Pan Genome

The Introduction of Pan Genome Sequencing

The concept of the pan-genome encompasses the entirety of genes present across all strains within a given species, thereby offering a comprehensive perspective on genetic diversity that transcends the limitations of individual genome sequences. It includes two primary components:

• Core Genome: This segment comprises genes ubiquitously present across all strains of the species. These core genes are typically associated with fundamental biological functions and primary phenotypic traits, thereby reflecting the evolutionary stability of the species. For instance, in Escherichia coli, core genes include those implicated in essential cellular processes such as DNA replication and transcription.
• Variable (Accessory/Dispensable) Genome: In contrast, this segment encompasses genes that are found in only a subset of strains or individuals within the species. These accessory genes often encode for specific adaptations or unique traits, including factors such as antibiotic resistance or virulence. For example, in Streptococcus pneumoniae, accessory genes contribute to variations in pathogenicity and resistance profiles among different strains.

Through the comprehensive study of the pan-genome, researchers can gain insights into the full spectrum of genetic variability within a species, facilitating a deeper understanding of its evolutionary dynamics, functional adaptations, and potential response to environmental pressures.

Figure 1. Composition of a pan genome

The pursuit of pan-genome sequencing involves leveraging high-throughput sequencing technologies alongside sophisticated bioinformatics tools. This approach entails the meticulous construction of sequencing libraries followed by comprehensive sequencing of individuals, subspecies, or lineages within a species. Subsequent assembly of these sequences leads to the development of a pan-genome map. This map serves to enrich the genetic repository of the species and enables the investigation of crucial biological questions, contributing significantly to our understanding of genetic diversity and evolutionary processes.

Why is Pan-Genome Research Essential

In the extensive course of evolution, influenced by geographical and environmental factors, individual organisms develop highly unique genetic traits. A single reference genome is insufficient to encompass the complete genetic information of an entire species. In other words, relying solely on a single reference genome for studies on genetic domestication and variation can result in the loss of significant genomic content, as many unique sequences are not represented in the reference genome.

Moreover, the decreasing cost of genome sequencing has made pan-genome research increasingly viable in recent years. This reduction in cost facilitates the exploration of genetic diversity at a depth and scale that was previously unattainable. Consequently, the study of pan-genomes has become a burgeoning field, offering profound insights into the complexity of genomic information and the adaptive potential of species.

Difference Between the Pan-Genome and the Whole Genome

The concept of the whole genome pertains to the complete set of genetic material found within a single individual or strain, typically leveraged as a reference in genomic research. In contrast, the pan-genome amalgamates genetic information from multiple individuals or strains, offering a more holistic and comprehensive genetic landscape of the species.

Key Differences

• Scope: The whole genome delineates the genetic architecture of a single strain. By contrast, the pan-genome encapsulates all genetic variants present across multiple strains, thereby capturing a broader and more inclusive spectrum of genetic diversity.
• Resolution: Pan-genome analysis elucidates genetic variations that may remain undetected when relying solely on a single reference genome. This encompasses unique accessory genes that drive strain-specific traits and adaptations.

For instance, examination of the pan-genome of Mycobacterium tuberculosis reveals considerable genetic variability among different strains, a factor of paramount importance for understanding mechanisms of drug resistance and for the development of effective therapeutic interventions.

Advantages of Pan Genome

• Enrich genome information of the species through sequencing the subspecies and individuals
• Quickly find genes or structural variations of genes related to important traits based on study of variable genome
• Study the differences within species from the perspective of unique gene sequences
• Small population, cost and time efficient

Applications of Pan Genome

• Species Evolution and Phylogenetics: Assists in tracing evolutionary relationships and genetic diversity among species.
• Trait Discovery and Breeding: Identifies genes associated with desirable traits for improved crop breeding.
• Pathogen Research: Reveals genetic variations in pathogens related to virulence and resistance, informing control measures.
• Ecological and Environmental Studies: Provides insights into species' adaptations to different environments and ecological niches.

Pan Genome Workflow

Service Specifications

	Sample Requirements Sample Type: Genomic DNA; Small fragment library: ≥1 μg; 2 Kb to 6 Kb large fragment library: ≥20 μg; 10 Kb large fragment library: ≥30 μg; 20 Kb and 40 Kb large fragment libraries: ≥60 μg; For whole-genome sequencing, the required amount of sample DNA is approximately 500 μg to 1 mg; Sample Concentration: Small fragment library ≥30 ng/μl; Large fragment library: ≥133 ng/μl; Sample Purity: OD260/280 ratio should be between 1.8 and 2.0. All DNA should be RNase-treated and should show no degradation or contamination. Note: Sample amounts are listed for reference only. For detailed information, please contact us with your customized requests.
Click	Sequencing Strategy Simple genome (genome size <2Gb, heterozygosity <0.5%, repeated sequence ratio <50%); Complex genome (genome size >2Gb, heterozygosity >0.5%, repeated sequence ratio >50%); ONT long reads ONT ultra-long reads PacBio continuous long reads (CLRs) PacBio HiFi reads
	Bioinformatics Analysis We provide multiple customized bioinformatics analyses: Pan-genome build Assembly evaluation Genome annotation Repeat sequence annotation Gene function annotation Non-coding RNA annotation Comparative genomic analysis Biological analysis …and more Note: Recommended data outputs and analysis contents displayed are for reference only. For detailed information, please contact us with your customized requests.

Analysis Pipeline

Deliverables

• The original sequencing data
• Experimental results
• Data analysis report
• Details in Pan Genome for your writing (customization)