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

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

• Research Article • Previous Articles Next Articles

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

Abstract

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

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.

Figures/Tables 7

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Table 1

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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
7195857	Pt_Myb1R_SHAQKYF1b	PHATRDRAFT_49526	MYB
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

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

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