Table 5.

List of differentially expressed SAS in the ancestral genotype in relation to the reference (RB867515)

SAS	Functional category	Annotation	S. officinarum			S. robustum			S. spontaneum
			In1	In5	L	In1	In5	L	In1	In5	L
SCEQLB1065B01.g	Carbohydrate metabolism	Sucrose synthase		↑
SCACRZ3111E02.g	Carbohydrate metabolism	Putative SnRK1-interacting protein 2				↓	↓		↓	↓
SCCCLR1079B06.g	Carbohydrate metabolism	Phosphoglycerate kinase	↓	↓		↓
SCMCRT2089E02.g	Carbohydrate metabolism	Pyruvate decarboxylase	↓	↓
SCSBFL1105F08.g	Carbohydrate metabolism	6-phosphofructokinase 3							↑		↑
SCSBSB1057D05.g	Carbohydrate metabolism	Starch phosphorylase			↓			↓
SCUTAM2089E05.g	Carbohydrate metabolism	Beta-amylase	↓		↓		↑	↑			↑
SCJLFL3014G01.g	Oxidative phosphorylation	ATP synthase subunit epsilon							↑	↑	↑
SCCCRT2002G08.g	Transport	Bidirectional sugar transporter SWEET14			↓					↓
SCEQRT3C03F06.g	Transport	putative hexose carrier protein HEX6			↑
SCCCRZ2C01E03.g	Transport	Bidirectional sugar transporter SWEET11		↑
SCSFRT2067F07.g	Transport	Putative sugar transporter type 2a						↓			↓
SCEQRT2091A08.g	Cell wall metabolism	Xyloglucan endotransglycosylase hydrolase (XTH)			↓
SCJLST1020H07.g	Cell wall metabolism	Xyloglucan endotransglycosylase hydrolase (XTH)		↓
SCRUFL3067G01.b	Cell wall metabolism	Xyloglucan endotransglycosylase hydrolase (XTH)				↑
SCCCCL4006H09.g	Cell wall metabolism	Beta-Expansin	↓
SCCCCL5072C04.g	Cell wall metabolism	Beta-Expansin					↓
SCCCLB1023H08.g	Cell wall metabolism	Beta-Expansin							↑
SCCCLR1048B09.g	Cell wall metabolism	Alpha-Expansin		↑			↑
SCEZLB1008D12.g	Transport	Aquaporin TIP4-2					↓	↓
SCAGLR2033E03.g	Transport	Aquaporin PIP1-2							↓	↓	↓
SCEQRT2028C04.g	Transport	Aquaporin PIP1-5	↓		↓	↑	↑
SCQGFL1096G10.g	Transport	Aquaporin PIP2-1			↓
SCJFRT1060F02.g	DNA metabolism	Histone H3	↓	↓	↓
SCQGLR1041C10.g	DNA metabolism	Histone H2B	↑	↑	↑
SCCCRZ2C04H07.g	DNA metabolism	Histone H1				↓			↓
SCCCLR1C04B01.g	DNA metabolism	Histone H2B				↓	↓	↓	↓	↓	↓
SCCCLR2C02B06.g	DNA metabolism	Histone H2B.1	↑	↑				↓
SCCCRZ2002A05.g	DNA metabolism	Histone H3							↓		↓
SCCCLR1068F12.g	DNA metabolism	histone H3 (H3-1.1)							↓	↓	↓
SCRFLR2038C05.g	DNA metabolism	Histone H4							↓		↓
SCCCLR2001D01.g	DNA metabolism	Histone H4 variant TH091		↑
SCCCLR1067B01.g	Signal transduction	LIM-domain binding protein				↓	↓	↓	↓	↓	↓

In1, immature internodes; In5, intermediate internodes; L, leaf+1

This list shows only some DEGs of interest. Complete list of DEGs can be found at Online Resource 2