Table 2.

Summary and identification of the down-regulated genes associated with phytohormone pathways in response to TSA treatment

Gene ID	Gene name	Annotation	Regulated type	Fold change (Log2)	Associated pathway
Gh_A10G1020	GhIAA3_A10	INDOLE-3-ACETIC ACID INDUCIBLE 3	Down	− 2.0372	Auxin
Gh_D02G0405	GhIAA4_D02	INDOLE-3-ACETIC ACID INDUCIBLE 4	Down	− 2.2086	Auxin
Gh_A09G1945	GhIAA4_A09		Down	− 2.7903	Auxin
Gh_A02G0340	GhIAA4_A02		Down	− 1.5551	Auxin
Gossypium_hirsutum _newGene_23351	GhIAA4_N		Down	− 1.0348	Auxin
Gh_D01G0947	GhIAA4_D01		Down	− 2.7321	Auxin
Gh_A02G0341	GhIAA14_A02	INDOLE-3-ACETIC ACID INDUCIBLE 14	Down	− 1.1472	Auxin
Gh_A11G1164	GhIAA16_A11	INDOLE-3-ACETIC ACID INDUCIBLE 16	Down	− 2.6413	Auxin
Gh_D05G0472	GhIAA18_D05	INDOLE-3-ACETIC ACID INDUCIBLE 18	Down	− 3.8157	Auxin
Gh_A05G0356	GhIAA18_A05		Down	− 1.5554	Auxin
Gh_A06G1644	GhIAA19_A06	INDOLE-3-ACETIC ACID INDUCIBLE 19	Down	− 3.9605	Auxin
Gh_D10G1512	GhIAA19_D10		Down	− 6.1937	Auxin
Gh_A05G1607	GhIAA24_A05	INDOLE-3-ACETIC ACID INDUCIBLE 24	Down	− 1.319	Auxin
Gh_D05G1792	GhIAA24_D05		Down	− 1.1334	Auxin
Gh_D11G1228	GhIAA29_D11	INDOLE-3-ACETIC ACID INDUCIBLE 29	Down	− 1.8453	Auxin
Gh_D11G0514	GhGH3.1_D11	ENCODING A PROTEIN SIMILAR TO IAA-AMIDO SYNTHASES GH3.1	Down	− 2.4801	Auxin
Gh_A11G1077	GhGH3.3_A11	ENCODING AN PROTEIN SIMILAR TO IAA-AMIDO SYNTHASES GH3.3	Down	− 1.6851	Auxin
Gh_D13G0668	GhGH3-10_D13	ENCODING AN PROTEIN SIMILAR TO IAA-AMIDO SYNTHASES GH3-10	Down	− 2.692	Auxin
Gh_A11G0443	GhGH3-10_A11		Down	− 2.0607	Auxin
Gh_A13G0480	GhGH3-10_A13		Down	− 1.2652	Auxin
Gh_D02G2216	GhSAUR1_D02	SMALL AUXIN UP-REGULATED RNA11	Down	− 2.3625	Auxin
Gh_D12G0291	GhSAUR12_D12	SMALL AUXIN UPREGULATED RNA12	Down	− 2.747	Auxin
Gh_A13G0578	GhSAUR48_A13	SMALL AUXIN UPREGULATED RNA48	Down	− 1.0704	Auxin
Gh_D12G0289	GhSAUR52_D12	SAUR52, SMALL AUXIN UPREGULATED RNA52	Down	− 1.0695	Auxin
Gh_D10G0616	GhPAP1_D10	PURPLE ACID PHOSPHATASE 1	Down	− 1.998	Auxin
Gh_A02G1156	GhPAP2_A02	PURPLE ACID PHOSPHATASE 2	Down	− 1.7051	Auxin
Gh_A05G1076	GhPAP2_A05		Down	− 1.289
Gh_A03G1804	GhLAX2_A03	LIKE AUXIN RESISTANT 2	Down	− 2.3804	Auxin
Gh_D01G1617	GhLAX2_D01		Down	− 3.069	Auxin
Gh_A01G1374	GhLAX2_A01		Down	− 2.3246	Auxin
Gh_D09G1378	GhTIR1_D09	AUXIN RECEPTOR, TRANSPORT INHIBITOR RESPONSE 1	Down	− 3.9574	Auxin
Gh_D09G2152	GhTIR1_D09		Down	− 2.3805	Auxin
Gh_A12G1016	GhARF11_A12	AUXIN RESPONSE FACTOR 11	Down	− 1.6769	Auxin
Gh_A07G1254	GhARF18_A07	AUXIN RESPONSE FACTOR 18	Down	− 1.345	Auxin
Gh_Sca005214G02	GhARR2_S	RESPONSE REGULATOR 2	Down	− 1.8818	Cytokinin
Gh_D05G2656	GhARR7_D05	RESPONSE REGULATOR 7	Down	− 1.2673	Cytokinin
Gh_A11G2364	GhAHP5_A11	HISTIDINE-CONTAINING PHOSPHOTRANSFER FACTOR 5	Down	− 1.0153	Cytokinin
Gh_A11G1389	GhAHK2_A11	HISTIDINE KINASE 2	Down	− 1.151	Cytokinin
Gh_D01G1042	GhCYCD3;2_D01	CYCLIN D3;2	Down	− 2.2107	Cytokinin
Gh_D05G0138	GhTGA7_D05	TGACG SEQUENCE-SPECIFIC BINDING PROTEIN 7	Down	− 1.4757	SA
Gh_A02G0775	GhTGA7_A02		Down	− 2.0558	SA
Gh_D12G1679	GhTGA8_D12	TGACG SEQUENCE-SPECIFIC BINDING PROTEIN 8	Down	− 3.7153	SA
Gh_A09G0903	GhTGA9_A09	TGACG SEQUENCE-SPECIFIC BINDING PROTEIN 9	Down	1.3068	SA
Gh_A07G1202	GhPIF3_A07	PHYTOCHROME INTERACTING FACTOR 3	Down	− 1.1952	GA
Gh_D13G1847	GhGID1C_D13	GA INSENSITIVE DWARF1C	Down	− 1.7948	GA
Gh_A05G0308	GhHAB1_A05	HYPERSENSITIVE TO ABA1, NEGATIVE IN ABA SIGNALING	Down	− 1.0137	ABA
Gh_D01G1881	GhBAK1_D01	BRI1-ASSOCIATED RECEPTOR KINASE	Down	− 1.1379	BR
Gh_D05G2975	GhJAI3_D05	JASMONATE-INSENSITIVE 3	Down	− 1.8414	JA