Chilling acclimation provides immunity to stress by altering regulatory networks and inducing genes with protective functions in Cassava

Table 1 The cleavage site of anti-correlated miRNA:mRNA pairs detected by 5′RACE assay

miR-Target	ID	Cleavage sites*			Anti-correlation^§						Annotation
miR-Target	ID	NC	CA + CCA	CS	CA/NC	CCA/NC	CS/NC	CCA/CA	CS/CA	CS/CCA	Annotation
novel7a-DHDSP2	010211 m	4,±			+						dihydrodipicolinate synthase
Novel53-RPL27	016749 m		21,±	±	+		-				ribosomal protein large subunit 27
miR171hi-HAM3(1)	002034 m		10(5),7(2),-	10,7,3,-	+	+					GRAS family transcription factor
miR395-ATRX	000210 m		9(11)	9,-	+		+				P-loop containing nucleoside triphosphate
miR395-ATRX	000210 m		9(11)	9,-	+		+				hydrolases superfamily protein
novel16-POS	033835 m		±	5,0,±	+						Peroxidase superfamily protein
Novel42-LMDH	007889 m		-	11,±				-			lactate/malate dehydrogenase family protein
miR394-FY	002500 m		4,3,1(2),-	4,-						+	Transducin/WD40 repeat-like superfamily protein
miR171hi-HAM3(2)	034057 m		10(3),7,-	10(5),7(3),-						+	GRAS family transcription factor
miR319-TCP4	004517 m			8,-			+			+	TCP family transcription factor 4
novel30-CP	014450 m	12,10			+	+	+		-		Cyclase family protein
miR164-NAC	029889 m		10(7)	10(9)		+	+		+		NAC domain containing protein 1
Novel53-SWEET17	014996 m		22,17(2),-	±		+		+	-		Nodulin MtN3 family protein
miR398-EC	011902 m		±	10(2),±		-				+	copper ion binding/electron carrier
miR319-GSTU8	015766 m						-	-	-	-	glutathione S-transferase TAU 8
miR172-TUA	007502 m	-			-						tubulin alpha-2 chain
miR172-LMP	002489 m		+	-	-	-					LMBR1-like membrane protein
miR394-IIL1	005847 m			-	-			-	-		isopropyl malate isomerase large subunit 1

The cleavage sites of 13 (out of 17, 76.5%) miRNA:mRNA pairs were detected within miRNA binding regions. Five (the first five from the top), three (the subsequent three) and five pairs (the next subsequent five) of them were anti-correlated in the three chilling stress conditions with respect to the NC condition, in the other three comparisons and both two comparisons according to RNA-seq data, respectively. The cleavage sites of the remaining four pairs (the last four) failed to be detected in the basepairing regions of corresponding target genes. The “*” column lists number of miRNAs that are complementary with target cleavage sites in binding regions; the “+” and “-” symbols refer to cleavage sites located in upstream and downstream of miRNA:target binding regions, respectively. In the “§” column, “+” means that there is an anti-correlation between a miRNA and its target gene based on sequencing data, and the cleavage site of miRNA:target is located in the basepairing region in 5′RACE assay, and “-” means that there is an anti-correlation in sequencing data, whereas the cleavage site of miRNA:target is not within the basepairing region but either upstream or downstream to the basepairing region.

ISSN: 1471-2229