Ella Walter
In molecular biology and genetics, a pan-genome is the entire set of genes from all strains within a clade, including the core genome, accessory genome, and species- or strain-specific genes. The core genome is the set of genes shared by all individuals of a species, while the accessory genome is composed of genes present in two or more strains but not all. The pan-genome can be classified as open or closed, with an open pan-genome continuously increasing the number of gene families as new genomes are added to the analysis, and a closed pan-genome remaining limited in its gene pool. The core genome can be further divided into a hard core, consisting of homologous genes shared by every genome, and a soft core, with gene families distributed above a certain threshold. The pan-genome concept was first introduced in 2005 by Tettelin et al. to describe the genomic diversity within a clade, and has since been applied to various bacterial and plant species, providing insights into evolutionary history and the importance of considering the entire gene repertoire in a species.
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What You'll Learn
- The core genome is the set of genes shared by all analysed microorganisms
- The pan-genome is divided into subgroups: core, shell, and cloud
- The core genome is further divided into hard and soft core
- The shell genome is influenced by gene loss and gain dynamics
- The cloud genome is also known as the peripheral genome or accessory genome
The core genome is the set of genes shared by all analysed microorganisms
In the fields of molecular biology and genetics, a pan-genome is the entire set of genes from all strains within a clade. The core genome is the set of genes shared by all analysed microorganisms. It is part of the pan-genome that is shared by every genome in the tested set.
The core genome is made up of genes that are present in all strains, while the dispensable or accessory genome is composed of genes that are absent from one or more strains and genes that are unique to each strain. The core genome is essential for the survival of bacteria and may also be involved in pathogenicity and virulence in some bacterial species.
The concept of a pan-genome was first introduced in 2005 by Tettelin et al., who analysed the genomes of Streptococcus agalactiae. They found that the core genome, shared by all isolates, accounted for approximately 80% of any single genome. The remaining 20% was made up of the dispensable genome, consisting of partially shared and strain-specific genes.
The size and proportion of the core genome to the pan-genome depend on several factors, including the phylogenetic similarity of the considered genomes. For example, the core genome of two identical genomes would be the same as the complete pan-genome. The core genome of a genus will always be smaller than that of a species.
Clustering of core and pan-genomes has shown that evolutionary history is traceable in the core genome, and that clustering of the core genome is sufficient to explore relationships between species.
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The pan-genome is divided into subgroups: core, shell, and cloud
In the fields of molecular biology and genetics, a pan-genome is the entire set of genes from all strains within a clade. It is the union of all the genomes of a clade. The term was defined by Tettelin et al. in 2005, who applied it specifically to bacteria. The pan-genome can be broken down into three subgroups: the core, the shell, and the cloud.
The core pangenome contains genes present in all individuals of a species. It is shared by every genome in the tested set. The core genome size depends on several factors, especially 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.
The shell pangenome contains genes present in two or more strains. There is no universally accepted threshold to define the shell genome, but some authors consider a gene family as part of the shell pangenome if it is shared by more than 50% of the genomes in the pangenome. A family can become part of the shell through several evolutionary dynamics, such as gene loss or gene gain and fixation.
The cloud pangenome contains genes found in only a single strain. It includes singletons or genes present in only one of the genomes. It is also known as the peripheral genome or accessory genome. Estimating the size of the cloud genome can be challenging due to its dependence on the occurrence of rare genes and genomes. Some authors question the use of the term "dispensable" to describe the cloud genome, as these genes play an important role in genome evolution and the complex interplay between the genome and the environment.
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The core genome is further divided into hard and soft core
The distinction between the hard and soft core is important in understanding the genetic composition of a species. The hard core genes are highly conserved and essential for the functioning and survival of the organism. They are often related to housekeeping functions and primary metabolism. On the other hand, soft core genes are still prevalent in the majority of genomes but may exhibit some variation between individuals or strains.
In the context of the pan-genome, the core genome represents the conserved genes shared by all individuals of a species. It forms the basis of the species' genetic identity and plays a crucial role in defining its characteristics. The pan-genome, on the other hand, encompasses the entire set of genes within a species, including both the core genome and the 'dispensable' genome, which consists of genes that are not present in all individuals.
The concept of the pan-genome was first introduced in 2005 by Tettelin et al., who analysed the genomes of Streptococcus agalactiae. They found that the core genome accounted for approximately 80% of any single genome, while the remaining 20% consisted of a dispensable genome with strain-specific genes. This discovery highlighted the importance of considering the entire gene repertoire of a species, as many agronomically important genes were found in the dispensable genome.
Since then, the concept of the pan-genome has been further explored and expanded beyond bacterial species. Improvements in genome sequencing technologies have facilitated the assembly and study of pan-genomes for more complex organisms, such as plants and humans. By analysing multiple genomes within a species, researchers can gain a more comprehensive understanding of the genetic diversity and identify novel genes that may play a role in important functions such as disease resistance.
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The shell genome is influenced by gene loss and gain dynamics
The pangenome, a term coined in 2005, refers to the entire set of genes within a species. It is comprised of a core genome, which contains sequences shared between all individuals of the species, and a dispensable or accessory genome, which contains genes absent from one or more strains and unique strain-specific genes. The dispensable genome is also referred to as the cloud genome or peripheral genome.
The core genome can be further divided into a hard core, which includes families of homologous genes with at least one copy shared by every genome, and a soft core or extended core, which includes gene families distributed above a certain threshold (typically 90-95%). The shell genome, also known as the cloud genome, contains gene families present in two or more strains, but not all individuals. There is no universally accepted threshold to define the shell genome, but it generally includes gene families shared by more than 50% of the genomes in the pangenome.
The dynamics of gene gain and loss are particularly evident in bacterial and archaeal evolution, where they play a significant role in molecular evolution and genome sequence divergence. Mathematical models, such as those developed by Iranzo et al., help explain how homologous recombination maintains the cohesiveness of the core genome while allowing extensive gene gain and loss within the accessory genome. This dynamic process of gene gain and loss contributes to the diversification of bacterial and archaeal genomes, with turnover rates that can exceed the rate of nucleotide substitution.
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The cloud genome is also known as the peripheral genome or accessory genome
In the fields of molecular biology and genetics, a pan-genome is the entire set of genes from all strains within a clade. The pan-genome can be broken down into the core pangenome, shell pangenome, and cloud pangenome. The core pangenome contains genes present in all individuals of a species, the shell pangenome contains genes present in two or more strains, and the cloud pangenome contains genes only found in a single strain.
The concept of the pan-genome was first introduced by Tettelin et al. in 2005 when they analyzed the genomes of Streptococcus agalactiae. They found that the core genome accounted for approximately 80% of any single genome, with the remaining 20% consisting of a dispensable genome with partially shared and strain-specific genes. Since then, the pan-genome concept has been applied to various species, including bacteria, plants, and humans.
The size of the cloud genome can be challenging to estimate due to its dependence on the occurrence of rare genes and genomes. However, it is an important component of the pan-genome, contributing to the overall genetic diversity and variability within a species.
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Frequently asked questions
A pan-genome is the entire set of genes from all strains within a clade. It is the union of all the genomes of a clade.
A core genome is the set of genes shared by all individuals of a species. It contains genes present in all strains.
An accessory genome, also known as a dispensable genome, is the set of genes that are present in two or more genomes but not all.
Pan-genome analysis is a technique used to identify the set of orthologous and unique genes of a specific group of organisms. It involves homogenizing genome annotation and using software to calculate the pan-genome.
The core genome is a subset of the pan-genome. It is the intersection of all the gene sets in a pan-genome, representing the genes shared by all individuals of a species.
