Comparative genomic analysis of the R2R3 MYB secondary cell wall regulators of Arabidopsis, poplar, rice, maize, and switchgrass

Zhao, Kangmei; Bartley, Laura E

doi:10.1186/1471-2229-14-135

Table 4 Groups of homologous proteins from poplar, rice, maize and switchgrass relative to the Arabidopsis R2R3 MYB secondary cell wall (SCW) regulators

From: Comparative genomic analysis of the R2R3 MYB secondary cell wall regulators of Arabidopsis, poplar, rice, maize, and switchgrass

Class	Arabidopsis	Poplar POPTR_00	Sequence identity (%)	Rice LOC_Os	Sequence identity (%)	Maize GRMZM	Sequence identity (%)	Switchgrass	Sequence identity (%)
I	AtMYB26	01s20370	47	01g51260	45	2G0887834	45	AP13ISTG69224	44
I	AtMYB103	03s13190	60	08g05520	50	2G325907	48	AP13CTG15561	51
		01s09810	62					AP13ISTG58495	50
I	AtMYB69	07s04140	53	11g10130	47	5G803355	48	Pavirv00031864m	50
				05s06410	53			Pavirv00029353m	50
								Pavirv00020802m	49
II	AtMYB46^a	PtrMYB3	58^b	OsMYB46	47 ^a	ZmMYB46	49 ^a	AP13ISTG55479	50 ^a
	AtMYB83^b	PtrMYB20	57^b					AP13ISTG55477	51 ^b
		09s05860	53^a
		01s26590	54^a
II	AtMYB20 ^a	04s08480	58^b	09g23620	54^a	2G169356	55 ^a	Pavirv00023586m	69 ^a
	*AtMYB43* ^b	*17s02850*	58 ^a	*08g33150*	56 ^a	2G126566	52 ^a	*KanlCTG16207*	53 ^a
								*AP13ISTG67468*	51 ^a
								Pavirv00053167m	60^a
								AP13ISTG57686	56^a
								Pavirv00069978m	56^a
								Pavirv00023587m	53^a
								Pavirv00051815m	57^a
								Pavirv00011866m	57^a
II	AtMYB42 ^a	03s11360	61 ^b	09g36250	51 ^a	2G104551	52 ^b	AP13ISTG65795	52 ^b
	*AtMYB85* ^b	01s07830	61^a			2G138427	53^b	AP13CTG22878	52 ^b
		15s14600	55^b			2G037650	52^b	AP13CTG08064	53^b
		12s14540	57^b
II	AtMYB52 ^a	17s04890	55 ^a	03g51110	52 ^a	2G455869	53 ^a	AP13ISTG34280 ^d	59 ^a
	AtMYB54 ^b	15s05130	57^b			2G077147	52^a	AP13ISTG43780 ^d	54 ^b
		12s03650	58^b					Pavirv00048592m ^d	54 ^b
		07s01430	53^a					Pavirv00048591m ^d	55 ^b
								Pavirv00005610m	52^b
III	AtMYB58 ^a	07s08190	48 ^a	02g46780	49 ^a	5G833253	46 ^a	Pavirv00055045m	47 ^b
	AtMYB63 ^b	05s09930	48^a	04g50770	48^a	2G097636	47^a	AP13ISTG56055	38^a
						2G097638	50^a	Pavirv00019950m	49^a
						2G038722	47^a	Pavirv00047040m	51^b
								AP13ISTG56056	49^a
								Pavirv00053415m	50^a
III	AtMYB61 ^a	05s00340	53 ^a	05g04820	57 ^b	2G127490	56 ^b	AP13CTG04029	56 ^b
	AtMYB50^b	13s00290	60 ^a	01g18240	57 ^b	2G171781	56 ^b	Pavirv00042495m	56 ^b
	AtMYB55^c	02s18700	56^c			2G017520	56 ^b	Pavirv00021467m	56 ^b
		14s10680	57^c					Pavirv00035679m	58 ^b
								Pavirv00041312m	58 ^b
III	AtMYB4 ^a	05s11410	67 ^a	09g36730	68 ^a	2G000818	75 ^a	AP13ISTG73550	68 ^a
	*AtMYB32* ^b	09s13640	66^a	08g43550	56^b	ZmMYB31	65 ^a	AP13ISTG73836	70 ^a
		04s18020	70^a			*ZmMYB42*	65 ^a	PvMYB4.a ^d	64 ^a
						(2G084583)	66 ^a	(PvMYB4.b ^d )	64 ^a
								(PvMYB4.c ^d )	64 ^a
								(PvMYB4.d ^d )	64 ^a
								(PvMYB4.e ^d )	64 ^a
IV	AtMYB75	05s14450	67 ^a
	AtMYB90	05s14460	67 ^a
	AtMYB113	05s14470	67 ^a
	AtMYB114 ^a	05s14480	70 ^a
		05s14490	72 ^a

Classes refer to the phylogentic relationships between the Arabidopsis and rice proteins in the clade as described in the text. Proteins are divided within each class based on maximum likelihood phylogenic reconstruction. Bold font indicates putative orthologous and paralogous relationships based on OrthoMCL analysis. Italic and round brackets indicate additional OrthoMCL groups within the clade.
^{a, b, c}Indicate proteins with highest sequence identity to the indicated Arabidopsis MYB.
^dMYBs that have ≥99% protein sequence similarity that are likely allelic to each other.
^eArabidopsis MYBs implicated in functions besides SCW regulation with higher sequence identity to proteins from the other species compared with the At SCW MYBs in the same clade.

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ISSN: 1471-2229

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