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BMC Genomics

Title:		"Identification of differentially expressed genes in flower, leaf and bulb scale of Lilium oriental hybrid 'Sorbonne' and putative control network for scent genes"
Author(s):		Du F; Fan J; Wang T; Wu Y; Grierson D; Gao Z; Xia Y;
Address:		"College of Horticulture, Shanxi Agricultural University, Taigu, 030801, China. Department of Horticulture, College of Agriculture & Biotechnology, Zhejiang University, Hangzhou, 310058, China. Plant & Crop Sciences Division, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD, UK. Department of Horticulture, College of Agriculture & Biotechnology, Zhejiang University, Hangzhou, 310058, China. gaozhongshan@zju.edu.cn. Department of Horticulture, College of Agriculture & Biotechnology, Zhejiang University, Hangzhou, 310058, China. ypxia@zju.edu.cn"
Journal Title:		BMC Genomics
Year:		2017
Volume:		20171122
Issue:		1
Page Number:		899 -
DOI:		10.1186/s12864-017-4303-4
ISSN/ISBN:		1471-2164 (Electronic) 1471-2164 (Linking)
Abstract:		"BACKGROUND: Lily is an economically important plant, with leaves and bulbs consisting of overlapping scales, large ornamental flowers and a very large genome. Although it is recognized that flowers and bulb scales are modified leaves, very little is known about the genetic control and biochemical differentiation underlying lily organogenesis and development. Here we examined the differentially expressed genes in flower, leaf and scale of lily, using RNA-sequencing, and identified organ-specific genes, including transcription factors, genes involved in photosynthesis in leaves, carbohydrate metabolism in bulb scales and scent and color production in flowers. RESULTS: Over 11Gb data were obtained and 2685, 2296, and 1709 differentially expressed genes were identified in the three organs, with 581, 662 and 977 unique DEGs in F-vs-S, L-vs-S and L-vs-F comparisons. By functional enrichment analysis, genes likely to be involved in biosynthetic pathways leading to floral scent production, such as 1-deoxy-D-xylulose-5-phosphate synthase (DXS), 3-ketoacyl-CoA thiolase (KAT), hydroperoxide lyase (HPL), geranylgeranyl pyrophosphate (GGPP) 4-hydroxy-3-methylbut-2-en-1-yl diphosphate (HDS) and terpene synthase (TPS), and floral color genes, such as dihydroflavonol 4-reductase (DFR), chalcone synthase (CHS), chalcone isomerase (CHI), flavonol synthase (FLS) were identified. Distinct groups of genes that participate in starch and sucrose metabolism, such as sucrose synthase (SS), invertase (INV), sucrose phosphate synthase (SPS), starch synthase (SSS), starch branching enzyme (SBE), ADP-glucose pyrophosphorylase (AGP) andbeta-amylase (BAM) and photosynthesis genes (Psa, Psb, Pet and ATP) were also identified. The expression of six floral fragrance-related DGEs showed agreement between qRT-PCR results and RPKM values, confirming the value of the data obtained by RNA-seq. We obtained the open reading frame of the terpene synthase gene from Lilium 'Sorbonne', designated LsTPS, which had 99.55% homology to transcript CL4520.Contig5_All. In addition, 54, 48 and 50 differently expressed transcription factor were identified by pairwise comparisons between the three organs and a regulatory network for monoterpene biosynthesis was constructed. CONCLUSIONS: Analysis of differentially expressed genes in flower, leaf and bulb scale of lily, using second generation sequencing technology, yielded detailed information on lily metabolic differentiation in three organs. Analysis of the expression of flower scent biosynthesis genes has provided a model for the regulation of the pathway and identified a candidate gene encoding an enzyme catalyzing the final step in scent production. These digital gene expression profiles provide a valuable and informative database for the further identification and analysis of structural genes and transcription factors in different lily organs and elucidation of their function"
Keywords:		"Alkyl and Aryl Transferases/genetics Chimera/genetics/metabolism Cloning, Molecular Flowers/genetics/metabolism *Gene Expression Regulation, Plant Gene Ontology *Gene Regulatory Networks Lilium/*genetics/metabolism Monoterpenes/metabolism Plant Leaves/gen;"
Notes:		"MedlineDu, Fang Fan, Junmiao Wang, Ting Wu, Yun Grierson, Donald Gao, Zhongshan Xia, Yiping eng 201601D011077/Natural Science Foundation of Shanxi/ 2014ZZ02/Introductory talent research project of Shanxi Agricultural University/ 31772337/National Natural Science Foundation of China/ England 2017/11/24 BMC Genomics. 2017 Nov 22; 18(1):899. doi: 10.1186/s12864-017-4303-4"