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The pangenome (or pan-genome) is the entire set of genes for all strains within a clade.

The pan-genome includes the core genome containing genes present in all individuals, an accessory or dispensable genome containing shell genes present in two or more strains, and finally unique cloud genes specific to single strains. Soft-core genes have also been found in most strains or ecotypes (95%) analyzed, leaving room for assembly and annotation errors. These distinctions are not completely objective, since they depend on which genomes are included in the analysis. Moreover, the term "dispensable" has been questioned.

The significance of the pan-genome arises in an evolutionary context, especially with relevance to metagenomics, but is also used in a broader genomics context. The study of the pangenome is called pangenomics.

History
Originally applied to species in bacteria and archaea, but also to plant species.

From https://academic.oup.com/bib/article/19/1/118/2566735:

The term ‘pan-genome’ was first used by Sigaux [13] to describe a public database containing an assessment of genome and transcriptome alterations in major types of tumors, tissues and experimental models. Later, Tettelin et al. [9] defined a microbial pan-genome as the combination of a ‘core’ genome, containing genes present in all strains, and a ‘dispensable’ genome (also known as flexible or accessory genome) composed of genes absent from one or more of the strains.

The original pan-genome concept was developed by Tettelin et al. when they sequenced six strains of Streptococcus agalactiae which could be described as 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. Extrapolation suggested that the gene reservoir in the S. agalactiae pan-genome is vast and that new unique genes will continue to be identified even after sequencing hundreds of genomes.

Core concepts
There are two generalised types of pan-genomes, categorised by the number of new genes added to the pan-genome per sequenced genome. Clades with a closed pan-genome would have very few genes added per sequenced genome after sequencing many strains, and the size of the full pan-genome could theoretically be predicted. Clades with an open pan-genome have enough genes added per additional sequenced genome that predicting the size of the full pan-genome is not possible. Population size and niche versatility have been suggested as the most influential factors in determining pan-genome size.

Prokaryotes


A similar pattern was found in Streptococcus pneumoniae when 44 strains were sequenced (see figure). With each new genome sequenced fewer new genes were discovered. In fact, the predicted number of new genes dropped to zero when the number of genomes exceeds 50 (note, however, that this is not a pattern found in all species). The main source of new genes in S. pneumoniae was Streptococcus mitis from which genes were transferred horizontally. The pan-genome size of S. pneumoniae increased logarithmically with the number of strains and linearly with the number of polymorphic sites of the sampled genomes, suggesting that acquired genes accumulate proportionately to the age of clones.

Another example for the latter can be seen in a comparison of the sizes of the core and the pan-genome of Prochlorococcus. The core genome set is logically much smaller than the pan-genome, which is used by different ecotypes of Prochlorococcus. A 2015 study on Prevotella bacteria isolated from humans, compared the gene repertoires of its species derived from different body sites of human. It also reported an open pan- genome showing vast diversity of gene pool.

Plants
Plant studies have shown that pan-genome dynamics is linked to transposable elements.

Software tools
As interest in pan-genomes increased, there have been a number of software tools developed to help analyze this kind of data. In 2015, a group reviewed the different kinds of analyses and tools a researcher may have available. There are seven kinds of analyses software developed to analyze pangenomes: cluster homologous genes; identify SNPs; plot pangenomic profiles; build phylogenetic relationships of orthologous genes/families of strains/isolates; function-based searching; annotation and/or curation; and visualizations.

Prokaryotes
The two most cited software tools at the end of 2014 were Panseq and the pan-genomes analysis pipeline (PGAP). Other options include BPGA – A Pan-Genome Analysis Pipeline for prokaryotic genomes, GET_HOMOLOGUES or Roary.

Plants
A similar review focused on plant pan-genomes was published also in 2015. The first software designed for plant pan-genomes is GET_HOMOLOGUES-EST.