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

Lai B, Hu B, Qin YH, Zhao JT, Wang HC, Hu GB - BMC Genomics (2015)

Bottom Line: 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.Since most of the unigenes were annotated, they provide a platform for litchi functional genomic research within this species.

View Article: PubMed Central - PubMed

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.

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.

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Related in: MedlinePlus

The pathway of chlorophyll breakdown and expressions of chlorophyll breakdown genes. (A) The PAO pathway of chlorophyll breakdown. (B) A heat map of the expressions of genes for chlorophyll breakdown in the pericarp during coloration. Chl, chlorophyll; CLH, chlorophyllase; HCAR, hydroxy-Chl a reductase; MCS, metal chelating substance; NCCs, nonfluorescent Chl catabolites; NOL, NYC1-like; NYC1, non-yellow coloring 1; PAO, pheide a oxygenase; pFCC, primary fluorescent Chl catabolite; Pheide, pheophorbide; PPH, pheophytinase; RCC, red Chl catabolite; RCCR, RCC reductase; SGR, stay-green protein.
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Fig7: The pathway of chlorophyll breakdown and expressions of chlorophyll breakdown genes. (A) The PAO pathway of chlorophyll breakdown. (B) A heat map of the expressions of genes for chlorophyll breakdown in the pericarp during coloration. Chl, chlorophyll; CLH, chlorophyllase; HCAR, hydroxy-Chl a reductase; MCS, metal chelating substance; NCCs, nonfluorescent Chl catabolites; NOL, NYC1-like; NYC1, non-yellow coloring 1; PAO, pheide a oxygenase; pFCC, primary fluorescent Chl catabolite; Pheide, pheophorbide; PPH, pheophytinase; RCC, red Chl catabolite; RCCR, RCC reductase; SGR, stay-green protein.

Mentions: One of the most distinct developmental changes in the pericarp of litchi is degreening, which results from rapid chlorophyll degradation. In land plants, chlorophyll is broken down to colorless linear tetrapyrroles in a highly conserved multi-step pathway termed the ‘PAO pathway’ (Figure 7A); so named because the opening of the chlorin macrocycle present in chlorophyll is catalyzed by pheophorbide a oxygenase (PAO) [4]. In the present study, eleven candidate genes related to chlorophyll degradation were identified from the litchi pericarp transcriptome database, including genes encoding chlorophyll catabolic enzymes, non-yellow coloring (NYC), chlorophyllase (CLH), hydroxy-Chl a reductase (HCAR), pheophytinase (PPH), pheide a oxygenase (PAO), and red Chl catabolite reductase (RCCR), and a stay green protein (SGR). The expression patterns were showed in Figure 7B. The expressions of Unigene 0024586 (PPH) and Unigene 0048135 (SGR) were similar, with the lowest expression at the green stage, moderate expression at the yellow stage, and highest expression at the red stage. The opposite pattern was seen for Unigene 0020901 (HCAR), whose expression decreased during pericarp coloration. For NYC, CLH and PAO, more than one gene was identified and the different gene family members displayed different expression patterns in all cases. The expression of Unigene 0039534 (CLH), Unigene 0016475 (NYC), and Unigene 0027254 (PAO) decreased sharply from the green to the yellow stage before showing up-regulation as fruit reached full maturity. The expression of the remaining genes belonging to these families remained relative stable throughout fruit coloration.Figure 7


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

Lai B, Hu B, Qin YH, Zhao JT, Wang HC, Hu GB - BMC Genomics (2015)

The pathway of chlorophyll breakdown and expressions of chlorophyll breakdown genes. (A) The PAO pathway of chlorophyll breakdown. (B) A heat map of the expressions of genes for chlorophyll breakdown in the pericarp during coloration. Chl, chlorophyll; CLH, chlorophyllase; HCAR, hydroxy-Chl a reductase; MCS, metal chelating substance; NCCs, nonfluorescent Chl catabolites; NOL, NYC1-like; NYC1, non-yellow coloring 1; PAO, pheide a oxygenase; pFCC, primary fluorescent Chl catabolite; Pheide, pheophorbide; PPH, pheophytinase; RCC, red Chl catabolite; RCCR, RCC reductase; SGR, stay-green protein.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4376514&req=5

Fig7: The pathway of chlorophyll breakdown and expressions of chlorophyll breakdown genes. (A) The PAO pathway of chlorophyll breakdown. (B) A heat map of the expressions of genes for chlorophyll breakdown in the pericarp during coloration. Chl, chlorophyll; CLH, chlorophyllase; HCAR, hydroxy-Chl a reductase; MCS, metal chelating substance; NCCs, nonfluorescent Chl catabolites; NOL, NYC1-like; NYC1, non-yellow coloring 1; PAO, pheide a oxygenase; pFCC, primary fluorescent Chl catabolite; Pheide, pheophorbide; PPH, pheophytinase; RCC, red Chl catabolite; RCCR, RCC reductase; SGR, stay-green protein.
Mentions: One of the most distinct developmental changes in the pericarp of litchi is degreening, which results from rapid chlorophyll degradation. In land plants, chlorophyll is broken down to colorless linear tetrapyrroles in a highly conserved multi-step pathway termed the ‘PAO pathway’ (Figure 7A); so named because the opening of the chlorin macrocycle present in chlorophyll is catalyzed by pheophorbide a oxygenase (PAO) [4]. In the present study, eleven candidate genes related to chlorophyll degradation were identified from the litchi pericarp transcriptome database, including genes encoding chlorophyll catabolic enzymes, non-yellow coloring (NYC), chlorophyllase (CLH), hydroxy-Chl a reductase (HCAR), pheophytinase (PPH), pheide a oxygenase (PAO), and red Chl catabolite reductase (RCCR), and a stay green protein (SGR). The expression patterns were showed in Figure 7B. The expressions of Unigene 0024586 (PPH) and Unigene 0048135 (SGR) were similar, with the lowest expression at the green stage, moderate expression at the yellow stage, and highest expression at the red stage. The opposite pattern was seen for Unigene 0020901 (HCAR), whose expression decreased during pericarp coloration. For NYC, CLH and PAO, more than one gene was identified and the different gene family members displayed different expression patterns in all cases. The expression of Unigene 0039534 (CLH), Unigene 0016475 (NYC), and Unigene 0027254 (PAO) decreased sharply from the green to the yellow stage before showing up-regulation as fruit reached full maturity. The expression of the remaining genes belonging to these families remained relative stable throughout fruit coloration.Figure 7

Bottom Line: 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.Since most of the unigenes were annotated, they provide a platform for litchi functional genomic research within this species.

View Article: PubMed Central - PubMed

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.

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.

Show MeSH
Related in: MedlinePlus