Tiffany Haney
The pan-genome of a species is a collection of all the DNA sequences that occur in a species, consisting of a core genome (containing sequences shared between all individuals of the species) and a dispensable or variable genome. The core genome can also contain some genes that differentiate the species from other species of the genus. The pan-genome of a species can be open or closed. An open pan-genome occurs when the number of new gene families in one taxonomic lineage keeps increasing without appearing to be asymptotic, regardless of how many new genomes are added. On the other hand, a closed pan-genome occurs when only a few gene families are added when new genomes are incorporated, and the total number of gene families seems to be asymptotic to one number.
| Characteristics | Values |
|---|---|
| Definition | The pan-genome represents the entire set of genes within a species. |
| Core genome | The core genome contains sequences shared between all individuals of the species. |
| Dispensable genome | The dispensable genome contains sequences that are not present in all individuals of the species. |
| Open pan-genome | An open pan-genome occurs when the number of new gene families continues to increase without appearing to reach a limit, regardless of how many new genomes are added. |
| Closed pan-genome | A closed pan-genome occurs when only a few new gene families are added when new genomes are incorporated, and the total number of gene families appears to be approaching a limit. |
| Examples | Escherichia coli is an example of a species with an open pan-genome. Streptococcus pneumoniae has a closed pan-genome. |
| Applications | The pan-genome can be used to identify genes associated with important traits, such as disease resistance in crop plants, or to develop vaccines for disease-causing microbes. |
| Limitations | Creating a pan-genome can be challenging due to the large amount of data involved, the need for high-quality sequencing, and the computational demands of analyzing and storing the data. |
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What You'll Learn
Pan-genome analysis
The process of pan-genome analysis has evolved with advancements in sequencing technologies, particularly long-read sequencing, enabling researchers to study more complex genomes beyond bacteria. The analysis typically begins with homogenizing genome annotation using software like GeneMark or RAST. Several software tools are available to aid in the analysis, such as ITEP, GET_HOMOLOGUES, PanGP, and tools for detecting homologous and orthologous genes.
The analysis focuses on the variation in the genome, often in the form of mutations, and considers factors such as the rate of variation, effective population size, and the proportion of neutral structural variants. By studying multiple genomes, researchers can identify new genes and understand their functions, as well as gain insights into the evolution of pathogenic species. For example, in a study of Streptococcus pneumoniae bacteria, the number of new genes discovered decreased with each additional genome sequenced.
Overall, pan-genome analysis offers a more comprehensive understanding of genetic diversity within a species, revealing unique sequences that contribute to biological adaptability, phenotype, and economically important traits. It highlights the limitations of relying on a single reference genome and provides valuable insights for fields such as agriculture and medicine.
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Open and closed pan-genomes
In the fields of molecular biology and genetics, a pan-genome is the entire set of genes from all strains within a species. It can be broken down into a "
An open pangenome occurs when the number of new gene families in a taxonomic lineage keeps increasing without appearing asymptotic, regardless of how many new genomes are added. This means that the size of the full pangenome cannot be predicted. Escherichia coli is an example of a species with an open pangenome, with a genome size of 4000-5000 genes, and a pangenome size of 89,000 different gene families. Open pan-genomes have been observed in environmental isolates such as Alcaligenes sp. and Serratia sp., showing a sympatric lifestyle.
A closed pangenome occurs when few gene families are added when new genomes are incorporated into the analysis, and the total number of gene families in the pangenome appears asymptotic to one number. This means that the size of the full pangenome can be predicted. An example of a species with a closed pangenome is Streptococcus pneumoniae bacteria, which shows few new genes discovered with each new genome sequenced.
The core genome size and proportion to the pangenome depend on several factors, especially the phylogenetic similarity of the considered genomes. The core genome includes most of the housekeeping genes, which may remain unknown for other genomes. The core genome may also contain some genes that differentiate the species from other species of the genus, such as those related to pathogenicity or niche adaptation.
The maturation of high-throughput sequencing technology has caused a surge in genome sequencing across many different species. Pangenomes were originally constructed for species of bacteria and archaea, but more recently eukaryotic pan-genomes have been developed, particularly for plant species.
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The core genome
In bacterial species, the core genome has been a key focus of study. For example, in Streptococcus agalactiae, the core genome was found to contain 80% of the genes, with the remaining 20% comprising the dispensable genome. This dispensable genome consists of genes that are absent in some strains or unique to specific strains. The analysis of the core genome in bacteria has provided insights into bacterial virulence genes and non-essential biological pathways, which are crucial for developing vaccines and subtyping different bacterial strains.
The concept of the core genome extends beyond bacteria, with studies exploring it in plants and animals as well. In plant pan-genomes, the core genome typically represents a significant proportion of the total pan-genome. For instance, in Glycine soja, the core genome accounted for approximately 80% of the pan-genome. However, the dispensable genome in plants should not be underestimated, as it often contains genes involved in important functions such as biotic stress response and development.
In summary, the core genome is an essential component of the pan-genome, providing insights into the shared genetic foundation of a species. Its size and composition can vary depending on the phylogenetic similarity of the genomes under study. By studying the core genome, researchers can gain a deeper understanding of the evolutionary history, genetic diversity, and unique characteristics of different species.
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Dispensable genome
The concept of a pangenome was first introduced in 2005, specifically for bacterial species. A pangenome is the entire set of genes within a species, consisting of a core genome and a 'dispensable' or 'variable' genome. The core genome contains sequences shared between all individuals of the species, while the dispensable genome contains genes that are absent from one or more strains and genes that are unique to each strain.
The dispensable genome is also referred to as the 'accessory' genome, and it has been questioned whether this genome is truly 'dispensable', as these accessory genes play "an important role in genome evolution and in the complex interplay between the genome and the environment". The dispensable genome is made up of 'cloud' and 'shell' genomes. The cloud genome contains gene families shared by a minimal subset of the genomes in the pangenome, including genes present in only one of the genomes. The shell genome contains gene families shared by more than 50% of the genomes in the pangenome.
The dispensable genome is an important aspect of pangenomics, as it allows for the exploration of missing genetic components and the identification of large structural variants. It also provides insight into the biological adaptability, phenotype, and economically important traits of a species. For example, in plants, many agronomically important genes are most often found in the dispensable genome, such as those involved in biotic stress response, development, and disease resistance.
The concept of the dispensable genome is particularly relevant when considering the open or closed nature of a pangenome. A pangenome is considered open when the number of new gene families in a lineage continues to increase without appearing asymptotic, regardless of how many new genomes are added. In contrast, a closed pangenome occurs when only a few gene families are added when new genomes are incorporated, and the total number of gene families appears to be asymptotic. The presence of a large dispensable genome suggests a more open pangenome, as there is a higher potential for the addition of new genes with each sequenced genome.
Overall, the dispensable genome is a critical component of the pangenome concept, providing insight into the genetic diversity, evolution, and adaptability of a species. By understanding the dispensable genome, scientists can better explore the procedures that create genetic and morphological diversity and the potential for species to adapt to different environmental conditions.
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Pan-genome in human research
The pan-genome is the entire set of genes from all strains within a species, consisting of a core genome and a 'dispensable' or variable genome. The core genome contains sequences shared between all individuals of the species, while the variable genome displays information unique to each individual. The pan-genome can be further 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 concept of the pan-genome was first conceived for bacterial species in 2005, and it has since been studied extensively in both bacteria and viruses. The first plant pan-genome was published in 2014, and subsequent plant pan-genomes have shown the importance of looking at the entire gene repertoire in a species.
The human pangenome is an active area of research, with the Human Pangenome Reference Consortium aiming to create a more sophisticated and complete human reference genome that represents global genomic diversity. In 2023, a draft human pangenome reference was published based on 47 diploid genomes from individuals of varied ethnicities, with about half of African ancestry and the rest from Latin America, South Asia, and East Asia. This draft pangenome showed that the human pangenome captured nearly all human genome variants and identified more than 1,100 cases of gene duplication that were missing from the existing reference genome, GRCh38. The consortium ultimately aims to produce a more detailed pangenome that incorporates genomes from 350 individuals to ensure that future genomic research can benefit people of all backgrounds.
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Frequently asked questions
A pan genome is a collection of all the DNA sequences that occur in a species. It represents the entire set of genes within a species, consisting of a core genome and a dispensable genome.
The core genome contains sequences shared between all individuals of the species. It often includes housekeeping genes and genes that differentiate the species from other species of the genus.
The dispensable genome contains genes that are absent in some individuals of the species or genes that are unique to specific individuals. These genes can be involved in important functions such as biotic stress response, development, and disease resistance.
Studying pan genomes allows us to better understand the genetic diversity within a species. This is particularly important for developing vaccines, improving crop species, and studying the impact of genetic variations on human health.
A pan genome is created by sampling a diverse set of individuals from a species and assembling their DNA sequences. Advances in genome sequencing technologies, such as long-read sequencing, have facilitated the creation of pan genomes for complex organisms.
