龙眼<i>PIFs</i>家族全基因组鉴定及其表达分析

李小芳; 林晓艺; 苏炳茜; 张城瑜; 罗彬彬; 陈裕坤; 杜迎刚; 赖钟雄

doi:10.19303/j.issn.1008-0384.2022.008.008

龙眼PIFs家族全基因组鉴定及其表达分析

doi: 10.19303/j.issn.1008-0384.2022.008.008

李小芳^1,,
林晓艺¹,
苏炳茜¹,
张城瑜¹,
罗彬彬¹,
陈裕坤¹,
杜迎刚^{1, 2, ,},
赖钟雄^1, ,

1.
福建农林大学园艺植物生物工程研究所，福建　福州　350002
2.
潍坊科技学院山东省高校设施园艺实验室，山东　潍坊　261000

基金项目: 国家自然科学基金项目（31572088）；福建省高原学科建设经费项目（102/71201801101）；福建农林大学科技创新专项基金（CXZX2020027A）

详细信息

作者简介:
李小芳（1996−），女，硕士，主要从事果树生物技术研究（E-mail：1585913092@qq.com）

通讯作者:
杜迎刚（1977−），男，博士，教授，主要从事害虫生物防治、园艺害虫生物技术研究（E-mail:eduyingang@163.com）

赖钟雄（1966−），男，博士，研究员，主要从事园艺植物的生物技术与遗传资源研究（E-mail:laizx01@163.com）

中图分类号: S 667.2
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出版历程
- 收稿日期: 2022-04-19
- 修回日期: 2022-05-04
- 网络出版日期: 2022-08-08
- 刊出日期: 2022-08-28

Genome-wide Identification and Expressions of PIF Family in Longan

1.
Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian　350002, China
2.
Facility Horticulture Laboratory of Universities in Shandong, Weifang University of Science and Technology, Weifang, Shandong　261000, China

摘要

摘要: 目的 PIFs属于 basic helix-loop-helix（bHLH）转录因子家族的第 15 亚族，研究其在龙眼（ Dimocarpus longan Lour.）中的表达特征可为其参与调控植物的生长发育和抵御逆境胁迫过程中的作用机制提供参考。方法基于龙眼基因组和转录组数据进行PIFs基因家族的鉴定与生物信息学分析，对其启动子序列进行顺式作用元件分析；基于龙眼体胚发生早期3个阶段[胚性愈伤组织（ Embryogenic callus，EC）、不完全胚性紧实结构（Incomplete embryotic compacted structure，ICpEC）、球形胚（Spherical embryo，GE）]、不同组织部位（花、花蕾、叶、果皮、果肉、根、种子、茎、幼果）、不同温度（15 ℃、25 ℃、35 ℃）和不同光质（蓝光、白光和黑暗）处理下龙眼EC转录组数据，通过龙眼PIFs的FPKM值分析其表达模式，并采用实时荧光定量 PCR（Quantitative real-time polymerase chain reaction，qRT-PCR）分析DlPIFs在龙眼体胚发生早期、不同生长调节剂[生长素（2,4-D)、脱落酸（ABA）、赤霉素（GA₃）、水杨酸（SA）、茉莉酸甲酯（MeJA）]处理下的表达情况。结果生物信息学分析表明所鉴定的龙眼PIFs家族8个成员均具有bHLH结构域，编码区长度介于975～2298 bp，包含5～8个外显子和6个motif，亚细胞定位预测均定位于细胞核。DlPIFs启动子中不仅含有响应光、激素和非生物胁迫的作用元件，还具有与种子生长和胚胎发育过程相关的作用元件。系统进化树分析显示DlPIFs分布在4大分支上，与拟南芥（Arabidopsis thaliana）、甜橙[Citrus sinensis (L.) Osbeck]亲缘关系较近。不同组织器官的转录组数据分析结果表明，DlPIF1-1的表达量在种子中最高，DlPIF1-2的表达量在果肉中最高，DlPIF4的表达量在茎中最高，DlPIF5的表达量在花蕾中最高，DlPIF7和DlPIF8的表达量在叶中最高。不同光质转录组数据分析结果表明，DlPIF1-1、DlPIF5和DlPIF8在蓝光处理下的表达量明显高于对照，DlPIF4在白光和蓝光处理下的表达量均明显高于对照，DlPIF1-2在3种光质处理下的表达量差别不明显。不同温度的转录组数据分析结果表明，相对高温（35 ℃）促进DlPIF4和DlPIF6的表达，抑制DlPIF1-1、DlPIF1-2、DlPIF3和DlPIF8的表达；相对低温（15 ℃）促进DlPIF1-1、DlPIF3和DlPIF5的表达，抑制DlPIF1-2、DlPIF4、DlPIF6和DlPIF8的表达。qRT-PCR结果显示，DlPIF1-1、DlPIF5、DlPIF6和DlPIF8的表达量随着龙眼体胚早期的发育不断下降，DlPIF1-2和DlPIF3的表达量在EC到ICpEC阶段下降，在ICpEC到GE阶段上升，DlPIF4和DlPIF7的表达模式与之相反。与其他成员相比，DlPIF5和DlPIF7的表达量在5种生长调节剂处理下都具有明显变化。结论 DlPIFs家族在龙眼的生长发育进程中可能具有不同的功能，并可能参与生物胁迫和非生物胁迫的响应过程。
- 龙眼 /
- 光敏色素互作因子 /
- 基因家族鉴定 /
- 表达分析
Abstract: Objective Belonging to the 15^th subgroup of basic helix-loop-helix (bHLH) transcription factor family that associated with the growth, development, and stress resistance of plants, PIF family of Dimocarpus longan Lour were identified and their expressions studied. Method PIFs were identified, and bioinformatics extracted from the longan genome and transcriptome database. Cis-acting elements were analyzed for the promoter sequence. Expressions of DlPIFs during early SE (i.e., embryogenic callus or EC, incomplete embryotic compacted structure or ICpEC, and spherical embryo or GE), in different tissues (including flower, flower bud, leaf, pericarp, pulp, root, seed, stem, and young fruit), under different light (e.g., blue, bright, and dark), and at varied temperatures (i.e., 15℃, 25℃, and 35℃) were obtained from the FPKM values. In addition, expressions of the genes in early SE exposed to exogenous hormones such as 2,4-D, ABA, GA3, SA, MeJA were determined by qRT-PCR. Result All DlPIFs had the bHLH domain. The lengths of their coding region ranged from 975 bp to 2298 bp each consisted of 5–8 exons, 4–7 introns, and 6 motifs. The DlPIFs were in the nucleus with promoters containing not only the acting elements in response to light, hormone, and abiotic stress but also those to seed growth and embryonic development. The phylogenetic tree of DlPIFs distributed in 4 branches closely related to Arabidopsis thaliana and Citrus sinensis (L.) Osbeck. The transcriptomes of different tissues and organs showed the highest expression of DlPIF1-1 in the seeds, that of DlPIF1-2 in the pulp, that of DlPIF4 in the stems, that of DlPIF5 in the flower buds, and those of DlPIF7 and DlPIF8 in the leaves. The photometric transcriptomes indicated that the expressions of DlPIF1-1, DlPIF5, and DlPIF8 under blue light were significantly higher than that of control, that of DlPIF4 under white or blue light significantly higher than that of control, and that of DlPIF1-2 did not differ significantly under different light exposures. At 35^oC, the relatively high temperature heightened the expressions of DlPIF4 and DlPIF6 but depressed those of DlPIF1-1, DlPIF1-2, DlPIF3, and DlPIF8. At 15 ℃, on the other hand, the expressions of DlPIF1-1, DlPIF3, and DlPIF5 were enhanced, while those of DlPIF1-2, DlPIF4, DlPIF6, and DlPIF8 inhibited. qRT-PCR results showed that the expressions of DlPIF1-1, DlPIF5, DlPIF6, and DlPIF8 decreased with the longan embryonic development at the early stage. Those of DlPIF1-2, and DlPIF3 decreased from EC to ICpEC, those of DlPIF4 and DlPIF7 decreased from ICpEC to GE, and those of DlPIF4 and DlPIF7 were the opposite. In response to the exposure to 5 exogenous hormones, DlPIF5 and DlPIF7 expressed significantly different from the others. Conclusion DlPIFs might have varied functions associated with the growth and development, as well as biological and/or abiotic stress responses, of longan.
- Dimocarpus longan Lour. /
- photosensitive pigments interaction factor /
- gene family identification /
- expression analysis

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图 1 龙眼PIFs保守结构域

Figure 1. Conserved domain of DlPIFs

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图 2 龙眼PIFs家族基因结构和蛋白质保守基序分布

Figure 2. Gene structure and protein conserved motifs of DlPIFs

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图 3 DlPIFs染色体定位

Figure 3. Chromosome distribution of DlPIFs

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图 4 DlPIFs家族启动子顺式作用元件分析

Figure 4. Cis-acting elements of DlPIFs

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图 5 龙眼、拟南芥、水稻、甜橙PIFs家族系统进化树

Figure 5. Phylogenetic tree of PIF families in Arabidopsis thaliana, Oryza sativa L., Citrus sinensis, and D. longan

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图 6 DlPIFs家族在非胚性和胚性培养物和不同组织器官的表达量热图

Figure 6. Heat map of expressions of DlPIFs in non-embryogenic and embryogenic cultures and various tissues and organs

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图 7 DlPIFs家族在不同光质条件下的表达量热图

Figure 7. Heat map of expressions of DlPIFs exposed to varied light

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图 8 DlPIFs家族在不同温度条件下的表达量热图

Figure 8. Heat map of expressions of DlPIFs under different temperatures

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图 9 龙眼PIFs家族体胚发生阶段表达分析

Figure 9. Expressions of DlPIFs during somatic embryogenesis

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图 10 生长调节剂处理下DlPIFs基因的相对表达量

不同小写字母表示处理间差异显著（P ＜ 0.05）。

Figure 10. Expressions of DlPIFs in response to exogenous hormones

Data with different lowercase letters indicate significant differences at P＜0.05.

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表 1 DlGRF基因家族qRT-PCR引物

Table 1. qRT-PCR primers of DlPIFs

引物名称 Primer name		序列 Sequences（5′-3′）
DlPIF1-1	F	GCAAAACGGTCAGGTGGT
DlPIF1-1	R	TTGGCGTCGTTGAGAGG
DlPIF1-2	F	CACATCACCACCACCGAA
DlPIF1-2	R	TCCTCGCTATCACAGTCATCA
DlPIF3	F	TCTCAAACCGCGAAAACC
DlPIF3	R	TCCAGACAACTCAGGCAAGA
DlPIF4	F	AGGGACCGACACATTTTCTG
DlPIF4	R	TCGAAGGGTCCATAGTGAGC
DlPIF5	F	TACAGGGGCAGAAAATGAGC
DlPIF5	R	TGAATCCACGAGACTGTTTCA
DlPIF6	F	GATGACCAATCCGAAGCTGT
DlPIF6	R	CACTAAGATCAGCAGACCAC
DlPIF7	F	ATTCGTTCCATCTCCGTTTCT
DlPIF7	R	AGAGTGCTGCCATCTTGTTGT
DlPIF8	F	TGATGCCCCCATGTTAGAC
DlPIF8	R	AGCTTGTGGCTTGGTTGAC
FSD-Q	F	GGTCAGATGGTGAAGCCGTAGAG
FSD-Q	R	GTCTATGCCACCGATACAACAAACCC

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表 2 龙眼PIFs成员基本理化性质

Table 2. Basic physicochemical properties of DlPIFs

三代基因ID Third generation gene ID	二代基因ID Second generation gene ID	基因名称 Gene name	注释 Annotated	CDS长度 Length/bp	氨基酸数 Amino acid number	等电点 PI	分子量 Molecular weight/Da	不稳定系数 Instability index	亲水性 Gravy
Dlo012584	Dlo_012166.1	DlPIF1-1	AtPIF1-1	1605	534	6.39	59036.32	62.06	−0.696
Dlo015892	Dlo_000274.1	DlPIF1-2	AtPIF1-2	1197	398	5.44	43473.33	56.83	−0.545
Dlo034359		DlPIF3	AtPIF3	2298	765	6.10	82158.84	54.69	−0.586
Dlo028134	Dlo_000977.1	DlPIF4	AtPIF4	1617	538	6.73	58258.97	62.25	−0.647
Dlo014068	Dlo_018063.1	DlPIF5	AtPIF5	975	324	5.48	35089.75	68.21	−0.624
Dlo011892		DlPIF6	AtPIF6	1695	540	9.21	62892.14	57.87	−0.741
Dlo031044	Dlo_031800.1	DlPIF7	AtPIF7	1362	453	8.39	49786.89	74.28	−0.776
Dlo012986	Dlo_028817.1	DlPIF8	AtPIF8	1431	476	8.55	50818.37	58.46	−0.579

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表 3 龙眼PIFs家族二级结构及亚细胞定位

Table 3. Secondary structure and subcellular localization of DlPIFs

基因 Gene	α-螺旋 Alpha helix/%	β-转角 Beta turn/%	延伸链 Extended strand/%	无规卷曲 Random coil/%	亚细胞定位 Subcellular localization
DLPIF1-1	23.97	2.62	7.12	66.29	细胞核
DLPIF1-2	21.36	1.26	8.04	69.35	细胞核
DLPIF3	17.12	2.09	7.45	73.33	细胞核
DLPIF4	20.26	1.86	5.39	72.49	细胞核
DLPIF5	24.38	3.70	8.33	63.58	细胞核
DLPIF6	23.05	2.30	4.96	69.68	细胞核
DLPIF7	30.02	1.32	3.75	64.9	细胞核
DLPIF8	29.41	1.47	5.04	64.08	细胞核

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