of Duplicated Genes andMulti-Gene Families 98 Ruijia Wang and Zhanjiang Liu 7 Dealing with Complex Polyploidy Genomes: Considerations for Assembly and Annotation of the Common Carp Genome 110 Peng Xu, Jiongtang Li and Xiaowen Sun Part II Bioinformatics Analysis of Transcriptomic Sequences 123 8 Assembly of RNA-Seq Short Reads into Transcriptome Sequences 125 Jun Yao, Chen Jiang, Chao Li, Qifan Zeng and Zhanjiang Liu 9 Analysis of Differentially Expressed Genes and Co-expressed Genes Using RNA-Seq Datasets 135 Chao Li, Qifan Zeng, Chen Jiang, Jun Yao and Zhanjiang Liu 10 Gene Ontology, Enrichment Analysis, and Pathway Analysis 150 Tao Zhou, Jun Yao and Zhanjiang Liu 11 Genetic Analysis Using RNA-Seq: Bulk Segregant RNA-Seq 169 Jun Yao, RuijiaWang and Zhanjiang Liu 12 Analysis of Long Non-coding RNAs 179 Ruijia Wang, Lisui Bao, Shikai Liu and Zhanjiang Liu 13 Analysis of MicroRNAs and Their Target Genes 200 Shikai Liu and Zhanjiang Liu 14 Analysis of Allele-Specific Expression 228 Yun Li, Ailu Chen and Zhanjiang Liu 15 Bioinformatics Analysis of Epigenetics 247 Yanghua He and Jiuzhou Song Part III Bioinformatics Mining and Genetic Analysis of DNA Markers 275 16 Bioinformatics Mining of Microsatellite Markers from Genomic and Transcriptomic Sequences 277 Shaolin Wang, Yanliang Jiang and Zhanjiang Liu 17 SNP Identification from Next-Generation Sequencing Datasets 288 Qifan Zeng, Luyang Sun, Qiang Fu, Shikai Liu and Zhanjiang Liu 18 SNP Array Development, Genotyping, Data Analysis, and Applications 308 Shikai Liu, Qifan Zeng, Xiaozhu Wang and Zhanjiang Liu 19 Genotyping by Sequencing and Data Analysis: RAD and 2b-RAD Sequencing 338 Shi Wang, Jia Lv, Jinzhuang Dou, Qianyun Lu, Lingling Zhang and Zhenmin Bao 20 Bioinformatics Considerations and Approaches for High-Density Linkage Mapping in Aquaculture 356 Yun Li, Shikai Liu, Ruijia Wang, Zhenkui Qin and Zhanjiang Liu 21 Genomic Selection in Aquaculture Breeding Programs 380 Mehar S. Khatkar 22 Quantitative Trait Locus Mapping in Aquaculture Species: Principles and Practice 392 Alejandro P. Gutierrez and Ross D. Houston 23 Genome-wide Association Studies of Performance Traits 415 Xin Geng, Degui Zhi and Zhanjiang Liu 24 Gene Set Analysis of SNP Data from Genome-wide Association Studies 434 Shikai Liu, Peng Zeng and Zhanjiang Liu Part IV Comparative Genome Analysis 461 25 Comparative Genomics Using CoGe, Hook, Line, and Sinker 463 Blake Joyce, Asher Baltzell, Matt Bomhoff and Eric Lyons 26 NCBI Resources Useful for Informatics Issues in Aquaculture 491 Zihao Yuan, Yujia Yang, Shikai Liu and Zhanjiang Liu 27 Resources and Bioinformatics Tools in Ensembl 508 Yulin Jin, Suxu Tan, Jun Yao and Zhanjiang Liu 28 iAnimal: Cyberinfrastructure to Support Data-driven Science 527 Blake Joyce, Asher Baltzell, Fiona McCarthy, Matt Bomhoff and Eric Lyons Conclusion 544 Acknowledgments 545 References 545 Index 547