白桦BpNAC012基因调控白桦木质部发育表达谱分析

doi:10.7525/j.issn.1673-5102.2021.02.013

摘要/Abstract

摘要：

NAC转录因子成员被认为是调控植物次生壁合成的开关。前期研究结果显示BpNAC012基因的表达能够调控白桦次生细胞壁的合成。为研究BpNAC012调控的下游靶基因，本研究分别以该基因的过表达，抑制表达株系茎为材料构建转录组，以野生型为对照分析差异表达基因。结果显示：与对照相比，过表达株系OE中上调的基因有627条，下调的基因有229条，抑制表达株系中上调的基因有299条，下调表达的基因有207条。过表达BpNAC012相对于抑制表达能够调控更多的基因表达变化。而抑制表达BpNAC012更多的是影响蛋白修饰和转运类基因的表达变化。在差异表达基因中，涉及受体信号通路，营养代谢，氨基酸合成，及苯丙烷生物合成相关代谢通路基因比较富集。BpNAC012能够调控纤维素、木质素合成及木质部发育相关基因的表达变化，同时能够调控多种转录因子的表达变化。该研究为深入分析BpNAC012在白桦次生细胞壁合成的分子调控机制奠定基础。

关键词: 白桦, BpNAC012, 表达谱分析, 木质部发育

Abstract:

NAC transcription factors have been considered to be the switches that regulate the formation of plant secondary cell walls. Our previous work indicated that the gene BpNAC012 was involved in the secondary cell wall biosynthesis of birch. In order to identify the downstream target genes regulated by BpNAC012， transcriptome sequencing of stems from BpNAC012over-expression and RNAi plants was conducted， and the differentially expressed genes were identified compare to the wild type birch. The results showed that， in contrast to the wild type plants， 627 genes were up-regulated and 229 genes were down-regulated in the over-expression transgenic line， and 299 up-regulated genes and 207 down-regulated genes were identified in the RNAi lines. The expression changes of downstream genes in the overexpression transgenic lines were much greater than that in the RNAi plants. Inhibition of BpNAC012 expression significantly affected the expression of genes related to protein modification and transport. The differentially expressed genes were enriched in pathways such as receptor signaling pathways， nutritional metabolism， amino acid synthesis， and phenylpropane biosynthesis. In addition， BpNAC012 can regulate the expression of genes related to cellulose， lignin bio-synthesis and xylem development， as well as a variety of transcription factors. This study laid the foundation for further analysis of the molecular regulatory mechanism of BpNAC012 in secondary cell wall bio-synthesis of birch.

Key words: Betula platyphylla, BpNAC012, expression profile analysis, xylem development

中图分类号:

S792.153

郭依萍, 刘佳欣, 于颖, 王超, 杨传平. 白桦BpNAC012基因调控白桦木质部发育表达谱分析[J]. 植物研究, 2021, 41(2): 251-261.

Yi-Ping GUO, Jia-Xin LIU, Ying YU, Chao WANG, Chuan-Ping YANG. Expression Profile Analysis ofXylem Development Regulated by BpNAC012 Gene from Betula platyphylla[J]. Bulletin of Botanical Research, 2021, 41(2): 251-261.

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过表达株系木质部发育相关上调表达基因

基因ID Gene_id	log2倍数变化 log2 fold change	基因长度 Gene length	NR GI	NR ID	NR评估 NR Evalue	NR说明 NR Description
Cluster-12857.118958	4.8343	1483	359497539	XP_003635559.1	1.90E-159	PREDICTED:cellulose synthase-like protein E6 isoform X1[Vitis vinifera]
Cluster-12857.76168	2.3144	2522	225457723	XP_002277713.1	1.70E-274	PREDICTED: probable cellulose synthase A catalytic subunit 5 [UDP-forming][Vitis vinifera]
Cluster-12857.74320	3.2946	681	571534195	XP_003549490.2	5.30E-93	PREDICTED: probable xyloglucan endotransglucosylase/hydrolase protein 23-like[Glycine max]
Cluster-12857.86571	3.5818	375	590661748	XP_007035759.1	1.10E-60	Xyloglucan endotransglucosylase/hydrolase family protein [Theobroma cacao]
Cluster-12857.94374	3.8561	1450	590683434	XP_007041599.1	7.30E-108	Fructose-1,6-bisphosphatase, cytosolic[Theobroma cacao]
Cluster-12857.94375	6.9966	1771	590683434	XP_007041599.1	7.20E-118	Fructose-1,6-bisphosphatase, cytosolic[Theobroma cacao]
Cluster-12857.76506	2.2768	2951	567877365	XP_006431272.1	1.20E-266	hypothetical protein CICLE_v10011622mg[Citrus clementina]
Cluster-12857.90286	5.2815	1523	645249297	XP_008230687.1	4.90E-155	PREDICTED:probable galacturonosyltransferase-like 10[Prunus mume]
Cluster-12857.59289	1.0271	7112	658001427	XP_008393176.1	9.70E-222	PREDICTED:galactoside 2-alpha-L-fucosyltransferase-like[Malus domestica]
Cluster-12857.85038	2.3215	3248	694386135	XP_009368869.1	5.40E-151	PREDICTED:glucan endo-1,3-beta-glucosidase 14-like[Pyrus x bretschneideri]
Cluster-12857.105697	1.9631	2202	802652705	XP_012080173.1	7.50E-181	PREDICTED:probable beta-1,3-galactosyltransferase 19[Jatropha curcas]
Cluster-12857.77676	3.1264	1772	645247636	XP_008229928.1	3.70E-69	PREDICTED:fasciclin-like arabinogalactan protein 2[Prunus mume]
Cluster-12857.82137	8.2031	1984	166209291	ABY85195.1	2.50E-268	p-coumaryl-CoA 3'-hydroxylase[Populus alba×Populus grandidentata]
Cluster-12857.97128	10.632	2699	720084019	XP_010243074.1	2.60E-159	PREDICTED:probable phenylalanine—tRNA ligase alpha subunit[Nelumbo nucifera]
Cluster-12857.41401	4.3742	1547	854930414	AKN79297.1	8.70E-67	peroxidase 4[Betula platyphylla]
Cluster-12857.76083	9.0528	1305	470108362	XP_004290489.1	5.90E-141	PREDICTED:peroxidase 12[Fragaria vesca subsp.vesca]
Cluster-12857.113235	5.9308	1124	255542656	XP_002512391.1	6.40E-35	serine-threonine protein kinase,plant-type, putative[Ricinus communis]
Cluster-8794.3	6.5661	2512	255555051	XP_002518563.1	3.40E-105	serine-threonine protein kinase, plant-type, putative[Ricinus communis]
Cluster-12857.119083	2.6264	1800	225452312	XP_002272486.1	3.40E-38	PREDICTED: serine/threonine-protein kinase HT1[Vitis vinifera]
Cluster-12857.118054	4.7784	2738	645224059	XP_008218928.1	6.30E-270	PREDICTED: serine/threonine-protein kinase-like protein CCR4[Prunus mume]
Cluster-12857.61436	5.542	320	568883219	XP_006494380.1	6.20E-28	PREDICTED: wall-associated receptor kinase-like 8-like[Citrus sinensis]
Cluster-12857.80854	1.1382	3198	590591190	XP_007016945.1	1.40E-143	Leucine-rich repeat protein kinase family protein, putative isoform 1[Theobroma cacao]
Cluster-12857.46913	2.5993	1991	590640151	XP_007029875.1	2.40E-178	Leucine-rich repeat containing protein, putative isoform 1[Theobroma cacao]

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参考文献 16

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样本 Sample	原始序列 Original sequence	过滤数据 Filter data	测序量 Sequencing volume	错误率 Error rate（%）	Q20（%）	Q30（%）	GC（%）
WT_1	56242018	55322414	8.3G	0.03	97.48	92.81	46.34
WT_2	58518124	56683910	8.5G	0.03	97.55	92.97	46.30
WT_3	52203502	50544932	7.58G	0.03	97.42	92.71	46.30
OE_1	58644414	57292724	8.59G	0.03	97.81	93.58	46.46
OE_2	59189588	57679272	8.65G	0.03	97.34	92.52	46.55
OE_3	56973490	56366534	8.45G	0.03	97.81	93.59	46.45
RS_1	51023786	50389048	7.56G	0.03	97.52	92.95	46.56
RS_2	54950226	54540828	8.18G	0.03	97.33	92.47	46.51
RS_3	57784458	57021886	8.55G	0.03	97.26	92.35	46.37

	基因数量 Number of genes	百分率 Percentage（%）
NR数据库所占比例Proportion of NR database	117 364	65.57
NT数据库所占比例Proportion of NT database	92 957	51.93
KO数据库所占比例Proportion of KO database	44 707	24.97
SwissProt数据库所占比例Proportion of SwissProt database	86 603	48.38
PFAM数据库所占比例Proportion of PFAM database	84 724	47.33
GO数据库所占比例Proportion of GO database	86 008	48.05
KOG数据库所占比例Proportion of KOD database	29 536	16.50
7大数据库共同出现的比例The proportion of 7 major databases	18 243	10.19
至少一个数据库注释成功的比例Proportion of at least one database annotation success	129 213	72.19
总基因数Total genes	178 983	100.00

数据库中唯一的标号信息 GO accession gene ontology	功能的描述信息 Description gene ontology	为该GO的类别 Term type	富集分析统计学显著水平 Over represented p-value	校正后的p-value Corrected p-value	DEG item	DEG list
GO:0001071	nucleic acid binding transcription factor activity	molecular_function	5.8636e-17	1.7558e-13	60	581
GO:0003700	transcription factor activity, sequence-specific DNA binding	molecular_function	5.8636e-17	1.7558e-13	60	581
GO:0005667	transcription factor complex	cellular_component	7.2294e-14	1.4432e-10	66	581
GO:0006355	regulation of transcription, DNA-templated	biological_process	1.0952e-08	1.3118e-05	85	581

基因ID Gene_id	log2倍数变化log2 fold change	基因长度 Gene length	NR GI	NR ID	NR评估 NR evalue	NR注释 NR description
Cluster-12857.66427	13.492	2 378	118132570	ABK60177.1	4.80E-16	conserved hypothetical protein[Streptomyces ghanaensis ATCC 14672]
Cluster-12857.79868	11.786	4 286	645227348	XP_008220472.1	0.00E+00	PREDICTED: glycine dehydrogenase（decarboxylating）,mitochondrial[Prunus mume]
Cluster-12857.83191	11.500	3 565	802581682	XP_012069851.1	2.40E-205	PREDICTED:probable methyltransferase PMT3[Jatropha curcas]
Cluster-12857.66430	11.254	2 133	566183478	XP_002311438.2	8.50E-190	DNA-binding protein RAV2[Populus trichocarpa]
Cluster-12857.97128	10.632	2 699	720084019	XP_010243074.1	2.60E-159	PREDICTED:probable phenylalanine--tRNA ligase alpha subunit[Nelumbo nucifera]
Cluster-12857.60814	10.592	8 563	645275167	XP_008242682.1	0.00E+00	PREDICTED:dnaJ homolog subfamily C GRV2 isoform X2[Prunus mume]
Cluster-12857.62522	10.323	3 186	590658081	XP_007034748.1	1.50E-294	No lysine kinase 1 isoform 1[Theobroma cacao]
Cluster-12857.109476	10.191	1 118	590634122	XP_007028287.1	3.30E-116	2,4-dienoyl-CoA reductase isoform 2[Theobroma cacao]
Cluster-12857.80721	9.689 3	2 946	645260833	XP_008236004.1	1.20E-197	PREDICTED: amino acid permease 3-like[Prunus mume]
Cluster-12857.54251	9.565 4	945	723712802	XP_010323300.1	1.50E-21	PREDICTED: cucumber peeling cupredoxin-like[Solanum lycopersicum]

基因ID Gene_id	log2倍数变化 log2 fold change	基因长度 Gene length	NR GI	NR ID	NR评估 NR evalue	NR说明 NR description
Cluster-12857.25938	-11.44 8	2 910	645278673	XP_008244338.1	4.70E-183	PREDICTED:kinesin-3[Prunus mume]
Cluster-12857.85041	-9.912 4	4 383	449456208	XP_004145842.1	1.60E-126	PREDICTED:UTP--glucose-1-phosphate uridylyltransferase[Cucumis sativus]
Cluster-12857.98081	-9.167 2	4 075	297745750	CBI15806.3	3.60E-35	unnamed protein product[Vitis vinifera]
Cluster-12857.25935	-9.037 2	2 757	645278673	XP_008244338.1	4.50E-183	PREDICTED:kinesin-3[Prunus mume]
Cluster-12857.74657	-8.754 7	2 186	719976857	XP_010248668.1	1.90E-112	PREDICTED:uncharacterized protein LOC104591513[Nelumbo nucifera]
Cluster-12857.45080	-8.609 6	3 854	645230669	XP_008222040.1	2.60E-277	PREDICTED:ankyrin repeat and sterile alpha motif domain-containing protein 1B-like[Prunus mume]
Cluster-12857.58236	-8.509 5	3 080	590658081	XP_007034748.1	1.40E-294	No lysine kinase 1 isoform 1[Theobroma cacao]
Cluster-12857.27318	-8.495 4	2 146	596174565	XP_007223177.1	5.00E-105	hypothetical protein PRUPE_ppa009157mg[Prunus persica]
Cluster-12857.135896	-8.463 2	1 217	590566763	XP_007010326.1	4.60E-132	Catalytic,putative isoform 1[Theobroma cacao]
Cluster-12857.69484	-8.311 2	2 496	567877953	XP_006431535.1	1.20E-38	hypothetical protein CICLE_v10003979mg,partial[Citrus clementina]