Hogg et al. [ 14], reported a finite pan-genome for Haemophilus influenzae, extrapolating from 12 whole genome sequences, while results for Streptococcus agalactiae indicate an infinite asymptotic pan-genome [ 21].
In the study of Cornejo et al. [ 10], they proposed a finite pan-genome for S. mutans, after they used a special "pseudogene cluster" identification process to exclude about 30% of the rare genes that are considered to be pseudogenes.
Both the fitting results of using y = a + bx c and y = a − b ln(x + c) indicated an infinite pan-genome, while the fitting result of using y = a × e− x / b + c resulted in a negative value of the parameter a, suggesting a finite pan-genome However, the last fitting shows obvious deviations to many of the data points.
Hogg et al. [ 24] proposed a finite supragenome model for pan-genome based on a different supposition that contingency genes are sampled from the pan-genome with unequal probability.
The role of the core and dispensable genes in defining bacterial species and the question of whether pan-genomes are finite or infinite remain unclear.
Such a low influx of foreign genes is indicative of a closed pan-genome with a finite gene set.
An alternative explanation for the difference of mean-field and cellular automaton results could be that it is the finite size effect that kills off the pan-sexual population from the spatial model at many parameter combinations.
Much speculation has centered around the origin, composition, and size of bacteria pan-genomes and whether they are finite or infinite (Tettelin et al. 2008; Lapierre and Gogarten 2009).
Nevertheless, we expect the logarithmic (power-law) dependence of pan (core) genome size also to hold for a finite gene pool (as long as the gene pool is much larger than the set of genes observed in the sample).
A recent comparison of the pan-genome model of Tettelin et al. with our finite supragenome model demonstrated that the two models make highly similar predictions when provided the same dataset [ 26], thus serving as a validation for both.
Thus, our analysis indicates that the pan-genome of C. coli and C. jejuni is indeed finite and that sequencing any further genomes would likely recover only a few putative pseudogenes.
