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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

From: Diel rewiring and positive selection of ancient plant proteins enabled evolution of CAM photosynthesis in Agave

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
  1. *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