Buffering by gene duplicates: an analysis of molecular correlates and evolutionary conservation

BMC Genomics

Table 1 Essentiality and gene duplicates in ten bacterial and eukaryotic organisms.

Organism	Essentiality test	No. of tested genes	No. of essential genes	Number of genes with duplicates (D≥ 1)	Contribution of duplicates to buffering C	R² of *P(S)* vs. Effective family size D	R² of *P(S)* vs. E-value
*M. genitalium*	Random insertion (clones)	460	364	89	-0.13	0.35	0.16
*H. pylori*	Random insertion (population)	1,559	329	358	0.13***	0.26	0.14
*H. influenzae*	Random insertion (population)	1,704	631	400	0.01*	0.27	0.20
*M. tuberculosis*	Random insertion (population)	3,920	614	1,683	0.06***	0.63*	0.40
*P. aeruginosa*	Random insertion (clones)	5,566	364	2,689	0.07***	0.64**	0.80**
*B. subtilis*	Targeted insertion (clones)	4,105	191	1,857	0.0045*	0.37	0.01
*E. coli*	Targeted knockout (clones)	3,221	291	1,940	0.06***	0.64**	0.82**
*S. cerevisiae*	Targeted knockout (clones)	5,318	952	2,531	0.12***	0.00	0.72*
*C. elegans*	Targeted knockdown (clones)	13,915	1,345	9,203	0.09***	0.74**	0.92***
*D. melanogaster*	Targeted knockdown in cell line (clones)	12,145	318	7,004	0.01***	0.00	0.60*
*M. musculus*	Collection of individual experiments	4,267	1,438	3,664	-0.07**	0.03	0.00

The table summarizes properties of the eleven organisms in our analysis, such as (from left to right) the names of the organims; the type of KO/KD experiment; the number of genes tested for their essentiality in gene-KO or KD experiments; the number of genes resulting in lethal phenotypes (essential genes); the number of genes with one or more duplicates (D ≥ 1) amongst the tested genes; the contribution of duplicates to buffering C = P(S|D ≥ 1)/P(S|D = 0) - 1; the correlation between P(S) and effective family size of the genes D (D ranges from 0 to 8+, see text); and the correlation between P(S) and distance of a gene to its nearest neighbor (measured in -log(E-value), bin size 5). In the experimental descriptions, 'clones' refers to clonal outgrowth on plates or in cultures; 'population' refers to (mixed) population outgrowth in liquid culture. P-value thresholds of 0.05, 0.01, and 0.001 are marked with *, **, and ***, respectively.
KD – knockdown; KO – knockout; P(S) – probability of survival; D – effective gene family size (number of additional gene duplicates)

ISSN: 1471-2164