Full-Length Transcriptome Sequencing and Modular Organization Analysis of the Naringin/Neoeriocitrin-Related Gene Expression Pattern in Drynaria roosii

doi:10.1093/pcp/pcy072

	Full-Length Transcriptome Sequencing and Modular Organization Analysis of the Naringin/Neoeriocitrin-Related Gene Expression Pattern in Drynaria roosii
	Sun, Mei-Yu ; Li, Jing-Yi ; Li, Dong ; Huang, Feng-Jie ; Wang, Di ; Li, Hui ; Xing, Quan ; Zhu, Hui-Bin ; Shi, Lei7,7
	2018
发表期刊	PLANT AND CELL PHYSIOLOGY
ISSN	0032-0781
卷号	59 期号:7 页码:1398-1414
摘要	Drynaria roosii (Nakaike) is a traditional Chinese medicinal fern, known as 'GuSuiBu'. The effective components, naringin and neoeriocitrin, share a highly similar chemical structure and medicinal function. Our HPLC-tandem mass spectrometry (MS/MS) results showed that the accumulation of naringin/neoeriocitrin depended on specific tissues or ages. However, little was known about the expression patterns of naringin/neoeriocitrin-related genes involved in their regulatory pathways. Due to a lack of basic genetic information, we applied a combination of single molecule real-time (SMRT) sequencing and second-generation sequencing (SGS) to generate the complete and full-length transcriptome of D. roosii. According to the SGS data, the differentially expressed gene (DEG)-based heat map analysis revealed that naringin/neoeriocitrin-related gene expression exhibited obvious tissue- and time-specific transcriptomic differences. Using the systems biology method of modular organization analysis, we clustered 16,472 DEGs into 17 gene modules and studied the relationships between modules and tissue/time point samples, as well as modules and naringin/neoeriocitrin contents. We found that naringin/neoeriocitrin-related DEGs distributed in nine distinct modules, and DEGs in these modules showed significantly different patterns of transcript abundance to be linked to specific tissues or ages. Moreover, weighted gene co-expression network analysis (WGCNA) results further identified that PAL, 4CL and C4H, and C3H and HCT acted as the major hub genes involved in naringin and neoeriocitrin synthesis, respectively, and exhibited high co-expression with MYB- and basic helix-leucine-helix (bHLH)-regulated genes. In this work, modular organization and co-expression networks elucidated the tissue and time specificity of the gene expression pattern, as well as hub genes associated with naringin/neoeriocitrin synthesis in D. roosii. Simultaneously, the comprehensive transcriptome data set provided important genetic information for further research on D. roosii.
关键词	Drynaria roosii Fern Modular organization Naringin/neoeriocitrin SMRT WGCNA
学科领域	Plant Sciences ; Cell Biology
DOI	10.1093/pcp/pcy072
收录类别	SCI
语种	英语
WOS关键词	SALVIA-MILTIORRHIZA ; BIOSYNTHESIS ; FLAVONOIDS ; NARINGIN ; IDENTIFICATION ; ARABIDOPSIS ; COMPLEXES ; CITRUS ; LEAVES ; FRUITS
WOS记录号	WOS:000438295800014
出版者	OXFORD UNIV PRESS
文献子类	Article
出版地	OXFORD
EISSN	1471-9053
资助机构	National Natural Science Foundation of ChinaNational Natural Science Foundation of China (NSFC) [81573519, 31600264] ; Chinese Academy of SciencesChinese Academy of Sciences [KZCC-EW-103-3]
作者邮箱	shilei_67@126.com
作品OA属性	Bronze
引用统计	被引频次：21[WOS] [WOS记录] [WOS相关记录]
文献类型	期刊论文
条目标识符	http://ir.ibcas.ac.cn/handle/2S10CLM1/20673
专题	中科院北方资源植物重点实验室
作者单位	1.[Sun, Mei-Yu 2.Li, Jing-Yi 3.Li, Dong 4.Huang, Feng-Jie 5.Wang, Di 6.Li, Hui 7.Xing, Quan 8.Chinese Acad Sci, Inst Bot, Key Lab Plant Resources, Beijing 100093, Peoples R China 9.Chinese Acad Sci, Inst Bot, Beijing Bot Garden, Beijing 100093, Peoples R China 10.Univ Chinese Acad Sci, Beijing 100049, Peoples R China 11.Hangzhou1gene Technol Co Ltd, Hangzhou 310053, Zhejiang, Peoples R China
推荐引用方式 GB/T 7714	Sun, Mei-Yu,Li, Jing-Yi,Li, Dong,et al. Full-Length Transcriptome Sequencing and Modular Organization Analysis of the Naringin/Neoeriocitrin-Related Gene Expression Pattern in Drynaria roosii[J]. PLANT AND CELL PHYSIOLOGY,2018,59(7):1398-1414.
APA	Sun, Mei-Yu.,Li, Jing-Yi.,Li, Dong.,Huang, Feng-Jie.,Wang, Di.,...&Shi, Lei.(2018).Full-Length Transcriptome Sequencing and Modular Organization Analysis of the Naringin/Neoeriocitrin-Related Gene Expression Pattern in Drynaria roosii.PLANT AND CELL PHYSIOLOGY,59(7),1398-1414.
MLA	Sun, Mei-Yu,et al."Full-Length Transcriptome Sequencing and Modular Organization Analysis of the Naringin/Neoeriocitrin-Related Gene Expression Pattern in Drynaria roosii".PLANT AND CELL PHYSIOLOGY 59.7(2018):1398-1414.

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