Tissue-specific Transcriptome analysis reveals lignocellulose synthesis regulation in elephant grass (Pennisetum purpureum Schum)

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.

Transcriptome Mining Provides Insights into Cell Wall Metabolism and Fiber Lignification in Agave tequilana Weber

“…In wheat, maize, and rice, 14, 10, and 11 CESAs members have identified, respectively [ 37 , 54 , 55 , 56 ]. In grasses, in Panicum virgatum 14 CESA genes have been reported [ 56 ], while an RNA-seq analysis revealed 27 CESA genes expressed during stem development of Pennisetum purpureum [ 57 ]. Here, we retrieved only six CESA orthologous in A. tequilana , which is quite comparable with that found in the hybrid H11648 (five CESA genes) [ 17 ] but contrasts with that reported recently in A. fourcroydes , A. sisalana , and H11648 (14 CESA genes) [ 19 ].…”

Transcriptomic resources for prairie grass (Bromus catharticus): expressed transcripts, tissue-specific genes, and identification and validation of EST-SSR markers

“…Few tissue-specific transcriptome works on forage grasses have been done to identify candidate genes involved in tissue development and forage quality improvement. Research on elephant grass ( Pennisetum purpureum ) stem lignocellulose identified 3,852 DEGs, and screened 43 candidate genes involved in lignocellulose biosynthesis, which might promote the development of high-quality elephant grass varieties [ 7 ]. We found 1,570 stem-specific genes, among which those significantly enriched in the phenylpropanoid biosynthesis pathway might affect the feed value of B. catharticus , as phenylpropanoid metabolism is a major pathway of lignocellulose biosynthesis [ 7 , 25 ].…”

“…Research on elephant grass ( Pennisetum purpureum ) stem lignocellulose identified 3,852 DEGs, and screened 43 candidate genes involved in lignocellulose biosynthesis, which might promote the development of high-quality elephant grass varieties [ 7 ]. We found 1,570 stem-specific genes, among which those significantly enriched in the phenylpropanoid biosynthesis pathway might affect the feed value of B. catharticus , as phenylpropanoid metabolism is a major pathway of lignocellulose biosynthesis [ 7 , 25 ]. While we identified 3,030 leaf-specific genes mainly related to the photosynthetic pathways, which might be of benefit in the improvement of leaf photosynthetic efficiency and biomass parameters.…”

“…Extensive transcriptomic studies have already been applied in various plant biological contexts. Where for instance, comparative transcriptome analysis on different tissues and stages was used to reveal the regulatory modules of tissues development [ 5 – 7 ], or the metabolism of specific biochemical components [ 8 – 10 ], and tissue-specific expression profiling has proved effective in uncovering biological pathways and regulatory networks. Despite general applications of genomic approaches, to date, these have not yet been applied to research on B. catharticus .…”

Transcriptome Analysis of Chinese Cabbage Provides Insights into the Basis of Understanding the Lignin Affected by Low Temperature

“…At present, RNA-seq technology can be applied to the study of various traits in various plants, such as using RNA-seq to study the identification of Lycium chinense biosynthesis genes and the accumulation of phenylpropanoids [ 19 ]. RNA-seq was used to investigate the protection of anthocyanins against Begonia semperflorens at low temperatures [ 20 ], and RNA-seq was used to study the regulation of elephant grass lignin synthesis [ 21 ]. In this study, Chinese cabbage was studied at a low temperature by the RNA-seq method, and the lignin synthesis pathway was further explored at a low temperature.…”