Genome-wide profiling of Populus small RNAs

BMC Genomics

Table 2 Predicted phased and trans-acting loci.

Location	Sequences	Phased sequences	Number of Targets (perfect match)	Phasing trigger	Genomic context
LG_III:13629357..13629608¹	7	6	0		CDS
LG_III:13638142..13638393¹	7	6	0		CDS
LG_III:13654756..13655007	7	5	1(0)		CDS/intergenic
LG_VI:551356..551607	25	9	4(0)	si39621	Intergenic
LG_VI:14747098..14747349	13	6	5(2) MYB	ptc- miR828	CDS
LG_X:19646453..19647187²	62	14	8(1)	ptc- miR482.2	UTR
LG_XII:9812366..9812617	20	7	2(0)		CDS/intergenic
LG_XV:5567507..5567758	13	6	3(0)		CDS/intergenic
LG_XIX:138605..138856	12	7	28(1) NBS- LRR		Intergenic
scaffold_70:624107..624358³	13	6	10(1) PPR	ptc- miR475c	CDS
scaffold_70:867516..867767	4	4	10(3) PPR	ptc- miR475c	CDS
scaffold_180:454350..454601	7	5	16(7) NBS- LRR		Intergenic

Predicted phased and trans-acting loci with p < 0.00001. Where a locus targets many genes from a particular class, this is shown after the number of targets. The number of predicted targets at each locus is shown with the number of perfect-match siRNA-targets indicated in parenthesis. Target predictions were made using the psRNATarget web tool. ¹These two loci are duplicates. ²Manually corrected coordinates, as described in Materials and Methods. ³There is a second locus just adjacent to this (scaffold_70:624403..624654) with p 0.000026, suggesting that the two may represent a single locus.

ISSN: 1471-2164