Month: September 2022

PAN GENOME. “Although the enforced stability of genomic content is ubiquitous among multi-cellular eukaryotes, the opposite is proving to be the case among prokaryotes, which exhibit remarkable and adaptive plasticity of genomic content.” https://lnkd.in/ewnQ9Vg View in LinkedIn

CORE, FLEX AND PAN GENOME. “Early bacterial whole-genome sequencing efforts discovered that whenever a particular “species” was re-sequenced, new genes were found that had not been detected earlier—entirely new genes, not merely new alleles. This led to the concepts of the bacterial core-genome, the set of genes found in all members of a particular “species”, and the flex-genome, the set of genes found in some, but not all members of the “species”. Together these make up the species’ pan-genome.” https://standardsingenomics.biomedcentral.com/articles/10.1186/s40793-016-0180-8 View in LinkedIn

TUMOR-LIKE GENOMES. “In many cases, a typical individual bacterial cell carries less than 50 % of the genes found in the species’ pan-genome—a level of genomic plasticity that in multi-cellular eukaryotes is only seen in highly unregulated tumors.” https://standardsingenomics.biomedcentral.com/articles/10.1186/s40793-016-0180-8 View in LinkedIn

STRAINS VERSUS SPECIES. “This is a stunning amount of variation within one “species” of bacteria. (Strains in the genus Shigella are now regarded as E. coli variants that need reclassification). If only strains currently named E. coli are considered, the number of core gene families rises from 993 to 1472, a slight increase of 6 % to 9 % of the total pan-genome.” https://standardsingenomics.biomedcentral.com/articles/10.1186/s40793-016-0180-8 View in LinkedIn

DOUBTFUL SPECIES UTILITY. “By comparison, current data suggest a 30 % overlap in gene content between humans and mice. That is, there may be more genetic similarity between a randomly selected human and a randomly selected mouse than there is between two bacterial cells of the same “species.” Clearly, a species concept that encompasses that much genetic variation is not compatible with the species concept as generally applied to multi-cellular eukaryotes.” https://standardsingenomics.biomedcentral.com/articles/10.1186/s40793-016-0180-8 View in LinkedIn

STRAIN GENE VARIATION. ““As the numbers of sequenced E. coli strains continues to grow, the number of discovered core genes remains about the same, while the number of flex genes grows linearly with the number of strains sequenced. Land et al., asserted that comparison of more than 2000 Escherichia coli genomes finds an E. coli core genome of about 3100 gene families and a total of about 89,000 gene families.” https://standardsingenomics.biomedcentral.com/articles/10.1186/s40793-016-0180-8 View in LinkedIn

NON-REPRODUCTIVE GENE SHARING. “Horizontal gene transfer can lead to the profound phenotypic change from benign commensal to lethal pathogen. “Horizontal” in this context refers to the lateral or “sideways” movement of genes between microbes via mechanisms not directly associated with reproduction.” Normally, gene sharing in other kingdoms is exclusively about reproduction. https://lnkd.in/ewnQ9Vg View in LinkedIn

PROMISCUOUS GENE SHARING. “Horizontal gene transfer among prokaryotes can occur between members of the same “species” as well as between microbes separated by vast taxonomic distances. As such, much prokaryotic genetic diversity is both created and sustained by high levels of horizontal gene transfer. Although horizontal gene transfer can occur for genes in the core-genome component of a pan-genome, it occurs much more frequently among genes in the optional, flex-genome component.” https://lnkd.in/ewnQ9Vg View in LinkedIn

FLOATING GENE ISLANDS. “In some cases, horizontal gene transfer has become so common that it is possible to think of some “floating” genes more as attributes of the environment in which they are useful rather than as attributes of any individual bacterium or strain or “species” that happens to carry them.” https://standardsingenomics.biomedcentral.com/articles/10.1186/s40793-016-0180-8 View in LinkedIn

HORIZONTAL GENE TRANSFERS. “This kind of genetic exchange can occur between widely unrelated taxa.” (This is huge). https://standardsingenomics.biomedcentral.com/articles/10.1186/s40793-016-0180-8 View in LinkedIn