板栗类黄酮合成通路13个基因家族的鉴定及表达分析

doi:10.13560/j.cnki.biotech.bull.1985.2024-0537

摘要/Abstract

摘要：

目的从板栗基因组中鉴定类黄酮合成通路13个基因家族，分析其在果实成熟过程和果实顶部芽组织PCD过程中的表达模式，为后续研究板栗类黄酮相关基因功能奠定基础。方法利用生物信息学技术鉴定板栗类黄酮合成通路13个基因家族，对其系统进化关系、蛋白理化性质、蛋白结构、基因结构、顺式作用元件、共线性关系、密码子偏好性等内容进行分析，同时，利用转录组和RT-qPCR分析不同发育时期板栗果实成熟过程和果实顶部芽组织PCD过程表达模式。结果板栗类黄酮合成通路13个基因家族57个成员分布在12个染色体及4个contig上。各基因家族包含1-2个关键结构域，各基因家族成员内含子数量具有一定的相似性。顺式作用元件分析结果显示，大量的生长发育相关元件、激素响应元件以及胁迫响应元件存在板栗中类黄酮合成通路基因家族成员启动子上。在板栗基因组内共发现7对共线性基因对，同时，发现4个基因与8个单双子叶植物均有共线性基因。密码子偏好性发现RSCU值大于1的偏好A/U结尾，且ENC值均超过35。转录组与RT-qPCR结果都显示，多个黄酮合成通路基因在板栗果实成熟过程和果实顶部芽组织PCD过程表达量上调。结论共鉴定57个板栗类黄酮合成通路基因，CmLAR2、CmCHI1、Cm4CL1、CmC4H3、CmPAL1、CmPAL2、Cm4CL6和CmANR3在板栗果实成熟过程和果实顶部芽组织PCD过程均表达量上调，可能参与板栗果实成熟过程和板栗芽组织PCD过程。

关键词: 板栗, 类黄酮, 基因家族, 共线性, 密码子

Abstract:

Objective Identifying 13 gene families of the flavonoid synthesis pathway from the chestnut genome and analyzing their expression patterns during fruit ripening and PCD of fruit top bud tissue may lay a foundation for subsequent studies on the function of flavonoids-related gene in chestnut. Method Bioinformatics techniques was used to identify 13 gene families in chestnut flavonoids synthesis pathway, and analyze their phylogenetic relationships, protein physicochemical properties, protein structure, gene structure, cis-acting elements, collinearity relationships, and codon preference. Both transcriptome and RT-qPCR were used to analyze the expression patterns during fruit ripening and PCD of fruit top bud tissue. Result The 57 members of 13 chestnut flavonoid synthesis pathway gene family distributed on 12 chromosomes and 4 contigs. Each gene family contained 1-2 key domains, and the number of introns of each gene families member was similar. The results of cis-acting element analysis showed that a large number of growth and development related elements, hormone response elements and stress response elements existed on the promoters of flavonoid synthesis pathway gene family members in chestnut. A total of seven collinear gene pairs were found within the chestnut genome, and four genes were also found to have collinear genes with eight monodicotydon plants. Codon usage bias analysis found preferred A/U endings with RSCU values greater than 1, and all ENC values were above 35. Both transcriptome and RT-qPCR results showed the upregulation of multiple flavonoids synthesis pathway genes during chestnut fruit ripening and PCD of fruit top bud tissues. Conclusion A total of 57 genes of the chestnut flavonoid synthesis pathway were identified. The genes of CmLAR2, CmCHI1, Cm4CL1, CmC4H3, CmPAL1, CmPAL2, Cm4CL6 and CmANR3 were upregulated in chestnut fruit ripening process and PCD of fruit top bud tissue, and these genes may be involved in chestnut fruit ripening process and PCD of chestnut bud tissue.

Key words: chestnut, flavonoids, gene family, collinearity, codon

杨涌, 曹蕊, 康肖肖, 刘静, 王旋, 张海娥. 板栗类黄酮合成通路13个基因家族的鉴定及表达分析[J]. 生物技术通报, 2025, 41(2): 270-283.

YANG Yong, CAO Rui, KANG Xiao-xiao, LIU Jing, WANG Xuan, ZHANG Hai-e. Identification and Expression Analysis of 13 Gene Families in the Chestnut Flavonoid Synthesis Pathway[J]. Biotechnology Bulletin, 2025, 41(2): 270-283.

图/表 13

表1 引物序列

Table 1 Primer sequences

基因 Gene	正向引物 Forward primer （5′-3′）	反向引物 Reverse primer （5′-3′）
CmLAR2	GTGGAACCAGCCCTGACC	GGTAGGGCCAAGCAGCAA
CmCHI1	AGCGTCTCTTCCGGGAGT	CGCCGAGGAACAGTGTGT
Cm4CL1	TGACTCAGGCCGACGAGA	CGACTTGTTGTGCCACGC
CmC4H3	AGGGTGTGGAGTTCGGGT	ATGCTCGCCGTAAACCGT
CmPAL1	AGGCCCTCCAATGCAACC	CGGCAGTGACCTGAGCAA
CmPAL2	CGACTCGTGCCGCTATGT	CGGAGTGGCAAGCATGGA
Cm4CL6	ATCCAGAGGCCACGGCTA	CTCGGCAGGGGCTACTTG
CmANR3	CACCGTTCGGTCTGACCC	GGGTGCATTGAAACTCTCTGG
CmActin	ATTCACGAGACCACCTACA	TGCCACAACCTTAATCTTCAT

图1 类黄酮合成通路基因家族系统进化树

Fig. 1 Phylogenetic tree of gene families of the flavonoid synthesis pathway

图2 13个基因家族染色体分布

Fig. 2 Chromosome distribution of the 13 gene families

图3 13个基因家族成员系统进化树（A）、蛋白结构（B）和基因结构（C）

Fig. 3 Phylogenetic tree （A）， protein structure （B）， and gene structure （C） of the 13 gene family members

表2 13个基因家族成员蛋白结构分析

Table 2 Analysis of the protein structures of the 13 gene family members

基因家族 Gene family	以马可夫模型编号 Pfam ID	结构域名称 Domain name
PAL	PF00221	芳香族氨基酸裂解酶 Aromatic amino acid lyase
4CL	PF13193， PF00501	AMP结合酶C末端结构域，AMP结合酶结构域 AMP-binding enzyme C-terminal domain， AMP-binding enzyme domain
CHS	PF02797， PF00195	查尔酮和二苯乙烯合酶，N/C末端结构域 Chalcone and stilbene synthases， N/C-terminal domain
CHI	PF02431	查尔酮黄烷酮异构酶 Chalcone-flavanone isomerase
LAR	PF05368	NmrA-like结构域 NmrA-like domain
DFR	PF01370	NAD依赖性差向异构酶结构域 NAD dependent epimerase domain
ANR	PF01370	NAD依赖性差向异构酶结构域 NAD dependent epimerase domain
F3H	PF03171， PF14226	2OG-FeII_Oxy结构域，DIOX_N结构域 2OG-FeII_Oxy domain， DIOX_N domain
FLS
ANS
C4H	PF00067	细胞色素P450 Cytochrome P450
F3′5′H
FNSII

图4 13个基因家族成员顺式作用元件统计

Fig. 4 Statistics of the cis-acting elements for the 13 gene family members

图5 13个基因家族基因组内共线性（A）和基因对复制类型（B）TRD、DSD、PD、TD及WGD代表转座子复制、分散复制、近端复制、串联复制及全基因组复制。下同

Fig. 5 Collinearity within 13 gene families （A） and gene pairs replication types （B）TRD, DSD, PD, TD and WGD indicate transposon duplication, dispersed duplication, proximal duplication, tandem duplication and whole genome duplication. The same below

表3 基因对Ka/Ks值的计算

Table 3 Calculations of the gene-pairs Ka/Ks values

复制类型 Duplication types	基因对 Gene pairs		非同义替换率 Ka	同义替换率 Ks	非同义替换率/同义替换率 Ka/Ks
WGD	CmPAL3	CmPAL2	0.123 822 763	1.465 415 048	0.084 496 719
WGD	Cm4CL2	Cm4CL11	0.383 354 993	1.384 646 007	0.276 861 372
WGD	CmANR5	CmANR2	0.549 975 334	2.288 010 781	0.240 372 702
WGD	CmC4H1	CmC4H3	0.085 827 583	1.945 979 279	0.044 105 086
WGD	CmANS3	CmANS1	0.219 052 838	1.816 044 933	0.120 620 825
WGD	Cm4CL8	Cm4CL2	0.366 520 820	1.302 665 198	0.281 362 257
WGD	Cm4CL8	Cm4CL11	0.372 236 766	1.132 735 123	0.328 617 661
PD	Cm4CL14	Cm4CL15	0.045 708 825	0.165 863 036	0.275 581 749
TD	Cm4CL3	Cm4CL4	0.143 933 551	0.443 981 508	0.324 188 167
TD	CmPAL5	CmPAL6	0.054 029 598	0.093 294 174	0.579 131 530
TD	CmFNSII2	CmFNSII3	0.139 352 161	0.427 416 010	0.326 034 023
TD	CmDFR1	CmDFR2	0.189 572 148	0.623 062 431	0.304 258 672
TD	CmANR3	CmANR4	0.137 094 524	0.393 608 899	0.348 301 384
TD	Cm4CL4	Cm4CL5	0.133 265 871	0.425 828 776	0.312 956 470
TD	Cm4CL9	Cm4CL10	0.103 441 680	0.273 134 833	0.378 720 204
TD	CmPAL4	CmPAL5	0.052 152 683	0.128 965 485	0.404 392 564
TRD	CmCHS1	CmCHS2	0.644 246 280	NaN （high sequence divergence）
TRD	CmCHS3	CmCHS4	0.587 247 232	2.429 515 767	0.241 713 694
TRD	CmLAR2	CmLAR1	0.263 851 247	1.291 720 422	0.204 263 432
TRD	CmF3'5'H1	CmF3'5'H2	0.090 142 821	0.211 897 324	0.425 408 022
TRD	CmFLS2	CmFLS3	0.190 856 593	1.395 097 547	0.136 805 196
TRD	CmANS2	CmANS1	0.636 070 470	3.657 827 926	0.173 892 945
TRD	CmFLS1	CmFLS3	0.467 506 223	3.335 289 988	0.140 169 588
TRD	CmANR7	CmANR6	0.015 019 275	0.051 683 849	0.290 599 013
TRD	Cm4CL6	Cm4CL1	0.148 018 360	1.985 685 394	0.074 542 705

图6 板栗与物种间类黄酮合成通路基因共线性Cm：板栗；Os：水稻；Zm：玉米；At：拟南芥；Md：苹果；Vv：葡萄；Qd：槲树；Cc：日本栗；Cd：美洲栗

Fig. 6 Collinearity of flavonoid synthesis pathway genes between chestnut and speciesCm: Castanea mollissima; Os: Oryza sativa; Zm: Zea mays; At: Arabidopsis thaliana; Md: Malus domestica; Vv: Vitis vinifera; Qd: Quercus dentata; Cc: Castanea crenata; Cd: Castanea dentata

图7 板栗类黄酮合成通路基因家族RSCU值

Fig. 7 RSCU values of the flavonoid synthesis pathway gene family in the chestnut

图8 板栗类黄酮合成通路基因家族成员A：中性绘图；B：ENC-plot绘图；C：PR2-plot绘图

Fig. 8 Members of the Chinese chestnut flavonoids synthesis pathway gene familyA: Neutrality curve; B: ENC-plot plot; C: PR2-plot plot

图9 板栗果实成熟过程（A）和果实顶部芽组织PCD过程（B）中类黄酮合成通路基因的表达模式Nut70、Nut82、Nut94分别代表70、82、94 d果实成熟时期； Bud20、Bud25、Bud30分别代表20、25、30 d芽组织PCD时期。下同

Fig. 9 Expression pattern of genes in flavonoid synthesis pathway in chestnut fruit ripening （A） and PCD process of fruit top bud tissue （B）Nut 70, Nut 82 and Nut 94 indicate 70, 82, and 94 d of fruit ripening period, respectively; Bud20, Bud25, and Bud30 indicate the 20, 25, and 30 d bud tissue PCD period, respectively. The same below

图10 板栗果实成熟过程（A）和果实顶部芽组织PCD过程（B）中类黄酮合成通路基因的相对表达量不同小写字母代表在0.05水差异显著

Fig. 10 Relative expressions of genes in flavonoid synthesis pathway in chestnut fruit ripening （A） and PCD process of fruit top bud tissue （B）Different lower letters indicate significantly difference at the 0.05 level

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