Table 3.

Distribution of gene co-expression modules in the gene sets with positive selection and diel shift in gene expression pattern, respectively, in Agave americana. Gene set 1a includes Agave genes with Ka/Ks ratio greater than one in the Agave-Arabidopsis, Agave-Oryza and Agave-Zea orthologous gene pairs. Gene set 1b includes Agave genes with Ka/Ks ratio greater than one in Agave-Arabidopsis and Agave-Oryza but not Agave-Zea pairs. Gene sets 2a and 2b includes Agave genes with morning-to-night shift and afternoon-to-night shift, respectively, in expression pattern as compared with the orthologous genes in Arabidopsis. The numbers represent the observed and expected (in parentheses) number of genes

Co-expression module	Gene set 1a	Gene set 1b	Gene set 2a	Gene set 2b
M01	14 (27)	17 (16)	10 (4)*	5 (4)
M02	13 (7)*	4 (4)	2 (1)	0 (1)
M03	16 (7) **	10 (4)*	0 (1)	0 (1)
M04	1 (5)	0 (3)	0 (1)	0 (1)
M05	0 (4)	0 (2)	1 (1)	0 (1)
M06	1 (4)	1 (2)	0 (1)	3 (1)*
M07	5 (10)	1 (6)	1 (1)	2 (1)
M08	2 (2)	0 (1)	0 (0)	0 (0)
M09	1 (9)	2 (5)	0 (1)	1 (1)
M10	49 (28)**	23 (16)	0 (4)	0 (4)
M11	5 (5)	2 (3)	4 (1)*	0 (1)
M12	0 (3)	0 (2)	0 (0)	0 (0)
M13	3 (11)	2 (6)	3 (2)	10 (1)**
M14	2 (8)	2 (5)	0 (1)	0 (1)
M15	0 (2)	1 (1)	0 (0)	0 (0)
M16	1 (2)	1 (1)	1 (0)	0 (0)
Non-module	47 (25)**	28 (15)*	0 (4)	0 (3)
Total	160	94	22	21

^*Overrepresentation (FDR adjusted p-value< 0.05, cumulative Poisson distribution) of co-expression modules in each category. ^**Overrepresentation (FDR adjusted p-value< 0.01, cumulative Poisson distribution) of co-expression modules in each category