白菜、甘蓝和甘蓝型油菜PAP1/2同源基因的鉴定及分析

doi:10.16420/j.issn.0513-353x.2021-0629

摘要/Abstract

摘要：

PAP1/2转录因子是参与形成MBW复合体从而调控花青素合成的主要MYB转录因子。以拟南芥PAP1/2转录因子核酸和蛋白序列比对及Pfam验证,研究白菜、甘蓝和甘蓝型油菜等芸薹属植物中PAP1/2转录因子调控花青素代谢的确切同源拷贝数、进化关系及表达情况：在白菜、甘蓝及甘蓝型油菜中鉴定到的PAP1/2转录因子同源拷贝数分别为3、4和9个;通过进化分析和PAP1/2转录因子同源拷贝所在区段微共线性分析进一步明确了其不同拷贝间的进化关系,厘清了A7和C6染色体上PAP1/2转录因子不同拷贝的相互关系;结合白菜、甘蓝和甘蓝型油菜不同组织转录组测序数据进行表达情况分析,阐明了PAP1/2转录因子同源拷贝在不同组织中的表达情况。

关键词: 白菜, 甘蓝, 甘蓝型油菜, 同源基因, 保守结构域, 花青素, R2R3-MYB转录因子, PAP1/2

Abstract:

PAP1/2 transcription factors are the main MYB transcription factors involved in the formation of MBW complex to regulate anthocyanin biosynthesis. Using Arabidopsis PAP1/2 transcription factor（TF）nucleic acid and protein sequence alignment and Pfam verification to study the exact homologous copy number,evolutionary relationship and expression of PAP1/2 TFs regulating anthocyanin metabolism in Brassica plants such as Brassica rapa,B. oleracea and B. napus. The number of homologous copies of PAP1/2 TFs identified in B. rapa,B. oleracea and B. napus were three,four and nine,respectively. The evolutionary relationship between different copies of PAP1/2 TFs was further clarified by evolution analysis and microcollinearity analysis of the segment where the homologous copies of PAP1/2 TFs were located. The relationship between different copies of PAP1/2 TFs on chromosomes A7 and C6 was clarified. Finally,combined with the transcriptome sequencing data of different tissues of B. rapa,B. oleracea and B. napus,the expression analysis was carried out,and the expression of homologous copies of PAP1/2TFs in different tissues was clarified.

Key words: Brassica rapa, B. Oleracea, B. Napus, homologous gene, conserved domain, anthocyanin, R2R3-MYB transcription factor, PAP1/2

中图分类号:

S635

陈道宗, 刘镒, 沈文杰, 朱博, 谭晨. 白菜、甘蓝和甘蓝型油菜PAP1/2同源基因的鉴定及分析[J]. 园艺学报, 2022, 49(6): 1301-1312.

CHEN Daozong, LIU Yi, SHEN Wenjie, ZHU Bo, TAN Chen. Identification and Analysis of PAP1/2 Homologous Genes in Brassica rapa,B. oleracea and B. napus[J]. Acta Horticulturae Sinica, 2022, 49(6): 1301-1312.

图/表 10

表1 拟南芥、白菜、甘蓝和甘蓝型油菜PAP1/2同源基因拷贝数及共线性关系

Table 1 Copy number and collinearity of PAP1/2 homologous genes in Arabidopsis,Brassica rapa,B. oleracea and B. napus

Function	拟南芥 A. thaliana	白菜 B. rapa	甘蓝 B. oleracea	甘蓝型油菜-AA B. napus-AA	甘蓝型油菜-CC B. napus-CC
PAP1(MYB75)	AT1G56650	BraA02g017040.3C	Bo00835s060.1	BnaA02G0160600ZS	BnaC02G0205500ZS
PAP1(MYB75)	AT1G56650	BraA03g040840.3C	Bo3g081880.1	BnaA03G0376600ZS	BnaC03G0461400ZS
PAP1(MYB75)	AT1G56650		Bo6g099880.1	BnaA07G0286900ZS	BnaC06G0328400ZS
PAP1(MYB75)	AT1G56650				BnaC06G0328700ZS
PAP2(MYB90)	AT1G66390	BraA07g032100.3C	Bo6g100940.1	BnaA07G0287000ZS	BnaC06G0329100ZS

图1 拟南芥、白菜、甘蓝和甘蓝型油菜PAP1/2同源基因进化分析

Fig. 1 Evolutionary analysis of PAP1/2 homologous genes in Arabidopsis,Brassica rapa,B. oleracea and B. napus

图2 拟南芥、白菜、甘蓝和甘蓝型油菜PAP1/2同源基因所在区段微共线性分析 A. A2-C2、A3-C3染色体PAP1/2同源基因所在区段微共线性分析;B. A7-C6染色体PAP1/2同源基因所在区段微共线性分析。

Fig. 1 The comparison map of the segment of PAP1/2 homologous genes in Arabidopsis,Brassica rapa,B. oleracea and B. napus A. The comparison map of the segment of PAP1/2 homologous genes on A2-C2,A3-C3 chromosome;B. The comparison map of the segment of PAP1/2 homologous genes on A2-C6 chromosome.

表2 拟南芥、白菜、甘蓝和甘蓝型油菜PAP1/2同源基因所在区段微共线性分析

Table 2 The comparison map of the segment of PAP1/2 homologous genes in Arabidopsis,Brassica rapa,B. oleracea and B. napus

	拟南芥 A. thaliana	白菜B. rapa Chiifu-A2	甘蓝B. oleracea TO1000-C2	甘蓝型油菜B. napus ZS11-A2	甘蓝型油菜B. napus ZS11-C2
A2-C2	AT1G66330	BraA02g017010.3C	Bo2g052820.1	BnaA02G0160200ZS	BnaC02T0204500ZS
	AT1G66390	BraA02g017040.3C	Bo00835s060.1	BnaA02T0160600ZS	BnaC02T0205500ZS
	AT1G66470	BraA02g017080.3C	Bo00835s050.1	BnaA02T0160700ZS	BnaC02T0205700ZS
A3-C3	AT1G66330	Null	Null	Null	Null
	AT1G56650	BraA03g040840.3C	Bo3g081880.1	BnaA03G0376600ZS	BnaC03G0461400ZS
	AT1G66470	Null	Null	Null	Null
A7-C6	AT1G66210	BraA07g032000.3C	Bo6g099780.1	BnaA07T0285500ZS	BnaC06T0327300ZS
	AT1G66390	BraA07g032100.3C	Bo6g099880.1	BnaA07G0286900ZS	BnaC06G0328400ZS
	AT1G66390	BraA07g032100.3C	Bo6g099880.1	BnaA07G0286900ZS	BnaC06G0328700ZS
	AT1G66390	BraA07g032100.3C	Bo6g099880.1	BnaA07G0287000ZS	BnaC06G0329100ZS
	AT1G66840	BraA07g032410.3C	Bo6g101320.1	BnaA07T0289800ZS	BnaC06T0333000ZS

图3 拟南芥、白菜、甘蓝和甘蓝型油菜PAP1/2同源基因R2、R3保守结构域基序

Fig. 3 R2,R3 conserved domain motif of PAP1/2 homologous genes in Arabidopsis,Brassica rapa,B. oleracea and B. napus

图4 拟南芥、白菜、甘蓝和甘蓝型油菜不同组织PAP1/2同源基因蛋白保守基序

Fig. 4 Protein conservation motif analysis of PAP1/2 homologous genes in different tissues of Arabidopsis,Brassica rapa,B. oleracea and B. napu

表3 拟南芥、白菜、甘蓝和甘蓝型油菜PAP1/2同源基因保守结构域基序

Table 3 Conserved motif sequence of PAP1/2 homologous genes in Arabidopsis,Brassica rapa,B. oleracea and B. napus

保守结构域名称 Motif name	保守结构域序列 Motif sequence	e值 e-value	宽度 Width
Motif 1	C[KN]T[KQ]M[KR]KRN[IV][PT][CF]S[SY]T[TQ]PAQK[IN][DE]V[FL]KPRPR[SL] FTVNNGCSH[LIF][NH]G[ML]P[EK][VA]D[VI][VI]P	1.4e-672	50
Motif 2	[YS]ELV[SN]NLMDG[EQ]N[MR]WW[EK]SLL[ED]ES[QK][DEQ]P[AD][AG][LI][VF] P[EK][AGS]T[AE]T[KE]K[GL]AT[SF]AFDVEQLW[SN]	3.1e-601	50
Motif 3	AWTAEED[SN]LLR[QR]CIDKYGEGKWHQVPLRAGL	8.7e-512	31
Motif 4	K[LF][SN]SDEVDLLLRLHKLLGNRWSLIAGRLPGRTAND[VI]KNYWNTHLSKKHEP	7.6e-799	50
Motif 5	RCRKSCRLRWLNYLKPSI[KN][RK]G	3.0e-340	21
Motif 6	[ND][TIA]NNV[CS]EN[SI][IFM]T[CY][NK][KN]D	2.0e-156	15
Motif 7	ME[GD]S[SP]KGL[RKT]KG	1.2e-113	11
Motif 8	[LM]LDGET[VG][ET]	7.2e-62	8
Motif 9	[LP][CF]LG[LFV]N	1.4e-20	6

图5 白菜（A）、甘蓝（B）和甘蓝型油菜（C）不同组织PAP1/2同源基因表达热图

Fig. 5 The expression heat map of PAP1/2 homologous genes in different tissues of Brassica rapa（A）,B. oleracea（B）and B. napus（C）

图6 白菜（A）、甘蓝（B）和甘蓝型油菜（C）PAP1/2同源基因的表达分析

Fig. 6 Expression analysis of PAP1/2 homologous genes in Brassica rapa（A）,B. oleracea（B）and B. napus（C）

图7 白菜（A）、甘蓝（B）和甘蓝型油菜（B）叶片PAP1/2同源基因qRT-PCR验证

Fig. 7 qRT-PCR analysis of PAP1/2 homologous genes in Brassica rapa（A）,B. oleracea（B）and B. napus（C）of leaf

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