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2@@ -5,18 +5,18 @@ In molecular biology, the concept of a genome has been central to the study of g
The concept of the pangenome was formally introduced in 2005 by *Tettelin et al* ^1^. This research group proposed that the increasing amount of genetic information challenged the old definition of bacterial species (strains sharing 70%+ of their DNA). Following this premise, they asked themselves how many genes are necessary to fully describe a species. They sequenced and analyzed 8 *Streptococcus agalactiae* strains. With mathematical modeling they extrapolated that the number of genes present in all their genomes would reach an asymptote. The implication being that even when sequencing an infinite amount of genomes, the core genome will remain constant
The concept of the pangenome was formally introduced in 2005 by *Tettelin et al* <sup>1</sup>. This research group proposed that the increasing amount of genetic information challenged the old definition of bacterial species (strains sharing 70%+ of their DNA). Following this premise, they asked themselves how many genes are necessary to fully describe a species. They sequenced and analyzed 8 *Streptococcus agalactiae* strains. With mathematical modeling they extrapolated that the number of genes present in all their genomes would reach an asymptote. The implication being that even when sequencing an infinite amount of genomes, the pool of genes common to all genomes (= the core genome) will remain constant
@@ -25,18 +25,18 @@ This idea revolutionized how we think about microbial genetic diversity. And it
- Core/accessory genes: The core genes are defined as being shared by a majority of the clade. This threshold is usually above 95%, but it is not standardized. Accessory genes are simply defined as not being part of the core genome. Other concepts such as "soft core", "shell genes", "hard core", "cloud genes" are have more loose definitions and thresholds.
- Open/closed pangenome: These terms are used to describe the genetic diversity of the observed clade. An open pangenome (3b) defines a clade with a small proportion of core genes and a high proportion of accessory genes. In this case, the number of new genes discovered when sequencing new isolates has no asymptote if extrapolated (3c). This is flipped for closed pangenomes (3a, 3c). This definition is pretty intuitive when looking at figure 3
- Open/closed pangenome: These terms are used to describe the genetic diversity of the observed clade. An open pangenome (3b) defines a clade with a small proportion of core genes and a high proportion of accessory genes. In this case, the number of new genes discovered when sequencing new isolates has no asymptote if extrapolated (3c). This is flipped for closed pangenomes (3a, 3c). This definition is pretty intuitive when looking at figure 3.
<figcaption align = "left"><i>Fig.3 - a) Closed pangenomes are characterized by large core genomes and small accessory genomes. b) Open pangenomes tend to have small core genomes and large accessory genomes. c) The size of open pangenomes tends to increase with every added genome, meanwhile closed pangenome's size tends to be asymptotic despite adding more genomes. Due to this characteristic, complete pangenome size for pangenomes can be predicted.</i></figcaption>
<figcaption align = "left"><i>Fig.3 - a) Closed pangenomes are characterized by large core genomes and small accessory genomes. b) Open pangenomes tend to have small core genomes and large accessory genomes. c) The size of open pangenomes tends to increase with every added genome, meanwhile closed pangenome's size tends to be asymptotic despite adding more genomes. Due to this characteristic, complete pangenome size for pangenomes can be predicted.<sup>2</sup></i></figcaption>
@@ -48,4 +48,24 @@ Many software are available for pangenome analysis, with many different approach
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