International Journal of Genomics

Research Article

Genome-Wide Analysis of the TCP Gene Family in Switchgrass (Panicum virgatum L.)

Table 3

Putative cis-acting DNA elements in the promoter of PvTCP genes.


Clade name	Element no.^a	Element name^b	Signal sequence^c	Putative function^d	FO^e

PCF	S000449	CACTFTPPCA1	YACT	Photosynthesis	237
	S000265	DOFCOREZM	AAAG	Photosynthesis; leaf and shoot development	213
	S000454	ARR1AT	NGATT	Cytokinin response	161
	S000198	GT1CONSENSUS	GRWAAW	HR reaction^f; systemic acquired resistance	146
	S000407	MYCCONSENSUSAT	CANNTG	Abiotic stress; salinity stress	143
	S000144	EBOXBNNAPA	CANNTG	Salinity stress; phenylpropanoid biosynthesis	143
	S000501	CGCGBOXAT	VCGCGB	Calmodulin; auxin response	108
	S000447	WRKY71OS	TGAC	Biotic and abiotic stress; GA response	97
	S000378	GTGANTG10	GTGA	Pollen development; pectin regulation	95
	S000493	CURECORECR	GTAC	Copper; oxygen; hypoxic reaction	92
	S000245	POLLEN1LELAT52	AGAAA	Pollen development	91
	S000415	ACGTATERD1	ACGT	Photosynthesis	74
	S000462	NODCON2GM	CTCTT	Root nodulin	66
	S000203	TATABOX5	TTATTT	Glutamine synthetase	45
	S000457	WBOXNTERF3	TGACY	Jasmonic acid response	43
	S000179	MYBPZM	CCWACC	Flavonoid biosynthesis; seed development	37
	S000176	MYBCORE	CNGTTR	Abiotic stress; salinity; flavonoid biosynthesis	35

CYC/TB1	S000449	CACTFTPPCA1	YACT	Photosynthesis	87
	S000265	DOFCOREZM	AAAG	Photosynthesis; leaf and shoot development	53
	S000407	MYCCONSENSUSAT	CANNTG	Abiotic stress; salinity stress	48
	S000144	EBOXBNNAPA	CANNTG	Salinity stress; phenylpropanoid biosynthesis	48
	S000198	GT1CONSENSUS	GRWAAW	HR reaction; systemic acquired resistance	38
	S000454	ARR1AT	NGATT	Cytokinin response	33
	S000378	GTGANTG10	GTGA	Pollen development; pectin regulation	32
	S000447	WRKY71OS	TGAC	Biotic and abiotic stress; GA response	21
	S000482	SORLIP1AT	GCCAC	phyA; phytochrome; light response	17
	S000203	TATABOX5	TTATTT	Glutamine synthetase	14
	S000030	CCAATBOX1	CCAAT	Heat shock response	13
	S000103	SEF4MOTIFGM7S	RTTTTTR	Seed globulin	10

CIN	S000449	CACTFTPPCA1	YACT	Photosynthesis	153
	S000454	ARR1AT	NGATT	Cytokinin response	132
	S000265	DOFCOREZM	AAAG	Photosynthesis; leaf and shoot dvelopment	103
	S000407	MYCCONSENSUSAT	CANNTG	Abiotic stress; salinity stress	77
	S000144	EBOXBNNAPA	CANNTG	Salinity stress; phenylpropanoid biosynthesis	77
	S000501	CGCGBOXAT	VCGCGB	Calmodulin; auxin response	69
	S000198	GT1CONSENSUS	GRWAAW	HR reaction; systemic acquired resistance	64
	S000447	WRKY71OS	TGAC	Biotic and abiotic stress; GA response	49
	S000493	CURECORECR	GTAC	Copper; oxygen; hypoxic reaction	48
	S000378	GTGANTG10	GTGA	Photosynthesis; leaf and shoot development	43
	S000203	TATABOX5	TTATTT	Glutamine synthetase	27
	S000103	SEF4MOTIFGM7S	RTTTTTR	Seed globulin	26
	S000245	POLLEN1LELAT52	AGAAA	Pollen development	21

^a-cThe ID number, name, and signal sequences of the element in the online PLACE program (https://sogo.dna.affrc.go.jp/). ^dThe putative function of each element predicted by the online PLACE program and references from NCBI. ^eFrequency of occurrence in the promoters of TCP genes in each clade. ^fCharacters in bold represent those functions related to stress response.