Table 2. Pathway annotation to KEGG of pre-squaring stage-specific DEG in G. hirsutum.

	Pathway	Gene number (40)	Pvalue	Qvalue	Pathway ID
1	Photosynthesis-antenna proteins	2 (5%)	0.001319016	0.09855362	ko00196
2	Isoquinoline alkaloid biosynthesis	2 (5%)	0.00323993	0.09855362	ko00950
3	Biosynthesis of secondary metabolites	13 (32.5%)	0.003478363	0.09855362	ko01110
4	Benzoxazinoid biosynthesis	2 (5%)	0.00914341	0.19429746	ko00402
5	Sesquiterpenoid and triterpenoid biosynthesis	2 (5%)	0.01309328	0.22258576	ko00909
6	Glycolysis/Gluconeogenesis	3 (7.5%)	0.01931683	0.27001173	ko00010
7	Chloroalkane and chloroalkene degradation	2 (5%)	0.02223626	0.27001173	ko00625
8	Fatty acid metabolism	2 (5%)	0.03182014	0.31785701	ko00071
9	Pentose and glucuronate interconversions	3 (7.5%)	0.03903229	0.31785701	ko00040
10	Retinol metabolism	1 (2.5%)	0.04813431	0.31785701	ko00830
11	Cell cycle-yeast	3 (7.5%)	0.04846708	0.31785701	ko04111
12	Glycerolipid metabolism	2 (5%)	0.04915537	0.31785701	ko00561
13	Two-component system	2 (5%)	0.04991741	0.31785701	ko02020
14	Tyrosine metabolism	4 (10%)	0.05235292	0.31785701	ko00350
15	Diterpenoid biosynthesis	2 (5%)	0.0561666	0.3182774	ko00904