Bioinformatics in Aquaculture Principles and Methods

About this book

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. Bioinformatics in Aquaculture: Principles and Methods 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.

Bioinformatics in Aquaculture: Principles and Methods is a vital tool for all those working in genomics, molecular biology, biochemistry and genetics related to aquaculture, and computational and biological sciences.

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 and Multi-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

Customer Reviews

Biography

Zhanjiang (John) Liu is currently the Associate Provost and Associate Vice President for Research at Auburn University, and a Professor in the School of Fisheries, Aquaculture and Aquatic Sciences, and Program of Cell and Molecular Biosciences, Auburn University, Auburn, Alabama, USA.