基于WGCNA发掘缺磷、红光和黄光处理下三角褐指藻岩藻黄素合成关键基因

doi:10.16288/j.yczz.22-336

遗传 ›› 2023, Vol. 45 ›› Issue (3): 237-249.doi: 10.16288/j.yczz.22-336

基于WGCNA发掘缺磷、红光和黄光处理下三角褐指藻岩藻黄素合成关键基因

吕娇¹(), 龚一富¹(), 章丽¹, 胡媛¹, 王何瑜²()

1.宁波大学海洋学院，浙江省海洋生物工程重点实验室，宁波 315832
2.宁波大学食品与药学学院，宁波 315832

收稿日期:2022-10-24 修回日期:2023-01-10 出版日期:2023-03-20 发布日期:2023-02-10
通讯作者: 龚一富,王何瑜 E-mail:1459336048@qq.com;gongyifu@163.com;wangheyu@nbu.edu.cn
作者简介:吕娇，在读硕士研究生，专业方向：生物学。E-mail: 1459336048@qq.com
基金资助:
宁波市社发重大项目(2017C510002);Supported by the Major Social Development Project of Ningbo City No.(2017C510002);宁波大学横向项目(HX2022000115);the Horizontal Project of Ningbo University No.(HX2022000115)

Exploring the key genes of fucoxanthin biosynthesis in Phaeodactylum tricornutum under phosphorus deficiency, red light and yellow light using WGCNA

Jiao Lv¹(), Yifu Gong¹(), Li Zhang¹, Yuan Hu¹, Heyu Wang²()

1. Key Laboratory of Marine Biotechnology of Zhejiang Province, School of Marine Sciences, Ningbo University, Ningbo 315832, China
2. College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315832, China

Received:2022-10-24 Revised:2023-01-10 Online:2023-03-20 Published:2023-02-10
Contact: Gong Yifu,Wang Heyu E-mail:1459336048@qq.com;gongyifu@163.com;wangheyu@nbu.edu.cn

摘要/Abstract

摘要：

加权基因共表达网络分析(weighted gene co-expression network analysis，WGCNA)是一种分析多个样本间基因表达模式的方法，可将表达模式相近的基因聚类并发掘与特定的性状或表型相关的关键基因。本研究采用转录组测序和WGCNA方法，分析了三角褐指藻(Phaeodactylum tricornutum)在缺磷、红光和黄光等非生物胁迫下对岩藻黄素积累的影响。结果表明，与对照组相比，岩藻黄素含量在缺磷和红光处理后显著提高(P<0.05)，但是在黄光处理后显著降低(P<0.05)。利用转录组测序得到的10,392个基因构建加权基因共表达网络，为了确保无标度网络，选择β=18(R²>0.8)作为软阈值。通过对岩藻黄素含量进行关联分析，共鉴定了10个共表达模块，其中purple模块与岩藻黄素含量呈正相关(r=0.9，P=1E-200)，并确定了9个关键基因，包括5个岩藻黄素合成通路上的基因(DXR、PSY、PDS1、ZEP2、VDL2)和4个转录因子基因(bHLH5、HOX2、CCHH13、HSF1b)。进一步利用qRT-PCR证实，关键基因在缺磷处理时表达量更高，线性回归分析结果表明基因相对表达量均与转录组数据高度相关。本研究结果为进一步研究三角褐指藻中岩藻黄素的复杂调控机制奠定了基础。

关键词: 三角褐指藻, 岩藻黄素, 加权基因共表达网络分析, 关键基因

Abstract:

Weighted gene co-expression network analysis (WGCNA) is a method for analysing gene expression patterns across multiple samples, clustering genes with similar expression patterns and identifying key genes associated with specific traits or phenotypes. In this study, we investigated the effects of fucoxanthin accumulation in Phaeodactylum tricornutum in response to abiotic stresses of phosphorus deficiency, red light, and yellow light using transcriptome sequencing and weighted gene co-expression network analysis. The results showed that compared to the control, the fucoxanthin content of P. tricornutum was significantly increased after phosphorus deficiency and red light treatment (P<0.05), but significantly decreased after yellow light treatment (P<0.05). A weighted gene co-expression network was constructed using 10,392 genes obtained from transcriptome sequencing, and β=18 (R²>0.8) was chosen as a soft threshold in order to ensure a scale-free network. A total of 10 co-expression modules were identified by correlation analysis of fucoxanthin content, with the purple module positively correlated with fucoxanthin content (r=0.9, P=1E-200), and 9 key genes were identified, including five genes in the fucoxanthin biosynthesis pathway (DXR, PSY, PDS1, ZEP2, VDL2) and 4 transcription factors (bHLH5, HOX2, CCHH13, HSF1b). Further qRT-PCR confirmed that key genes were more highly expressed in the phosphorus deficiency treatment and linear regression analysis showed that the relative gene expressions were all highly correlated with the transcriptome data. The results of this study provide a basis for further investigation of the complex regulatory mechanisms of fucoxanthin in P. tricornutum.

Key words: Phaeodactylum tricornutum, fucoxanthin, WGCNA, key gene

吕娇, 龚一富, 章丽, 胡媛, 王何瑜. 基于WGCNA发掘缺磷、红光和黄光处理下三角褐指藻岩藻黄素合成关键基因[J]. 遗传, 2023, 45(3): 237-249.

Jiao Lv, Yifu Gong, Li Zhang, Yuan Hu, Heyu Wang. Exploring the key genes of fucoxanthin biosynthesis in Phaeodactylum tricornutum under phosphorus deficiency, red light and yellow light using WGCNA[J]. Hereditas(Beijing), 2023, 45(3): 237-249.

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基因_ID	基因名称	转录因子_ID	所属基因家族
7195238	Pt_CXC4	PHATRDRAFT_48955	CXC/tesmin
7195642	Pt_HSF4.5d	PHATRDRAFT_39786	HSF
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7196438	Pt_CCCH6	PHATRDRAFT_42841	ZF
7197059	Pt_CXC1	PHATRDRAFT_32462	CXC/tesmin
7197406	Pt_bHLH5	PHATRDRAFT_43365	bHLH
7198282	Pt_HSF4.6c	PHATRDRAFT_49620	HSF
7198402	Pt_Myb2R8	PHATRDRAFT_49720	MYB
7198927	Pt_Hox2	PHATRDRAFT_ex44808	CCAAT-binding
7198996	Pt_CCCH11	PHATRDRAFT_50345	ZF
7199537	Pt_CCHH8	PHATRDRAFT_45032	ZF
7199623	Pt_CCHH3	PHATRDRAFT_54326	ZF
7199692	Pt_Myb1R5	PHATRDRAFT_45029	MYB
7200785	Pt_TAZ4_PHD2_ZZ2	PHATRDRAFT_45764	ZF
7201568	Pt_CCHH18	PHATRDRAFT_46478	ZF
7201958	Pt_HSF1b	PHATRDRAFT_47181	HSF
7202412	Pt_CCHH13	PHATRDRAFT_37547	ZF
7203253	Pt_MybR+R	PHATRDRAFT_48038	MYB
7204890	Pt_bZIP9	PHATRDRAFT_1724	bZIP

基于WGCNA发掘缺磷、红光和黄光处理下三角褐指藻岩藻黄素合成关键基因

Exploring the key genes of fucoxanthin biosynthesis in Phaeodactylum tricornutum under phosphorus deficiency, red light and yellow light using WGCNA

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[1]	李萌, 贺竹梅. 遗传学教学中性别决定关键基因的阐述[J]. 遗传, 2014, 36(6): 611-617.
[2]	唐建新，陈卓，胡晗华 . 利用抑制差减杂交技术分离三角褐指藻在缺氮条件下上调表达的基因[J]. 遗传, 2009, 31(8): 865-870.