title: Comparative transcriptome analysis of genes involved in anthocyanin biosynthesis in the red and yellow fruits of sweet cherry (Prunus avium L.).
abstract: BACKGROUND
  Fruit color is one of the most important economic traits of the sweet cherry (Prunus avium L.). The red coloration of sweet cherry fruit is mainly attributed to anthocyanins. However, limited information is available regarding the molecular mechanisms underlying anthocyanin biosynthesis and its regulation in sweet cherry.
  
  
  RESULTS
  In this study, a reference transcriptome of P. avium L. was sequenced and annotated to identify the transcriptional determinants of fruit color. Normalized cDNA libraries from red and yellow fruits were sequenced using the next-generation Illumina/Solexa sequencing platform and de novo assembly. Over 66 million high-quality reads were assembled into 43,128 unigenes using a combined assembly strategy. Then a total of 22,452 unigenes were compared to public databases using homology searches, and 20,095 of these unigenes were annotated in the Nr protein database. Furthermore, transcriptome differences between the four stages of fruit ripening were analyzed using Illumina digital gene expression (DGE) profiling. Biological pathway analysis revealed that 72 unigenes were involved in anthocyanin biosynthesis. The expression patterns of unigenes encoding phenylalanine ammonia-lyase (PAL), 4-coumarate-CoA ligase (4CL), chalcone synthase (CHS), chalcone isomerase (CHI), flavanone 3-hydroxylase (F3H), flavanone 3'-hydroxylase (F3'H), dihydroflavonol 4-reductase (DFR), anthocyanidin synthase (ANS) and UDP glucose: flavonol 3-O-glucosyltransferase (UFGT) during fruit ripening differed between red and yellow fruit. In addition, we identified some transcription factor families (such as MYB, bHLH and WD40) that may control anthocyanin biosynthesis. We confirmed the altered expression levels of eighteen unigenes that encode anthocyanin biosynthetic enzymes and transcription factors using quantitative real-time PCR (qRT-PCR).
  
  
  CONCLUSIONS
  The obtained sweet cherry transcriptome and DGE profiling data provide comprehensive gene expression information that lends insights into the molecular mechanisms underlying anthocyanin biosynthesis. These results will provide a platform for further functional genomic research on this fruit crop.
authors: College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, Shandong 271018, China; Key Laboratory for Fruit Biotechnology Breeding of Shandong, Shandong Institute of Pomology, Shandong Academy of Agricultural Sciences, Tai'an, Shandong 271000, China.
authors: Hairong
authors: H
authors: Wei
authors: Key Laboratory for Fruit Biotechnology Breeding of Shandong, Shandong Institute of Pomology, Shandong Academy of Agricultural Sciences, Tai'an, Shandong 271000, China.
authors: Xin
authors: X
authors: Chen
authors: Key Laboratory for Fruit Biotechnology Breeding of Shandong, Shandong Institute of Pomology, Shandong Academy of Agricultural Sciences, Tai'an, Shandong 271000, China.
authors: Xiaojuan
authors: X
authors: Zong
authors: College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, Shandong 271018, China.
authors: Huairui
authors: H
authors: Shu
authors: College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, Shandong 271018, China.
authors: Dongsheng
authors: D
authors: Gao
authors: Key Laboratory for Fruit Biotechnology Breeding of Shandong, Shandong Institute of Pomology, Shandong Academy of Agricultural Sciences, Tai'an, Shandong 271000, China.
authors: Qingzhong
authors: Q
authors: Liu
mesh_terms: D000872:Anthocyanins / Q000096:biosynthesis*; D030562:Databases, Protein; D005638:Fruit / Q000201:enzymology / Q000235:genetics; D020869:Gene Expression Profiling / Q000379:methods*; D018506:Gene Expression Regulation, Plant; D010940:Plant Proteins / Q000235:genetics*; D000068220:Prunus avium / Q000201:enzymology / Q000235:genetics*; D040641:Quantitative Trait Loci; D017422:Sequence Analysis, DNA
chemical_list: D000872:Anthocyanins; D010940:Plant Proteins