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Identification of differentially expressed genes in flower, leaf and bulb scale of Lilium oriental hybrid ‘Sorbonne’ and putative control network for scent genes

Overview of attention for article published in BMC Genomics, November 2017
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Title
Identification of differentially expressed genes in flower, leaf and bulb scale of Lilium oriental hybrid ‘Sorbonne’ and putative control network for scent genes
Published in
BMC Genomics, November 2017
DOI 10.1186/s12864-017-4303-4
Pubmed ID
Authors

Fang Du, Junmiao Fan, Ting Wang, Yun Wu, Donald Grierson, Zhongshan Gao, Yiping Xia

Abstract

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. 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) andβ-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. 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.

Twitter Demographics

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Mendeley readers

The data shown below were compiled from readership statistics for 36 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Unknown 36 100%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 5 14%
Researcher 5 14%
Student > Master 3 8%
Lecturer 2 6%
Student > Bachelor 2 6%
Other 4 11%
Unknown 15 42%
Readers by discipline Count As %
Agricultural and Biological Sciences 12 33%
Biochemistry, Genetics and Molecular Biology 4 11%
Unspecified 1 3%
Sports and Recreations 1 3%
Medicine and Dentistry 1 3%
Other 0 0%
Unknown 17 47%

Attention Score in Context

This research output has an Altmetric Attention Score of 1. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 22 June 2018.
All research outputs
#12,698,323
of 16,638,522 outputs
Outputs from BMC Genomics
#6,366
of 9,107 outputs
Outputs of similar age
#278,003
of 416,921 outputs
Outputs of similar age from BMC Genomics
#561
of 826 outputs
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