Transcriptomic analysis of Litchi chinensis pericarp during maturation with a focus on chlorophyll degradation and flavonoid biosynthesis

Abstract

BackgroundThe 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.ResultsCoincident 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.ConclusionsThis 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.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1433-4) contains supplementary material, which is available to authorized users.

Transcriptome analysis and anthocyanin-related genes in red leaf lettuce

“…Two pathways, the "Flavonoid biosynthesis" (ko00941) pathway and the "Flavone and flavonol biosynthesis" (ko00944) pathway, involved in the red color of the lettuce, and eight glucoside metabolic pathways related to synthetic substrates for anthocyanin were identified. In many plants, flavonoid pathways were found in colored tissues and were mainly responsible for color variation, as seen in Magnolia sprengeri , peach flowers (Chen et al, 2014), and the pericarp of L. chinensis (Lai et al, 2015). These data indicate that the sequencing and assembly were successfully performed, covering many metabolic pathways.…”

“…A series of transcriptomes of colored plant tissues have been sequenced using high-throughput sequencing technology, leading to the identification of many anthocyanin-related genes, as has been done in grape hyacinth (Lou et al, 2014), Camellia chekiangoleosa , and in the pericarp of Litchi chinensis (Lai et al, 2015). In this study, the transcriptome of red leaf lettuce was sequenced using an Illumina HiSeq 2500 platform.…”

Identification of MicroRNAs and Their Target Genes Related to the Accumulation of Anthocyanins in Litchi chinensis by High-Throughput Sequencing and Degradome Analysis

“…And now the PAP1 orthologs have been identified in many horticultural crops (Cutanda-Perez et al, 2009; Chagne et al, 2012; Schaart et al, 2013; Albert et al, 2014; Jin et al, 2016). Recently, our studies suggest that the structural gene LcUFGT and its regulator LcMYB1 play major roles in anthocyanin accumulation in litchi (Lai et al, 2014, 2015). In addition to MBW complex, additional TFs and regulatory genes have also been reported to affect anthocyanin biosynthesis, such as COP1 (Maier et al, 2013), JASMONATE ZIM-domain (JAZ) genes (Qi et al, 2011), the SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) gene (Gou et al, 2011), and NAC (Zhou et al, 2015).…”

“…Apart from the delicious taste, attractive red skin of litchi is another important aspect of the fruit quality. Recently, the gene involved in anthocyanin biosynthesis and sequestration from litchi has been reported (Wei et al, 2011; Lai et al, 2014, 2015, 2016; Li et al, 2015; Hu et al, 2016). However, the mechanism of miRNAs regulating anthocyanin biosynthesis in litchi has not been reported.…”

Transcriptional changes during ovule development in two genotypes of litchi (Litchi chinensis Sonn.) with contrast in seed size

“…In horticultural crops, only in a few cases, transcriptome sequence analysis has been used for the prediction of genes related to fruit development- as in case of Annona squamosa, Musa accuminata , Prunusavium , Pyrusbrets chneideri etc78910. Comparative analysis of transcriptome in litchi has been used to speculate on the processes involved in the regulation of floral initiation by phytohormones, expression of flowering related genes11, genes related to shading stress12, fruit cracking13, reactive oxygen species (ROS) induced abortion of rudimentary leaves14, fruit abscission15, maturation, coloration16, abscission induced by carbohydrate stress17 and fruit ripening after cold storage18. To the best of our knowledge, there is no report on transcription profiling of early stage developing ovules in litchi.…”