Pan-genomics: Applications, Challenges, and Future Prospects

Front Matter
Copyright
Dedication
Contributors
Editors biography
Preface
Pan-omics focused to Crick's central dogma
	Introduction
		Brief overview of pan-genomics
		Open and closed pan-genomes
		Computational methods used in pan-genomics
		Applications of pan-genomics in evolutionary studies
	Applications of Pan-genomics in Bacteria
		Applications of pan-genomics in model bacteria
		Applications of pan-genomics in Corynebacterium diphtheriae and Corynebacterium ulcerans
		Applications of pan-genomics in multidrug-resistant human pathogenic bacteria and pan-resistome
		Applications of pan-genomics in veterinary pathogens
		Applications of pan-genomics in aquatic pathogenic bacteria
		Pan-genomics applications for therapeutics
		Pan-genomics applications for probiotics
	Pan-genomics of virus and its applications
	Pan-genomics of plants and its applications
		Applications of pan-genomics in plant pathogens
	Genomics of algae and its applications
	Pan-metagenomics and human microbiome
	Pan-proteomics and its applications
	Pan-transcriptomics and its applications
	Pan-cancer analysis and its applications
	Conclusions
	References
Bioinformatics approaches applied in pan-genomics and their challenges
	Introduction
	Pan-genome analysis
		Pan-genome approaches
		Mathematical model: Heaps law
		Software packages and tools
			Composition and annotation
			Pan-genome tools
			Machine learning applied to pan-genome
	Challenges
		Pan-genome analysis with draft genomes
		Perspectives for pan-genome applied to the human genome
	Conclusion and future direction
	References
	Further reading
Evolutionary pan-genomics and applications
	Introduction
	Computational methods in evolutionary pan-genomics
	Evolutionary pan-genomics of prokaryotes
	Evolutionary pan-genomics of eukaryotes
	Orthology prediction and genomic plasticity in pan-genomics
	Phylogenomics and genomic epidemiology in pan-genomics
	Future directions
	Conclusion
	References
	Further reading
Insights into old and new foes: Pan-genomics of Corynebacterium diphtheriae and Corynebacterium ulcerans
	Corynebacterium diphtheriae and Corynebacterium ulcerans
	Phenotypic and genotypic separation of strains-A historical retrospective
	Beginning of the genome era
	Pan-genomics of C. diphtheriae
		Biochemical subdivision of C. diphtheriae into biovars
		Virulence characteristics and the variation in the degree of pathogenesis
		Genomic characterization of outbreak strains
	Genomics of C. ulcerans
		Virulence potential of C. ulcerans strains
		Genomic plasticity
		Zoonotic transmission
	Toxin variation and diphtheria toxoid vaccine
	Conclusions and future directions
	References
Pan-genomics of veterinary pathogens and its applications
	Introduction
	Pan-genomics studies of pathogenic bacteria causing veterinary and zoonotic diseases
		Corynebacterium pseudotuberculosis
		Corynebacterium ulcerans
		Streptococcus suis
		Brachyspira hyodysenteriae
		Moraxella bovoculi
		Pasteurella multocida
		Mannheimia haemolytica
		Clostridium botulinum
		Campylobacter
		Streptococcus agalactiae
		Francisella tularensis
		Corynebacterium diphtheriae
		Brucella spp.
	Conclusions
	References
Pan-genomics of plant pathogens and its applications
	Introduction
	Pan-genomics of plant pathogens
		Pan-genomics of plant pathogenic bacteria
			Pectobacteria
			Pectobacterium parmentieri
			Pantoea ananatis
			Erwinia amylovora
			Burkholderia
			Xylella fastidiosa
		Pan-genomics of plant pathogenic fungi
			Puccinia graminis
			Zymoseptoria tritici
	Applications of plant pathogen's pan-genomics
		Detection and characterization of new strains
		Evaluating strain diversity
		Revealing the pathogenic evolution
		Development of universal vaccines
		Role in SNP discovery
		Differentiation of virulent and nonvirulent strains
		Development of fungicides
	Analyzing pan-genomes
		Approaches
		Overview of pan-genome analysis tools
	Conclusions and future directions
	References
Pan-genomics of food pathogens and its applications
	Introduction
	Pan-genomics of E. coli
	Pan-genomics of Salmonella enterica
	Pan-genomics of Clostridium spp.
	Pan-genomics of L. monocytogenes
	Pan-genomics of S. aureus
	Conclusions and future directives
	References
Pan-genomics of aquatic animal pathogens and its applications
	Genome study of aquaculture pathogens
	The spread of aquatic pathogens and advent of next-generation sequencing
	The aquatic bacterial genome sequence and its open access data
	Using the comparative pan-genome to analyze aquatic pathogenic bacteria
		The proliferation of software packages and tools for infectious disease analysis
		Pan-genome composition of aquatic bacterial pathogens
			Introduction
			Inside the pan-genome of aquatic pathogenic bacteria
		Pan-genome analysis of aquatic pathogenic species: the case of Edwardsiella and Aeromonas
			Edwarsiella genus
			Aeromonas genus
	Conclusions and the avenues of pan-genome for analyzing aquatic pathogens
	References
Pan-genomics of model bacteria and their outcomes
	Introduction
	Technical approaches and their outcomes
	Pan-genomics of model bacteria
		Streptococcus agalactiae
		Neisseria meningitidis
		Staphylococcus aureus
		Escherichia coli
		Streptococcus pyogenes
		Haemophilus influenzae
		Streptococcus pneumoniae
	Conclusion
	References
Pan-genomics of multidrug-resistant human pathogenic bacteria and their resistome
	Introduction
	The pan-genomics of human pathogens
	The pan-genome of resistant bacteria
	The pan-genome of emergent resistant bacteria
	PATRIC and other databases
	Core and accessory genomes of antibiotic-resistant bacteria
	Pan-genome and resistome
	New challenges of pan-genome strategy
	Conclusion
	References
	Further reading
Pan-genomics of virus and its applications
	Next-generation sequencing strategies
	Genomic surveillance
	Genomic epidemiology
	Bioinformatic tools
		Bioinformatic tools used in pan-genomic studies
			Panseq-Pan-genome sequence analysis program
			PGAP-Pan-genome analysis pipeline
			EDGAR (efficient database framework for comparative genome analyses using BLAST score ratios)
			ITEP-Integrated toolkit for the exploration of microbial pan-genomes
			GET_HOMOLOGUES
			PanFunPro: PAN-genome analysis based on FUNctionalPROfiles
			CASTOR
			Genome Detective
		Future improvements
	Conclusions
	References
Pan-genomics of fungi and its applications
	Introduction
	Application of pan-genomics of fungi based on meta-analysis
		Application of pan-genomics on advantageous fungus
		Application of pan-genomics in disadvantageous fungus
	Conclusions and future prospective
	References
Genomics of algae: Its challenges and applications
	Diversity in algae and their evolutionary insights
	Advancements in genomics and its importance to ecologists
	Ecological and economic importance of algae
	Genomics of microalgae
		Picoplanktonic marine cyanobacterial species
		Eukaryotic phytoplankton
	Genomics of macroalgae
		Green algae
		Red algae
		Brown algae
	Conclusions
	References
	Further reading
Pan-genomics of plants and its applications
	Plant pan-genome concept
	Structure and dynamics of plant pan-genome
	Plant pan-genome studies
		Pan-genome of agronomically important crops
	Plant pan-genome analysis tools
		Approaches to characterize plant pan-genomes
			k-mer-based approaches
			Comparative de novo assembly approach
			Iterative assembly approach
	Applications of plant pan-genomics
		Genetic mapping approaches and plant pan-genomics
		Pan-genomics in crop diversity
		Pan-genomics in adaptations to climate changes
		Pan-genomics in plant breeding
		Pan-genomics in production of desirable traits
	Conclusions and future directions
	References
Pan-cancer analysis and applications
	Introduction
	Methods in pan-cancer analysis
	Pan-cancer analysis findings and applications
	Limitations of analysis
	Future prospects
	Summary
	References
	Further reading
Reverse vaccinology and drug target identification through pan-genomics
	Introduction and goals of pan-genomics and reverse vaccinology
		RV vs conventional vaccinology
	Outcomes of pan-genomics and RV
	Core genome as the basis of the novel and broad-spectrum drugs and vaccine candidates
	Pan-genomics
		Drug targets identification employing pan-genomics
			Determination of nonhomologous protein sequences to the human proteome
			Identification of virulence factors and essential proteins
			Metabolic pathway analysis
			Prediction of subcellular localization
			Assessment of protein involvement in conferring antibiotic resistance
			Druggability potential of shortlisted sequences
		Advantages and success stories
		Bioinformatics tools to determine pan-genome
	Reverse vaccinology
		RV methodology to predict potential vaccine candidates
			Selection of host nonhomologous, essential, and virulent proteins
			Subcellular localization check
			Transmembrane helices filter
			Physicochemical characterization
			Metabolic pathway analysis
			Epitope prediction
		Tools available for RV
		Currently available effective RV vaccines
	Limitations of RV and pan-genomics
	Future prospects
	References
	Further reading
Pan-metagenomics: An overview of the human microbiome
	Introduction
	Gut pan-metagenome
	Pan-microbiome and its built environment
	Pan-microbiome in pharmacokinetic studies
	The large-scale microbiome projects
	Conclusion
	References
Pan-transcriptomics and its applications
	Introduction
	Methodologies in transcriptomics
		Microarray
		Next-generation sequencing
	Computational framework of pan-transcriptomics
	Prokaryotic data analysis software
		WoPPER
		JCoast
		EDGAR
		Trimmomatic
		Roary
	Eukaryotic data analysis software
		AGAPE
		SHOE
		TaxMapper
	Applications
	Prokaryotic examples
		View of the pan-genome and pan-regulon of Dickeya solani
		Pan-regulon study of Listeria monocytogenes σB
	Eukaryotic examples
		Insight into maize pan-transcriptome
		Pan-transcriptome analysis of barley
		Pan-transcriptome reconstruction in Phaeoacremonium minimum
	Conclusion and future prospects
	References
Pan-proteomics: Technologies, applications, and challenges
	Introduction
	Pan-proteomics concept and proteomics technologies used in pan-proteomics
	Bioinformatics strategies/tools used in proteomics
	Pan-proteomics applications and outcomes in microbes
	Pan-proteomics applications and outcomes in plants
	Pan-proteomics applications and outcomes in animals
	Conclusions and future prospective
	References
Pan-metabolomics and its applications
	Introduction
	Methodologies of pan-metabolomics
		Sample collection and preparation
		Data collection
		Data analysis platform
		Database of metabolomics
	Application of pan-metabolomics
		Drug discovery
		Disease research
		Plant metabolomics
		Microbial research
		Nutritional research
		Environmental sciences
	Development of pan-metabolomics in the future
	References
Pan-interactomics and its applications
	Introduction
	Computational analysis of interactome
	Databases and its types
		Viral interactomes
		Bacterial interactomes
		Eukaryotic interactomes
		Predicted interactomics
	In vivo pan-interactome mapping
		Label-free technologies
			Y2H system
			Surface plasmon resonance
		Conventional label-based detection technologies
		Novel detection techniques for protein microarrays
	Applications
		Role in disease diagnosis
		Role in computational drug discovery
		Role in identification of novel orphan gene in a pathway
		Role in understanding the parallel evolution of organisms
		Role in mutation studies
	Conclusions and future perspectives
	References
Index
	A
	B
	C
	D
	E
	F
	G
	H
	I
	J
	K
	L
	M
	N
	O
	P
	Q
	R
	S
	T
	U
	V
	W
	X
	Y
	Z