smRNAome profiling to identify conserved and novel microRNAs in Stevia rebaudiana Bertoni

BMC Plant Biology

Table 4 Putative target genes of novel miRNAs identified using psRNATarget and TAPIR programs

Novel miRNA	Target Acc.	Tool used	Score	mfe	Start	Seed mismatch	Seed gu	Mismatch	gu	E	UPE	Inhibition	Annotation	e-value
Stv_1	BG523199	psRNA/TAPIR	2.5	0.7	55	0	1	1	1	2	9.668	Cleavage	AT1G55490 [Arabidopsis thaliana]	4e-71
Stv_2	BG525025	psRNA/TAPIR	0	1	418	0	0	0	0	0	10.485	Cleavage	Phosphoglycerate kinase [Arabidopsis thaliana]	8e-101
Stv_7	BG526734	psRNA/TAPIR	3.5	0.78	463	1	0	1	1	3	16.578	Cleavage	Pectinacetylesterase family protein [Arabidopsis thaliana]	3e-108
Stv_8	BG525715	psRNA/TAPIR	2	0.89	303	1	0	0	0	1.5	16.677	Cleavage	Predicted protein [Populus trichocarpa]	2e-06
Stv_10	BG521995	TAPIR	3.5	0.82	594	1	1	0	1	-	---	-------	Ribulose-1,5-biphosphate carboxylase activase [Oryza sativa]	1e-63

mfe: free energy ratio; start: start position of the duplex on the mRNA; seed gap: no.of gaps in seed region; seed mismatch: no.of mismatches in seed region; seed gu: number of G–U pairs in seed region; mismatches: number of mismatches, gu: number of G–U pairs; gap: number of gaps introduced by bulges and loop structures; Score: score calculated for each miRNA–mRNA duplex taking into account all the above described parameters. E (Expectation): scores < 3.0 considered as a potential target of miRNA; UPE :Target accessibility - allowed maximum energy to unpair the target site.

ISSN: 1471-2229