Tissue-specific Transcriptome analysis reveals lignocellulose synthesis regulation in elephant grass ( Pennisetum purpur
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RESEARCH ARTICLE
Open Access
Tissue-specific Transcriptome analysis reveals lignocellulose synthesis regulation in elephant grass (Pennisetum purpureum Schum) Wenqing Zhang1,2†, Shengkui Zhang1,2†, Xianqin Lu1,2, Can Li1,2, Xingwang Liu1,2, Geyu Dong1,2 and Tao Xia1,2*
Abstract Background: The characteristics of elephant grass, especially its stem lignocellulose, are of great significance for its quality as feed or other industrial raw materials. However, the research on lignocellulose biosynthesis pathway and key genes is limited because the genome of elephant grass has not been deciphered. Results: In this study, RNA sequencing (RNA-seq) combined with lignocellulose content analysis and cell wall morphology observation using elephant grass stems from different development stages as materials were applied to reveal the genes that regulate the synthesis of cellulose and lignin. A total of 3852 differentially expressed genes (DEGs) were identified in three periods of T1, T2, and T3 through RNA-seq analysis. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis of all DEGs showed that the two most abundant metabolic pathways were phenylpropane metabolism, starch and sucrose metabolism, which were closely related to cell wall development, hemicellulose, lignin and cellulose synthesis. Through weighted gene co-expression network analysis (WGCNA) of DEGs, a ‘blue’ module highly associated with cellulose synthesis and a ‘turquoise’ module highly correlated with lignin synthesis were exhibited. A total of 43 candidate genes were screened, of which 17 had function annotations in other species. Besides, by analyzing the content of lignocellulose in the stem tissues of elephant grass at different developmental stages and the expression levels of genes such as CesA, PAL, CAD, C4H, COMT, CCoAMT, F5H and CCR, it was found that the content of lignocellulose was related to the expression level of these structural genes. Conclusions: This study provides a basis for further understanding the molecular mechanisms of cellulose and lignin synthesis pathways of elephant grass, and offers a unique and extensive list of candidate genes for future specialized functional studies which may promote the development of high-quality elephant grass varieties with high cellulose and low lignin content. Keywords: Elephant grass (Pennisetum purpureum Schum.), RNA-Seq, KEGG (Kyoto encyclopedia of genes and genomes), WGCNA (weighted gene co-expression network analysis), Cellulose, Lignin
* Correspondence: [email protected] † Wenqing Zhang and Shengkui Zhang contributed equally to this work. 1 State Key Laboratory of Biobased Material and Green Papermaking, Jinan, China 2 School of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250353, Shandong, People’s Republic of China © The Author(s). 2020 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appro
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