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
收稿日期: 2022-10-24
修回日期: 2023-01-10
网络出版日期: 2023-02-10
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
Received date: 2022-10-24
Revised date: 2023-01-10
Online published: 2023-02-10
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
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 . DOI: 10.16288/j.yczz.22-336
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
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