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 |