百香果<i>YUCCA</i>基因家族鉴定与表达分析

潘佳怡; 潘若云; 江文洁; 任锐; 方庭

百香果YUCCA基因家族鉴定与表达分析

1.
福建农林大学园艺学院/福建农林大学园艺植物遗传育种研究所，福建　福州　350002

基金项目: 福建省自然科学基金项目（2021J05022）；福建省种业创新与产业化工程项目（zycxny2021010）；福建省高原学科建设项目（102/71201801101）

详细信息

作者简介:
潘佳怡（2000 —），女，硕士研究生，主要从事果树遗传育种方向研究，E-mail：1161621228@qq.com

通讯作者:
方庭（1990 —），男，副教授，主要从事果树遗传育种方向研究，E-mail：fangting@fafu.edu.cn

中图分类号: S667.9
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出版历程
- 收稿日期: 2023-09-11
- 修回日期: 2023-11-13
- 网络出版日期: 2024-03-28

Identification and expression analysis of YUCCA gene family in Passiflora edulis

1.
Institute of Horticultural Plant Genetics and Breeding, Fujian Agriculture and Forestry University, Fujian Fuzhou,　350002

摘要

摘要: 目的黄素单加氧酶（YUCCA）基因是吲哚-3-乙酸（Indole-3-acetic acid, IAA）生物合成的主要限速酶基因之一，在植物生长发育中起着重要调控作用。本研究利用生物信息学方法对百香果（Passiflora edulis Sims.）YUCCA基因家族成员进行鉴定，以期揭示百香果YUCCA家族基因在激素响应中的功能，同时为YUCCA家族基因在其他物种中的生物信息学研究提供参考。方法利用生物信息学方法分析百香果YUCCA基因编码蛋白质的理化性质和保守结构域，基因的染色体定位、基因结构、系统进化树、顺式作用元件等；利用qRT-PCR探究部分成员在植物生长调节剂IAA处理下的表达情况。结果百香果基因组中共鉴定出29个YUCCA家族成员，不均匀分布于8条染色体，基因长度（552～9210 bp）存在明显差异，含有1～8个内含子，同时具有8个保守基序。通过系统进化树分析，发现百香果YUCCA基因家族可划分为3类，聚在同一分类中的百香果YUCCA基因具有高度的保守性，同时发现百香果的YUCCA基因与苜蓿（Medicago sativa L.）、拟南芥（Arabidopsis thaliana）亲缘关系更近，而与水稻（Oryza sativa L.）的亲缘关系较远。顺式作用元件分析显示，百香果YUCCA基因家族启动子受多种激素所诱导，可响应多种逆境胁迫。转录组数据分析结果表明：PeYUCCA6、PeYUCCA11和PeYUCCA16在台农百香果和黄金百香果叶片中呈现较低表达或者不表达，其中PeYUCCA23在台农百香果和黄金百香果的表达量最高，推测该基因对百香果叶片的发育有较大影响。qRT-PCR分析结果表明，在100 μmol·L⁻¹ IAA处理后，PeYUCCA7、PeYUCCA13、PeYUCCA17、PeYUCCA24 和PeYUCCA26基因表达量显著升高。结论 YUCCA基因家族成员在 IAA处理下的表达差异较大，YUCCA基因可能在植物生长调节剂IAA处理下的百香果生长发育和抵御逆境环境过程中发挥重要作用。
- 百香果 /
- 吲哚-3-乙酸 /
- YUCCA 基因家族 /
- 生物信息学 /
- 定量分析
Abstract: Objective YUCCA gene encodes flavin monooxygenase, which is one of the main rate-limiting enzyme genes in the biosynthesis of Indole-3-acetic acid (IAA), and plays an important role in regulating plant growth and development. In this study, bioinformatics methods were used to identify members of the YUCCA gene family in Passiflora edulis Sims. In order to reveal the function of YUCCA family genes in hormone response, and provide references for bioinformatics studies of YUCCA family genes in other species. Methods The physicochemical properties and conserved domains of the encoded proteins, chromosome location, gene structure, phylogenetic tree and cis-acting elements of the genes were analyzed. qRT-PCR was used to explore the expression of some members treated with exogenous hormone IAA. Results A total of 29 YUCCA family members were identified in the passion fruit genome, unevenly distributed in 8 chromosomes. YUCCA gene structure analysis of passion fruit showed significant differences in the length of different genes, containing 1～8 introns and 8 conserved motifs. Through phylogenetic tree analysis, it was found that the YUCCA gene family of passion fruit can be divided into three distinct categories, and the YUCCA genes clustered in the same classification have high conservation. It was also found that the YUCCA gene of passion fruit was more closely related to alfalfa (Medicago sativa L.) and Arabidopsis thaliana, but more closely related to rice (Oryza sativa L.). Cis-acting element analysis showed that the promoter of YUCCA gene family of passion fruit was induced by various hormones and could respond to various stresses. Transcriptome data analysis showed that PeYUCCA6, PeYUCCA11 and PeYUCCA16 showed low or no expression in the leaves of Tainon and golden passion fruit, and the expression of PeYUCCA23 was the highest in Tainon and golden passion fruit, suggesting that this gene had a high effect on the development of passion fruit leaves. The results of qRT-PCR analysis showed that the expressions of PeYUCCA7, PeYUCCA13, PeYUCCA17, PeYUCCA24 and PeYUCCA26 genes were significantly increased after 100 μmol·L-1 IAA treatment. Conclusion The expression of YUCCA gene family members varies greatly under IAA treatment. YUCCA gene may play an important role in the growth and development of passion fruit and the resistance to adverse environment under growth regulator IAA.
- passion fruit /
- IAA /
- YUCCA gene family /
- Bioinformatics /
- Quantitative analysis

HTML全文

图 1 百香果YUCCA 基因家族染色体定位

Figure 1. Chromosome location of YUCCA gene family in Passion fruit

下载: 全尺寸图片幻灯片

图 2 百香果YUCCA 基因家族基因结构和保守基序

Figure 2. Gene structure and conserved motif of YUCCA gene family in passion fruit

下载: 全尺寸图片幻灯片

图 3 拟南芥、水稻、苜蓿和百香果YUCCA蛋白的基因家族进化树

Pe:百香果；At:拟南芥；Os:水稻：Mt:苜蓿。

Figure 3. Evolution tree of YUCCA protein gene family in At, Os, Mt and passion fruit

Pe: Passiflora edulis Sims; At: Arabidopsis thaliana（Linn.）Heynh；Os: Oryza sativa Linn; Mt:Medicago truncatula.

下载: 全尺寸图片幻灯片

图 4 百香果YUCCA 基因启动子的顺式作用元件预测

Figure 4. Prediction of cis-acting elements of YUCCA gene promoter in passion fruit

下载: 全尺寸图片幻灯片

图 5 YUCCA基因在台农百香果和黄金百香果叶中的表达量

Figure 5. YUCCA gene expression in Tainon passion fruit and Golden Passion fruit

下载: 全尺寸图片幻灯片

图 6 IAA处理后YUCCA基因的表达量分析

*、**分别表示在0.05水平差异显著和0.01水平差异极显著。ns代表无显著性差异。

Figure 6. Analysis of YUCCA gene expression after IAA treatment

*, ** indicate significant difference at 0.05 level and extremely significant difference at 0.01 level. ns means no significant difference.

下载: 全尺寸图片幻灯片

表 1 YUCCA基因家族成员实时荧光定量PCR引物

Table 1. Primers for real-time fluorescent quantitative PCR of YUCCA gene family members in passion fruit

基因 Gene	正向引物序列(5'-3') Forward primer（5'-3'）	反向引物序列(5'-3') Reverse primer (5'-3')
Pe60S	AGGTGGGTAACAGGATTATC	TGGCTGTCTTTTGGTGCTG
PeYUCCA7	GGGAAGAAAGTGCTGGTCGT	TGTCAACGAGCCAAAGTGGT
PeYUCCA13	TGCCAGAGTTTGTGGGGTTG	TGGGCAAGACATGAACCGAG
PeYUCCA17	GTTGGGTGCGGCAATTCAG	GTTGGCAGCTAGAAGGAGGA
PeYUCCA24	TGTCTGAGTTTGGTGGCGAT	TCTCGGCAGAACGTGAACC
PeYUCCA25	GGGGACCTATTCTGCACACC	GCATCTCTTGGGGCAAAACG
PeYUCCA26	GGGAATGGAGGTGTGTTTGGA	ACACATGGACAGCCCGAAAG

下载: 导出CSV

表 2 百香果YUCCA基因家族成员

Table 2. Analysis of YUCCA gene family members in passion fruit

基因ID Gene name	基因名称 Gene ID	基因全长 Full length of genes/bp	编码区长度 Coding area length/bp	G+C含量 C+G content/%	A+T含量 A+T content/%
PeYUCCA1	ZX.01G0002140	2265	1593	41	59
PeYUCCA2	ZX.01G0002210	2612	1200	40	60
PeYUCCA3	ZX.01G0002240	2263	1593	41	59
PeYUCCA4	ZX.01G0004710	552	516	43	57
PeYUCCA5	ZX.01G0004780	4609	1977	38	62
PeYUCCA6	ZX.01G0004800	1651	1092	40	60
PeYUCCA7	ZX.01G0017780	1964	1275	43	57
PeYUCCA8	ZX.01G0025770	1602	1155	42	58
PeYUCCA9	ZX.01G0025830	1450	1152	42	58
PeYUCCA10	ZX.01G0025850	1412	1215	42	58
PeYUCCA11	ZX.01G0029730	2216	1557	42	58
PeYUCCA12	ZX.01G0086000	2409	1593	41	59
PeYUCCA13	ZX.01G0115230	1809	1293	43	57
PeYUCCA14	ZX.01G0126750	1718	1146	40	60
PeYUCCA15	ZX.01G0137550	1733	1146	40	60
PeYUCCA16	ZX.03G0007260	3263	1374	40	60
PeYUCCA17	ZX.04G0004260	1787	1200	43	57
PeYUCCA18	ZX.04G0005300	2979	1629	37	63
PeYUCCA19	ZX.04G0017390	2275	783	39	61
PeYUCCA20	ZX.04G0031510	1769	1293	44	56
PeYUCCA21	ZX.05G0003260	1706	1092	40	60
PeYUCCA22	ZX.06G0015980	9210	918	41	59
PeYUCCA23	ZX.07G0012040	3758	1467	40	60
PeYUCCA24	ZX.08G0000090	1981	1275	44	56
PeYUCCA25	ZX.09G0006460	2339	1275	43	57
PeYUCCA26	ZX.09G0011010	3589	1323	44	56
PeYUCCA27	ZX.09G0020980	1460	1164	41	59
PeYUCCA28	ZX.09G0021020	1263	1023	39	61
PeYUCCA29	ZX.09G0026980	1457	1161	41	59

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表 3 百香果YUCCA蛋白的理化性质

Table 3. Physicochemical properties of YUCCA protein in passion fruit

蛋白名称 Protein	氨基酸数量 Number of amino acid	分子量 Molecular weight/Da	等电点 pI	不稳定指数 Instability index	脂肪系数 Aliphatic index	平均亲水指数 Grand average of hydropathicity
PeYUCCA1	530	60025.48	8.79	36.52	91.96	−0.108
PeYUCCA2	399	44952.88	8.77	36.33	90.35	−0.132
PeYUCCA3	530	59901.36	8.86	36.45	93.25	−0.089
PeYUCCA4	171	19496.11	6.70	33.86	83.74	−0.353
PeYUCCA5	658	74050.52	8.60	38.14	93.92	−0.1
PeYUCCA6	363	40948.6	8.44	33.65	97.19	0.006
PeYUCCA7	424	47517.87	8.70	50.74	88.47	−0.163
PeYUCCA8	384	42813.29	8.51	35.85	82.99	−0.164
0PeYUCCA9	384	42248.58	8.39	36.22	83.49	−0.142
PeYUCCA10	404	44826.99	9.10	35.42	94.03	−0.082
PeYUCCA11	519	59666.11	8.66	46.14	80.58	−0.17
PeYUCCA12	530	59791.11	8.80	34.27	93.25	−0.104
PeYUCCA13	430	48121.4	8.21	48.71	90.4	−0.109
PeYUCCA14	381	43169.1	9.36	36.67	87.98	−0.239
PeYUCCA15	381	43196	9.26	37.02	85.43	−0.251
PeYUCCA16	457	52147.09	5.61	43.24	85.67	−0.361
PeYUCCA17	399	44585.34	8.88	41.46	89.65	−0.242
PeYUCCA18	542	61911.37	7.57	45.29	86.48	−0.18
PeYUCCA19	260	29366.12	5.62	37.73	80.46	−0.345
PeYUCCA20	430	48033.36	9.36	47.03	84.72	−0.237
PeYUCCA21	363	41357.16	9.25	38.59	85.62	−0.23
PeYUCCA22	305	35045.45	8.69	39.78	81.77	−0.216
PeYUCCA23	488	55653.62	5.65	50.21	76.6	−0.449
PeYUCCA24	424	47483.77	8.70	49.26	87.1	−0.191
PeYUCCA25	424	47495.97	8.64	48.26	84.15	−0.124
PeYUCCA26	440	48908.67	8.59	44.73	87.07	−0.122
PeYUCCA27	388	42840.19	8.20	37.54	81.88	−0.173
PeYUCCA28	340	37800.42	7.63	32.03	89.35	−0.094
PeYUCCA29	386	42561	8.37	34.48	85.08	−0.145

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参考文献(29)

[1]	贾利霞, 齐艳华. 生长素代谢、运输及信号转导调控水稻粒型研究进展 [J]. 植物学报, 2022, 57(3):263−275. doi: 10.11983/CBB21227 JIA L X, QI Y H. Advances in the regulation of rice( Oryza sativa)grain shape by auxin metabolism, transport and signal transduction [J]. Chinese Bulletin of Botany, 2022, 57(3): 263−275. (in Chinese) doi: 10.11983/CBB21227
[2]	李中华. 多组学数据揭示棉花纤维发育转换期的遗传调控机制和重要代谢物[D]. 武汉: 华中农业大学, 2021. LI Z H. Multiomics data reveal the genetic regulation mechanism and important metabolites of cotton fiber development transition period[D]. Wuhan: Huazhong Agricultural University, 2021. (in Chinese)
[3]	莫福磊, 束艺, 陈秀玲, 等. 基于全基因组的番茄YUCCA基因家族生物信息学分析 [J]. 分子植物育种, 2020, 18(10):3159−3163. MO F L, SHU Y, CHEN X L, et al. Bioinformatics analysis of tomato YUCCA gene family based on whole genome [J]. Molecular Plant Breeding, 2020, 18(10): 3159−3163. (in Chinese)
[4]	刘华彬, 张秦莹, 门淑珍. YUCCA基因家族在拟南芥胚胎发育过程中的表达模式研究 [J]. 南开大学学报(自然科学版), 2017, 50(4):1−7. LIU H B, ZHANG Q Y, MEN S Z. The expression patterns of YUCCA during embryo development in Arabidopsis [J]. Acta Scientiarum Naturalium Universitatis Nankaiensis, 2017, 50(4): 1−7. (in Chinese)
[5]	李莉萍. 西番莲综合开发利用研究进展 [J]. 安徽农业科学, 2012, 40(28):13840−13843,13846. doi: 10.3969/j.issn.0517-6611.2012.28.062 LI L P. Research progress of comprehensive development and utilization of passionflower [J]. Journal of Anhui Agricultural Sciences, 2012, 40(28): 13840−13843,13846. (in Chinese) doi: 10.3969/j.issn.0517-6611.2012.28.062
[6]	LI C B, XIN M, LI L, et al. Characterization of the aromatic profile of purple passion fruit ( Passiflora edulis Sims) during ripening by HS-SPME-GC/MS and RNA sequencing [J]. Food Chemistry, 2021, 355: 129685. doi: 10.1016/j.foodchem.2021.129685
[7]	FONSECA A M A, GERALDI M V, JUNIOR M R M, et al. Purple passion fruit ( Passiflora edulis f. edulis): A comprehensive review on the nutritional value, phytochemical profile and associated health effects [J]. Food Research International, 2022, 160: 111665. doi: 10.1016/j.foodres.2022.111665
[8]	XU M X, LI A D, TENG Y, et al. Exploring the adaptive mechanism of Passiflora edulis in Karst areas via an integrative analysis of nutrient elements and transcriptional profiles [J]. BMC Plant Biology, 2019, 19(1): 185. doi: 10.1186/s12870-019-1797-8
[9]	XIA Z Q, HUANG D M, ZHANG S K, et al. Chromosome-scale genome assembly provides insights into the evolution and flavor synthesis of passion fruit ( Passiflora edulis Sims) [J]. Horticulture Research, 2021, 8: 14. doi: 10.1038/s41438-020-00455-1
[10]	CHENG Y F, DAI X H, ZHAO Y D. Auxin biosynthesis by the YUCCA flavin monooxygenases controls the formation of floral organs and vascular tissues in Arabidopsis [J]. Genes & Development, 2006, 20(13): 1790−1799.
[11]	YAMAMOTO Y, KAMIYA N, MORINAKA Y, et al. Auxin biosynthesis by the YUCCA genes in rice [J]. Plant Physiology, 2007, 143(3): 1362−1371. doi: 10.1104/pp.106.091561
[12]	LI W L, ZHAO X Y, ZHANG X S. Genome-wide analysis and expression patterns of the YUCCA genes in maize [J]. Journal of Genetics and Genomics, 2015, 42(12): 707−710. doi: 10.1016/j.jgg.2015.06.010
[13]	ZHAO B L, HE L L, JIANG C, et al. Lateral Leaflet Suppression 1 (LLS1), encoding the MtYUCCA1 protein, regulates lateral leaflet development in Medicago truncatula [J]. The New Phytologist, 2020, 227(2): 613−628. doi: 10.1111/nph.16539
[14]	袁美同, 李绍信, 纪丕钰, 等. 梨 YUCCA基因家族的鉴定与生物信息学分析 [J]. 分子植物育种, 2021, 19(19):6328−6337. YUAN M T, LI S X, JI P Y, et al. Identification and bioinformatics analysis of YUCCA gene family in Pyrus [J]. Molecular Plant Breeding, 2021, 19(19): 6328−6337. (in Chinese)
[15]	李志谦, 邹东方, 李靖雯, 等. 葡萄YUCCA家族基因的鉴定及在穗梗褪绿过程中的表达分析 [J]. 河南农业大学学报, 2022, 56(2):254−261. doi: 10.3969/j.issn.1000-2340.2022.2.hennannydxxb202202010 LI Z Q, ZOU D F, LI J W, et al. Genome-wide identification of YUCCA gene family in grape and expression analysis during rachis degreening [J]. Journal of Henan Agricultural University, 2022, 56(2): 254−261. (in Chinese) doi: 10.3969/j.issn.1000-2340.2022.2.hennannydxxb202202010
[16]	张倩倩, 田守蔚, 张洁, 等. 西瓜YUCCA基因家族鉴定及在果实成熟过程中的表达分析 [J]. 中国蔬菜, 2019, (3):21−29. ZHANG Q Q, TIAN S W, ZHANG J, et al. Identification of YUCCA gene family and expression analysis during watermelon fruit ripening process [J]. China Vegetables, 2019(3): 21−29. (in Chinese)
[17]	ZHANG Y Y, MAO Q S, MA R J, et al. Genome-wide identification and expression analysis of the PpYUCCA gene family in weeping peach trees ( Prunus persica ‘pendula’) [J]. Horticulturae, 2022, 8(10): 878. doi: 10.3390/horticulturae8100878
[18]	MA D N, DONG S S, ZHANG S C, et al. Chromosome-level reference genome assembly provides insights into aroma biosynthesis in passion fruit ( Passiflora edulis) [J]. Molecular Ecology Resources, 2021, 21(3): 955−968. doi: 10.1111/1755-0998.13310
[19]	CHEN C J, CHEN H, ZHANG Y, et al. TBtools: An integrative toolkit developed for interactive analyses of big biological data [J]. Molecular Plant, 2020, 13(8): 1194−1202. doi: 10.1016/j.molp.2020.06.009
[20]	何锐杰, 方庭, 余伟军, 等. 西番莲查尔酮合成酶(CHS)基因家族全基因组鉴定及表达模式 [J]. 应用与环境生物学报, 2022, 28(4):1066−1075. HE R J, FANG T, YU W J, et al. Genome-wide identification and expression analysis of the CHS gene family in passion fruit [J]. Chinese Journal of Applied and Environmental Biology, 2022, 28(4): 1066−1075. (in Chinese)
[21]	TRIPATHI P, TAYADE R, MUN B G, et al. Silicon application differentially modulates root morphology and expression of PIN and YUCCA family genes in soybean ( Glycine max L. ) [J]. Frontiers in Plant Science, 2022, 13: 842832. doi: 10.3389/fpls.2022.842832
[22]	梁栋. IAA和BR参与干旱胁迫影响烟草侧根发育的研究[D]. 北京: 中国农业科学院, 2021. LIANG D. Study on IAA and BR participating in drought stress affecting tobacco lateral root development[D]. Beijing: Chinese Academy of Agricultural Sciences, 2021. (in Chinese)
[23]	李真. 毛白杨PtoWOX11/12a基因的抗逆功能研究[D]. 北京: 中国林业科学研究院, 2017. LI Z. Functional characterization of A PtoWOX11/12a gene in stress resistance of Populus tomentosa[D]. Beijing: Chinese Academy of Forestry, 2017. (in Chinese)
[24]	李孟湛. SAUR15调控植物侧根及不定根发育的功能及分子机理研究[D]. 兰州: 兰州大学, 2022. LI M Z. Functions and molecular mechanisms of SAUR15 in regulating development of plant lateral and adventitious roots[D]. Lanzhou: Lanzhou University, 2022. (in Chinese)
[25]	阚东阳, 柯学, Walid Ghidan, 等. 拟南芥图位克隆快速初定位系统的建立 [J]. 西南农业学报, 2018, 31(9):1765−1771. KAN D Y, KE X, WALID G, et al. Establishment of rapid initial localization system of Arabidopsis based on map-based cloning [J]. Southwest China Journal of Agricultural Sciences, 2018, 31(9): 1765−1771. (in Chinese)
[26]	丁义峰. 生长素相关基因调控桃果实成熟分子机制研究[D]. 武汉: 华中农业大学, 2018. DING Y F. Molecular mechanism of auxin related genes regulating peach fruit ripening[D]. Wuhan: Huazhong Agricultural University, 2018. (in Chinese)
[27]	ABEL S, NGUYEN M D, THEOLOGIS A. The PS-IAA4/5-like family of early auxin-inducible mRNAs in Arabidopsis thaliana [J]. Journal of Molecular Biology, 1995, 251(4): 533−549. doi: 10.1006/jmbi.1995.0454
[28]	YAMAGUCHI N, WINTER C M, WU M F, et al. Gibberellin acts positively then negatively to control onset of flower formation in Arabidopsis [J]. Science, 2014, 344(6184): 638−641. doi: 10.1126/science.1250498
[29]	金晓蕾. 外源激素对甜荞开花结实的影响及调控机制研究[D]. 呼和浩特: 内蒙古农业大学, 2019. JIN X L. Effect and regulation mechanism of exogenous hormones on flowering and fruiting in common buckwheat[D]. Hohhot: Inner Mongolia Agricultural University, 2019. (in Chinese)