Conifer R2R3-MYB transcription factors: sequence analyses and gene expression in wood-forming tissues of white spruce (Picea glauca)

Bedon, Frank; Grima-Pettenati, Jacqueline; Mackay, John

doi:10.1186/1471-2229-7-17

Table 1 Predicted lengths and C-terminal motifs of spruce MYB proteins

From: Conifer R2R3-MYB transcription factors: sequence analyses and gene expression in wood-forming tissues of white spruce (Picea glauca)

Sg¹		Full length cDNA²	DNA Binding Domain³	C-terminal Domain³	Motifs	Consensus sequences	Angio-Gymno⁴	MEME E-value	Start motif⁵	Ref.
4	Pg MYB5	-b-	115	142	F	LlsrGiDP(at)tHrp(li)n	13/13-5/5	6.00^e-14	1	a)
					G	e(re)cpdLNLel(cr)ispp	13/13-4/5	3.31^e-16	67	a), b)
	Pg MYB10	-a-	115	95	F	LlsrGiDP(at)tHrp(li)n	13/13-5/5	6.52^e-14	1	a)
					G	e(re)cpdLNLel(cr)ispp	13/13-4/5	4.32^e-15	67	a), b)
	Pg MYB13	-b-	116	80	F	LlsrGiDP(at)tHrp(li)n	13/13-5/5	1.18^e-14	1	a)
					G	e(re)cpdLNLel(cr)ispp	13/13-4/5	5.43^e-14	65	a), b)
22	Pg MYB6	-a-	115	235	H	(cs)s(sv)DPpT(ls)LsLslPg	7/7-14/14	2.02^e-14	99	d)
					I	YlkaedaismmsaAv	0/7-13/14	1.87^e-13	141	d)
					J	vmremvakEVrsYmn	7/7-14/14	1.07^e-17	188	a), b), c)
	Pg MYB7	-c-	116	257	K	egdyEVesrgLKRln	0/7-13/14	1.34^e-12	43	d)
					H	(cs)s(sv)DPpT(ls)LsLslPg	7/7-14/14	4.28^e-13	113	d)
					I	YlkaedaismmsaAv	0/7-13/14	2.30^e-10	161	d)
					J	vmremvakEVrsYmn	7/7-14/14	6.15^e-16	206	a), b), c)
	Pg MYB9	-a-	119	297	K	egdyEVesrgLKRln	0/7-13/14	6.03^e-16	60	d)
					P	hRQSAFksYesqktp	0/7-11/14	1.19^e-13	116	d)
					H	(cs)s(sv)DPpT(ls)LsLslPg	7/7-14/14	2.91^e-13	144	d)
					I	YlkaedaismmsaAv	0/7-13/14	9.50^e-16	205	d)
					J	vmremvakEVrsYmn	7/7-14/14	1.09^e-16	256	a), b), c)
8	Pg MYB1	-b-	115	217	A	lr(kq)mGiDP(lv)THkpl	5/5-2/2	1.79^e-18	1	a)
21	Pg MYB3	-c-	130	177	C	(fg)Re(rq)S(rs)(is)(rg)(kr)R	4/5-2/2	4.69^e-14	1	d)
					D	e(en)s(l)(vs)(pt)ffDfl(g)vG(cn)	5/5-2/2	1.26^e-13	35	a), b)
					E	(cy)xi(sg)h(in)nh(v)q(sf)(jr)Kef	3/5-2/2	4.76^e-14	123	d)
13	Pg MYB8	-c-	115	411	L	LrrGIDP(n)THkpl	4/4-2/2	2.54^e-17	1	a)
					M	VC(dv)(yk)(np)SIm(al)nPsm(yn)	2/4-2/2	1.94^e-18	199	d)
					N	e(ye)(ae)vKWSEml	2/4-2/2	6.45^e-14	317	d)
					O	(pk)D(fl)(hq)R(im)Aa(vs)(lf)(dg)q	2/4-2/2	4.89^e-15	399	a)
9	Pg MYB11	-a-	115	384	Q	L(lv)kMGIDPvTHkp(k)	6/6-1/1	4.08^e-16	1	a), b), c)
					R	h(m)AQWEsARleAear	6/6-1/1	3.10^e-13	35	a), b), c)
					S	(yc)eDnknYw(nd)silnlV	4/6-1/1	6.79^e-12	360	c)
2	Pg MYB12	-a-	115	254	T	MdfW(fl)(dn)v(fl)(t)	5/5-1/1	2.39^e-09	237	a)
nd	Pg MYB2	-c-	115	333	B	(c)SylPPL(y)d(v)	2/2-2/2	3.29^e-13	249	d)
	Pg MYB4	-c-	120	214	none	none	0/3-0/2	none	none	none

Conserved amino acid regions were identified in angiosperm and gymnosperm C-terminal sequences by the use of MEME software (setting described in Methods). Motifs were detected among the sequences belonging to each phylogenetic clade comprised of at least one spruce MYB (Additional File 2). Sequences from Additional File 3 were used to identify more conifer members of the PgMYB6, 7, 9 clade. Within the consensus sequences, upper-case letters indicate amino acids found in all members of a subgroup, lower-case letters indicate amino acids conserved in more than 50% of the members, pairs of lower-case amino acid in brackets show the two most abundant amino acids present for 50% each and above, x indicates that no amino acid is conserved among the sequences.
¹Sg, MYB subgroups identified by Kranz et al. [18].
²Source of full length cDNA sequence: -a-, full length cDNA clone identified from EST of Picea glauca database; b- partial cDNA clone identified from EST database of P. glauca, extended by RACE amplifications and finally amplified as a single clone by PCR with gene specific primers, and -c-, from non degenerates primers based on Pinus taeda MYB sequences and used on spruce cDNA followed by RACE amplifications.
³Lengths are expressed in amino acid (aa) residues.
⁴The number of MYB sequences, separately from angiosperm and gymnosperms, sharing the motif among all those used in each case.
⁵The position of the motif relative to the beginning of the C-terminal domain (5' end).
Ref: references for previously reported motifs, a) Kranz et al. [18], b) Stracke et al. [31] and c) Jiang et al. [30] and d) new motifs.

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ISSN: 1471-2229

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