Novel and conserved miRNAs in the halophyte Suaeda maritima identified by deep sequencing and computational predictions using the ESTs of two mangrove plants

Gharat, Sachin Ashruba; Shaw, Birendra Prasad

doi:10.1186/s12870-015-0682-3

Table 3 Targets of the novel/conserved miRNAs that expressed in S. maritima

From: Novel and conserved miRNAs in the halophyte Suaeda maritima identified by deep sequencing and computational predictions using the ESTs of two mangrove plants

miRNAs	S. maritima target accession^a/	Inhibition type/	R. mangle target accession^a/Target description	Inhibition type/
miRNAs	Target description	miRNA-mRNA pairing	H. littoralis target accession^a/Target description	miRNA-mRNA pairing
Novel miRNAs with precursors identified in both S. maritima and mangrove plants
sma-miR2	S.maritima26422/	Cleavage/	SRX001383.184716/	Cleavage/
sma-miR2	Uncharacterized protein LOC104902506 isoform X1 [B. vulgaris subsp. vulgaris]	::::.:::::: :::::.:	Hypothetical protein [C. wallichii]	::::::::::::::::::::
	S.maritima1694886/	Cleavage/	SRX001383.195417/	Cleavage/
	4-coumarate--CoA ligase-like 7 [E. grandis]	: ::::::.:::::::…:	Transcriptional corepressor/coregulator seuss-like [P. trichocarpa]	:::.: :::::::::.:::
sma-miR5	S.maritima155512/	Cleavage/	SRX001383.67404/	Cleavage/
sma-miR5	Uncharacterized protein At4g38062 [B. vulgaris subsp. vulgaris]	:.::: :::.:::::::::	E3 ubiquitin-protein ligase MBR2 [P. euphratica]	:.:::::::::::::.::.:
	S.maritima714933/	Cleavage/	SRX001383.163041/	Cleavage/
	Serine/threonine-protein kinase PRP4 homolog isoform X3 [A. pisum]	::::::.:::::::…::	Serine/threonine-protein kinase TAO3 [T. cacao]	: :::::.:::.:::.::::
			SRX001410.05634/	Cleavage/
			Serine/threonine-protein kinase ATG1 [G. arboreum]	:::: :::::::::::::.
	S.maritima37141/	Translation/
	DEAD-box ATP-dependent RNA helicase 58, chloroplastic isoform X1 [B. vulgaris subsp. vulgaris]	: : :.:::::: :::::::::
sma-miR6	S.maritima26981/	Cleavage/	SRX001383.21117/	Translation/
sma-miR6	Uncharacterized protein LOC104904783 isoform X2 [B. vulgaris subsp. vulgaris]	::: :::.::::::.::::	Hypothetical protein [H. bilis]	..: : ::::: :::::.::::
	S.maritima41280/	Cleavage/
	Hypothetical protein (mitochondrion) [V. faba]	::::::::::::::::::::::
sma-miR7	S.maritima7497/	Translation/	SRX001383.178145/	Cleavage/
sma-miR7	Uncharacterized protein LOC100160261 [A. pisum]	:.::::::: :::::.:::	Hypothetical protein DICPUDRAFT_75074 [D. purpureum]	:::::::::::::::::::::
	S.maritima41831/	Cleavage/	SRX001383.116751/	Cleavage/
	Auxin response factor 3 isoform X2 [B. vulgaris subsp. vulgaris]	::::::.::::::::::::::	Auxin response factor 4 [M. notabilis]	::::::.::::::::::::::
			SRX001410.09075/	Cleavage/
			Auxin response factor 4 isoform 2 [T. cacao]	::::::.:::::::::::::
	S.maritima39489/	Translation/	SRX001383.156526/	Translation/
	Vacuolar protein sorting-associated protein 26A [B. vulgaris subsp. vulgaris]	:::: ::: :::::::.::	Vacuolar protein sorting-associated protein 26B-like [C. sativa]	:.:: ::: ::::::::::
Conserved miRNAs with precursors identified in both S. maritima and mangrove plants
sma-miR159a	S.maritima41732/	Cleavage/	SRX001383.120796/	Cleavage/
sma-miR159a	Uncharacterized protein LOC104883236 isoform X1 [B. vulgaris subsp. vulgaris]	:::::: ::::. ::::.::	Hypothetical protein TRIUR3_29875 [T. urartu]	:::::::::::::::::::::
	S.maritima43555/	Cleavage/	SRX001383.174703/	Cleavage/
	Uncharacterized protein LOC104908454 [B. vulgaris subsp. vulgaris]	::::::..:::.::::: ::	Conserved hypothetical protein [R. communis]	:.:::.:: ::::::::::::.
	S.maritima36986/	Cleavage/	SRX001383.35722/	Translation/
	F-box family protein [S. vulgaris]	:: : .:.:.:::::::::::	F-box protein [M. notabilis]	::::.::: :::::::::
	S.maritima44432/	Cleavage/	SRX001383.108393/	Cleavage/
	Zinc finger CCCH domain-containing protein 5 isoform X2 [B. vulgaris subsp. vulgaris]	::::.:: :::: :::::.:	Double-stranded RNA-binding protein 2 [M. notabilis]	::::: .::::::.:.:.::
sma-miR166a	S.maritima19497/	Cleavage/	SRX001383.65087/	Cleavage/
sma-miR166a	Uncharacterized protein LOC104904626 [B. vulgaris subsp. vulgaris]	:::::: :.::.::::..::	P-ATPase family transporter: calcium ion [O. lucimarinus CCE9901]	:::::::::::::::::::::
	S.maritima32700/	Cleavage/
	Homeobox-leucine zipper protein REVOLUTA-like [B. vulgaris subsp. vulgaris]	::.:::::::::::::::.
sma-miR171b	S.maritima13778/	Cleavage/	SRX001383.169033/	Translation/
sma-miR171b	F-box/kelch-repeat protein At3g23880-like isoform X1 [B. vulgaris subsp. Vulgaris]	::: ::::..::::::::::	RNA helicase 36, partial [D. oppositifolia]	::::::: : :::::::::
	S.maritima44824/	Cleavage/
	Scarecrow-like protein 6 isoform X1 [B. vulgaris subsp. vulgaris]	:::::::::.:::::::::::
sma-miR396b	S.maritima38649/	Translation/	SRX001383.11076/	Cleavage/
sma-miR396b	dnaJ protein ERDJ3A [B. vulgaris subsp. vulgaris]	.:.:::::::.:: :::::.:.:	Rhodanese-like domain-containing protein 14, chloroplastic [V. vinifera]	.:::::: : :::::::::::
	S.maritima27747/	Cleavage/	SRX001383.145227/	Cleavage/
	Growth-regulating factor 2-like [B. vulgaris subsp. vulgaris]	:::::::::::: :::::::	Hypothetical protein PHAVU_009G048400g [P. vulgaris]	.:::::: : :.:::::::::
	S.maritima36182/	Translation/	SRX001383.205893/	Cleavage/
	CRS2-associated factor 2, chloroplastic [B. vulgaris subsp. vulgaris]	:: ::::::::: :::::::	ABC transporter F family member 5 [M. notabilis]	::::: :: :.::.:::::::
Conserved miRNAs with precursors identified only in S. maritima
sma-miR169a^b	S.maritima467708/	Cleavage/
sma-miR169a^b	Oxysterol-binding protein-related protein 4C-like [B. vulgaris subsp. vulgaris]	:::::::::::::::::::::
sma-miR164a^b	S.maritima27444/	Cleavage/
sma-miR164a^b	Uncharacterized proteinLOC104894828 [B. vulgaris subsp. vulgaris])	:::: :::.:::::::::.::
	S.maritima37419/	Translation/
	Lipid phosphate phosphatase delta [B. vulgaris subsp. vulgaris]	: :.:::::: ::::::.::
sma-miR157a^b	S.maritima347871/	Cleavage/
sma-miR157a^b	Squamosa promoter-binding-like protein 3 [P. euphratica]	::::::::::::::::::::
	S.maritima95321/	Cleavage/
	Hypothetical proteinPRUPE_ppa003644mg [P. persica]	::::::::: ::::::::::
	S.maritima700613/	Cleavage/
	Putative F-box/kelch-repeat proteinAt4g12810 [B. vulgaris subsp. vulgaris]	::::::::.:.::.: ::::
	S.maritima34755/	Cleavage/
	Ubiquitin-fold modifier-conjugating enzyme 1 [B. vulgaris subsp. vulgaris]	::.:::.::::: ::::..:
	S.maritima15309/	Cleavage/
	Putative G3BP-like protein isoform X2 [B. vulgaris subsp. vulgaris]	::::: :: :.::.::::::

The targets were identified in S. maritima, and also in Rhizophora mangle and Heritiera littoralis, the mangrove plants as the ESTs of these plants were used initially for identification of the novel miRNAs in S. maritima. SRX001383 and SRX001410 are the accession numbers of R. mangle and H. littolalis, respectivey in NCBI database
^aFor sequence please see Additional file 10
^bPrecursor not identified in the mangrove plants R. mangle and H. littoralis

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