title: Transcriptomic analysis of Litchi chinensis pericarp during maturation with a focus on chlorophyll degradation and flavonoid biosynthesis.
abstract: BACKGROUND
  The fruit of litchi (Litchi chinensis) comprises a white translucent edible aril surrounded by a pericarp. The pericarp of litchi has been the focus of studies associated with fruit size, coloration, cracking and shelf life. However, research at the molecular level has been limited by the lack of genomic and transcriptomic information. In this study, an analysis of the transcriptome of litchi pericarp was performed to obtain information regarding the molecular mechanisms underlying the physiological changes in the pericarp, including those leading to fruit surface coloration.
  
  
  RESULTS
  Coincident with the rapid break down of chlorophyll, but substantial increase of anthocyanins in litchi pericarp as fruit developed, two major physiological changes, degreening and pigmentation were visually apparent. In this study, a cDNA library of litchi pericarp with three different coloration stages was constructed. A total of 4.7 Gb of raw RNA-Seq data was generated and this was then de novo assembled into 51,089 unigenes with a mean length of 737 bp. Approximately 70% of the unigenes (34,705) could be annotated based on public protein databases and, of these, 3,649 genes were significantly differentially expressed between any two coloration stages, while 156 genes were differentially expressed among all three stages. Genes encoding enzymes involved in chlorophyll degradation and flavonoid biosynthesis were identified in the transcriptome dataset. The transcript expression patterns of the Stay Green (SGR) protein suggested a key role in chlorophyll degradation in the litchi pericarp, and this conclusion was supported by the result of an assay over-expressing LcSGR protein in tobacco leaves. We also found that the expression levels of most genes especially late anthocyanin biosynthesis genes were co-ordinated up-regulated coincident with the accumulation of anthocyanins, and that candidate MYB transcription factors that likely regulate flavonoid biosynthesis were identified.
  
  
  CONCLUSIONS
  This study provides a large collection of transcripts and expression profiles associated with litchi fruit maturation processes, including coloration. Since most of the unigenes were annotated, they provide a platform for litchi functional genomic research within this species.
authors.affiliation: State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Horticulture, South China Agricultural University, Guangzhou, 510642, Guangdong, People's Republic of China. laibiaoscau@gmail.com.|Physiological Laboratory for South China Fruits, College of Horticulture, South China Agricultural University, Guangzhou, 510642, People's Republic of China. laibiaoscau@gmail.com.
authors.forename: Biao
authors.initials: B
authors.lastname: Lai
authors.affiliation: State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Horticulture, South China Agricultural University, Guangzhou, 510642, Guangdong, People's Republic of China. hubinghello@163.com.|Physiological Laboratory for South China Fruits, College of Horticulture, South China Agricultural University, Guangzhou, 510642, People's Republic of China. hubinghello@163.com.
authors.forename: Bing
authors.initials: B
authors.lastname: Hu
authors.affiliation: State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Horticulture, South China Agricultural University, Guangzhou, 510642, Guangdong, People's Republic of China. qinyh@scau.edu.cn.
authors.forename: Yong-Hua
authors.initials: YH
authors.lastname: Qin
authors.affiliation: State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Horticulture, South China Agricultural University, Guangzhou, 510642, Guangdong, People's Republic of China. zhaojietang@gmail.com.
authors.forename: Jie-Tang
authors.initials: JT
authors.lastname: Zhao
authors.affiliation: Physiological Laboratory for South China Fruits, College of Horticulture, South China Agricultural University, Guangzhou, 510642, People's Republic of China. wanghc1972@263.net.
authors.forename: Hui-Cong
authors.initials: HC
authors.lastname: Wang
authors.affiliation: State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Horticulture, South China Agricultural University, Guangzhou, 510642, Guangdong, People's Republic of China. guibing@scau.edu.cn.|Physiological Laboratory for South China Fruits, College of Horticulture, South China Agricultural University, Guangzhou, 510642, People's Republic of China. guibing@scau.edu.cn.
authors.forename: Gui-Bing
authors.initials: GB
authors.lastname: Hu
mesh_terms: D002734:Chlorophyll / Q000235:genetics / Q000378:metabolism*; D005419:Flavonoids / Q000096:biosynthesis*; D005638:Fruit / Q000254:growth & development / Q000378:metabolism*; D020869:Gene Expression Profiling; D032125:Litchi / Q000235:genetics* / Q000378:metabolism*; D010858:Pigmentation; D059748:Proteolysis
chemical_list: D005419:Flavonoids; D002734:Chlorophyll