Digital Gene Expression Profiling to Explore Differentially Expressed Genes Associated with Terpenoid Biosynthesis during Fruit Development in Litsea cubeba
AbstractMountain pepper (Litsea cubeba (Lour.) Pers.) (Lauraceae) is an important industrial crop as an ingredient in cosmetics, pesticides, food additives and potential biofuels. These properties are attributed to monoterpenes and sesquiterpenes. However, there is still no integrated model describing differentially expressed genes (DEGs) involved in terpenoid biosynthesis during the fruit development of L. cubeba. Here, we performed digital gene expression (DGE) using the Illumina NGS platform to evaluated changes in gene expression during fruit development in L. cubeba. DGE generated expression data for approximately 19354 genes. Fruit at 60 days after flowering (DAF) served as the control, and a total of 415, 1255, 449 and 811 up-regulated genes and 505, 1351, 1823 and 1850 down-regulated genes were identified at 75, 90, 105 and 135 DAF, respectively. Pathway analysis revealed 26 genes involved in terpenoid biosynthesis pathways. Three DEGs had continued increasing or declining trends during the fruit development. The quantitative real-time PCR (qRT-PCR) results of five differentially expressed genes were consistent with those obtained from Illumina sequencing. These results provide a comprehensive molecular biology background for research on fruit development, and information that should aid in metabolic engineering to increase the yields of L. cubeba essential oil. View Full-Text
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Description: Figure S1: RPKM distribution of all genes. A-E represent 60 DAF, 75 DAF, 90 DAF, 105 DAF and 135 DAF, respectively. (1): x-axis means the range of RPKM, y-axis denotes the number of genes. (2): x-axis represents the range of RPKM, y-axis means the total RPKM values of all the genes in this range. RPKM means the reads per kilo base transcriptome per million mapped reads. Figure S2: Terpenoid backbone biosynthesis pathway in L. cubeba. Red or green rectangles indicate up-regulated or down-regulated genes, respectively. Table S1: DEGs identity and Gene Ontology annotations. Table S2: Real-time PCR confirmation of differential gene expression Table S3: Chemical Composition (%) of the Essential Oil at different stages of fruit development Table S4: RPKM change of DEG related with some compounds during the development of L. cubeba fruit.
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Gao, M.; Lin, L.; Chen, Y.; Wang, Y. Digital Gene Expression Profiling to Explore Differentially Expressed Genes Associated with Terpenoid Biosynthesis during Fruit Development in Litsea cubeba. Molecules 2016, 21, 1251.
Gao M, Lin L, Chen Y, Wang Y. Digital Gene Expression Profiling to Explore Differentially Expressed Genes Associated with Terpenoid Biosynthesis during Fruit Development in Litsea cubeba. Molecules. 2016; 21(9):1251.Chicago/Turabian Style
Gao, Ming; Lin, Liyuan; Chen, Yicun; Wang, Yangdong. 2016. "Digital Gene Expression Profiling to Explore Differentially Expressed Genes Associated with Terpenoid Biosynthesis during Fruit Development in Litsea cubeba." Molecules 21, no. 9: 1251.
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