Tiffany Haney
A pan-genome is the entire set of genes from all strains within a clade. It is the sum of a clade's genomes and can be broken down into a core pan-genome, a shell pan-genome, and a cloud pan-genome. The core pan-genome contains genes present in all individuals, the shell pan-genome contains genes present in two or more strains, and the cloud pan-genome contains genes only found in a single strain. The pan-genome was first conceived for bacterial species in 2005 and has since been applied to other species, including humans.
| Characteristics | Values |
|---|---|
| Definition | The whole set of genes from all strains within a clade |
| Alternative Names | Pangenome, supragenome |
| Parts | Core pangenome, shell pangenome, cloud pangenome |
| Core Pangenome | Contains genes present in all individuals |
| Shell Pangenome | Contains genes present in two or more strains |
| Cloud Pangenome | Contains genes only found in a single strain |
| Cloud Pangenome Synonyms | Accessory genome, peripheral genome |
| Core Pangenome Synonyms | Hard core, soft core, extended core |
| Core Pangenome Genes | Often related to housekeeping functions and primary metabolism of the lineage |
| Dispensable Pangenome | Contains genes shared by a subset of the strains |
| Dispensable Pangenome Synonyms | Flexible regions |
| Core Pangenome Size | Depends on the phylogenetic similarity of the considered genomes |
| Open Pangenome | The number of new gene families in one taxonomic lineage keeps increasing |
| Closed Pangenome | Only a few gene families are added when new genomes are incorporated |
What You'll Learn
The pan-genome is the entire set of genes within a species
In the fields of molecular biology and genetics, a pan-genome is the entire set of genes from all strains within a species. It is the union of all the genomes of a species. The pan-genome can be divided into three sections:
- A "core pan-genome" that contains genes found in all individuals
- A "shell pan-genome" that contains genes found in two or more strains
- A "cloud pan-genome" that only has genes seen in one strain
The core genome is common to all individuals in the species, while the cloud genome is unique to individuals or a subset of individuals. The core genome includes genes responsible for the basic biology of the species and its major phenotypic traits. The cloud genome, also known as the dispensable or accessory genome, contributes to species diversity and may encode functions that confer selective advantages, such as adaptation to different environments, antibiotic resistance, or colonisation of a new host.
The idea of a pan-genome was first conceived for bacterial species in 2005. Since then, there have been efforts to elucidate the pan-genome of many species beyond bacteria, including plants and humans. Assembling and studying pan-genomes has shown that relying on a single reference genome for a species can be inadequate for understanding the genomic basis of diverse traits. For example, many agronomically important genes in plant species are found in the dispensable genome.
The pan-genome of a species can be open or closed. An open pan-genome means that the number of genes in the species is not fixed, and new genes will be discovered as more organisms are sequenced. In contrast, a closed pan-genome means that the gene pool is restricted, and sequencing additional strains will not reveal new genes.
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It can be divided into core, shell and cloud pangenomes
In the fields of molecular biology and genetics, a pan-genome is the entire set of genes from all strains within a clade. It can be divided into three sections: the core pangenome, the shell pangenome, and the cloud pangenome.
The core pangenome contains genes present in all individuals within a species. It is often related to housekeeping functions and the primary metabolism of the lineage. However, the core genome can also contain genes that differentiate the species from other species within the genus.
The shell pangenome contains genes present in two or more strains. Genes in the shell pangenome can be gained or lost through evolutive dynamics. For example, a gene family can be part of the shell pangenome if it is shared by more than 50% of the genomes in the pangenome.
The cloud pangenome contains gene families shared by a minimal subset of the genomes in the pangenome, including singletons or genes present in only one genome. It is also known as the peripheral genome or accessory genome. Gene families in this category are often related to ecological adaptation.
The use of the term "dispensable" to describe the cloud genome has been questioned, at least in plant genomes, as accessory genes play an important role in genome evolution and the complex interplay between the genome and the environment.
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The core pangenome contains genes present in all individuals
The pan-genome is a term used in the fields of molecular biology and genetics to describe the entire set of genes from all strains within a clade. It can be broken down into the core pangenome, the shell pangenome, and the cloud pangenome. The core pangenome contains genes present in all individuals of the species.
The idea of a pan-genome was first conceived for bacterial species in 2005, when the genomes of six strains of Streptococcus agalactiae were sequenced, revealing a core genome containing 80% of S. agalactiae genes. The core genome includes most of the housekeeping genes, which remain unknown for other genomes assembled later. These results indicated that there are additional implications in analysing the Group B Streptococcus pangenome.
The core genome size and proportion to the pangenome depend on several factors, but it is especially dependent on the phylogenetic similarity of the considered genomes. For example, the core of two identical genomes would also be the complete pangenome. The core of a genus will always be smaller than the core genome of a species. Genes that belong to the core genome are often related to housekeeping functions and primary metabolism of the lineage. Nevertheless, the core gene can also contain some genes that differentiate the species from other species of the genus, i.e. that may be related to pathogenicity or niche adaptation.
The maturity of technologies and methods such as third-generation sequencing, telomere-to-telomere genomes, graphic genomes, and reference-free assembly will further promote the development of pangenome research.
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The cloud pangenome contains genes unique to a single strain
The pan-genome is a term used in the fields of molecular biology and genetics to describe the entire set of genes from all strains within a clade. It is the union of all the genomes of a clade. The pan-genome can be divided into the core pangenome, the shell pangenome, and the cloud pangenome. The core pangenome contains genes present in all individuals, the shell pangenome contains genes present in two or more strains, and the cloud pangenome contains genes unique to a single strain.
The cloud pangenome, also referred to as the accessory genome, contains 'dispensable' genes present in a subset of the strains and strain-specific genes. The use of the term 'dispensable' has been questioned, particularly in relation to plant genomes, as accessory genes play an important role in genome evolution and the complex interplay between the genome and the environment.
The cloud pangenome is made up of gene families shared by a minimal subset of the genomes in the pangenome, including singletons or genes present in only one of the genomes. It is also known as the peripheral genome. Gene families in this category are often related to ecological adaptation.
The cloud pangenome is a useful tool for understanding the functional differences between closely related genomes within a species or genus. It can be used to establish the degree of horizontal gene transfer and aid in the understanding of phenotypic differences. The cloud pangenome can also be used to emphasise the shell or the cloud, depending on the weighting strategy chosen.
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The pan-genome was first conceived for bacterial species
The idea of a pan-genome was first conceived for bacterial species in 2005. The term 'pan-genome' was defined by Tettelin et al., who applied it specifically to bacteria.
The pan-genome represents the entire set of genes within a species, consisting of a core genome—containing sequences shared between all individuals of the species—and a 'dispensable' genome. The genetic repertoire of a bacterial species is much larger than the gene content of an individual strain.
The pan-genome can be broken down into a "core pangenome" that contains genes present in all individuals, a "shell pangenome" that contains genes present in two or more strains, and a "cloud pangenome" that contains genes only found in a single strain.
The original pangenome concept was developed by Tettelin et al. when they analysed the genomes of eight isolates of Streptococcus agalactiae, where they described a core genome shared by all isolates, accounting for approximately 80% of any single genome, plus a dispensable genome consisting of partially shared and strain-specific genes.
Since the conception of the pan-genome for bacterial species, there have been efforts to elucidate the pan-genome of many species beyond bacteria. Improvements in genome sequencing technologies, particularly long-read sequencing, have facilitated the assembly of pan-genomes for genomes more complex than those of bacterial species.
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