Decrease of gene expression diversity during domestication of animals and plants

Table 2 Gene expression diversity changes in the seven domestic and wild species

Species	Pair	All		Candidate selected genes			Non-CSGS
Species	Pair	WGGS	Dcv of WGGS	CSGS	PCSGS	Dcv of CSGS	Dcv of non-CSGS
Dog	Dog-Wolf	24,580	10.2%***	294	1.20%	16.1%*	10.2%***
Silkworm	Trimolter-Wild	15,665	37.7%***	421	2.69%	34.0%***	37.8%***
Chicken	AB-RJF	17,858	14.2%***	148	0.83%	19.1%	14.1%***
Rice (japoniaca)	Dome-Wild	91,080	5.1%***	6892	7.57%	7.0%**	5.0%***
Rice (nivara)	Dome-Wild	37,985	12.5%***
Soybean	Landrace-Wild	54,174	−0.4%	3614	6.67%	5.6%*	−0.8%
Soybean	Improved-Landrace	54,174	1.1%	2987	5.51%	4.3%	0.8%
Cotton	Dome-Wild	70,478	16.4%***	1777	2.52%	20.6%***	16.3%***
Cotton.At	Dome-Wild	32,032	15.9%***	549	1.71%	17.2%**	15.8%***
Cotton.Dt	Dome-Wild	34,402	17.1%***	1228	3.57%	21.9%***	16.9%***
Ear of maize	Maize-Teosinte	39,621	5.1%***	1606	4.05%	13.0%***	4.9%***
Leaf of maize	Maize-Teosinte		−1.0%			5.6%	−1.3%
Stem of maize	Maize-Teosinte		0.2%			4.4%	0%

WGGS: Number of genes in the whole genome gene set; D_cv of WGGS: Decreased percentages of the expression diversity for the WGGS; CSGS: Number of genes in candidate selected gene set; PCSGS: Percentage of the number of candidate selected genes; D_cv of CSGS: Decreased percentages of expression diversity for the CSGS; Non-CSGS: Number of non-candidate selected genes; and D_cv of non-CSGS: Decreased percentage of expression diversity for non-CSGS; the species whose P-value less than 0.05, 0.01 and 0.001 are marked with *, ** and ***, respectively. The decreased percentage of expression diversity (D_cv) is equal to 1-(CV_dome-CV_wild) and the expression diversity is represented by the coefficient of variation (CV) in expression level. For rice, genes in the CSGS are from our analyzed data (Additional file 2: Table S10), and the candidate selected genes of the other six pairs are based on previously published data [14, 18, 28, 31, 32, 34, 35]. Detail information about the expression diversity of the seven pairs can be found in the supplemental table (Additional file 2: Table S11)

ISSN: 2730-7182