Molecular Genetics and Genomics

, Volume 290, Issue 1, pp 399–412 | Cite as

De novo transcriptome characterization of Lilium ‘Sorbonne’ and key enzymes related to the flavonoid biosynthesis

  • Ming-fang Zhang
  • Ling-min Jiang
  • Dong-mei ZhangEmail author
  • Gui-xia JiaEmail author
Original Paper


Lily is an important cut-flower and bulb crop in the commercial market. Here, transcriptome profiling of Lilium ‘Sorbonne’ was conducted through de novo sequencing based on Illumina platform. This research aims at revealing basic information and data that can be used for applied purposes especially the molecular regulatory information on flower color formation in lily. In total, 36,920,680 short reads which corresponded to 3.32 GB of total nucleotides, were produced through transcriptome sequencing. These reads were assembled into 39,636 Unigenes, of which 30,986 were annotated in Nr, Nt, Swiss-Prot, KEGG, COG, GO databases. Based on the three public protein databases, a total of 32,601 coding sequences were obtained. Meanwhile, 19,242 Unigenes were assigned to 128 KEGG pathways. Those with the greatest representation by unique sequences were for ‘‘metabolic pathways’’ (5,406 counts, 28.09 %). Our transcriptome revealed 156 Unigenes that encode key enzymes in the flavonoid biosynthesis pathway including CHS, CHI, F3H, FLS, DFR, etc. MISA software identified 2,762 simple sequence repeats, from which 1,975 primers pairs were designed. Over 2,762 motifs were identified, of which the most frequent was AG/CT (659, 23.86 %), followed by A/T (615, 22.27 %) and CCG/CGG (416, 15.06 %). Based on the results, we believe that the color formation of the Lilium ‘Sorbonne’ flower was mainly controlled by the flavonoid biosynthesis pathway. Additionally, this research provides initial genetic resources that will be valuable to the lily community for other molecular biology research, and the SSRs will facilitate marker-assisted selection in lily breeding.


Lilium Transcriptome De novo sequencing SSR Flavonoid biosynthesis 



This work was supported by the National forestry public welfare industry research project (201204609) and the State Bureau of Forestry 948 project (Grant No. 2009-4-25) in People’s Republic of China.


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© Springer-Verlag Berlin Heidelberg 2014

Authors and Affiliations

  1. 1.Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture and College of Landscape ArchitectureBeijing Forestry UniversityBeijingChina
  2. 2.The Shanghai Gardening and Landscape Science InstituteShanghaiChina

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