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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

Differential gene expression profiles based on the library of the three coloration stages. (A) The numbers of up- and down-regulated genes in comparisons of the red-VS-yellow, red-VS-green, and yellow-VS-green fruit samples. (B) Venn diagram showing the comparison of differentially expressed genes between any two stages of the litchi pericarp.
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Fig4: Differential gene expression profiles based on the library of the three coloration stages. (A) The numbers of up- and down-regulated genes in comparisons of the red-VS-yellow, red-VS-green, and yellow-VS-green fruit samples. (B) Venn diagram showing the comparison of differentially expressed genes between any two stages of the litchi pericarp.

Mentions: Differences in gene expression in the pericarp at three coloration stages (green-VS-yellow, yellow-VS-red, and green-VS-red) were assessed and DEGs were identified by pairwise comparisons of the three libraries with the expression fold (log2Ratio ≥ 1) and false discovery rate (FDR ≤ 10−3) as the thresholds (Figure 4A). A total of 3,649 genes were found to be significantly differentially expressed in the pair-wise comparisons between any two stages, with 1,800 DEGs (1,154 down-regulated and 646 up-regulated) between the green and yellow libraries (Additional file 6). A total of 1,241 DEGs were detected between the yellow and red libraries, with 371 down-regulated and 870 up-regulated (Additional file 7). Finally, the greatest number of differentially expressed genes occurred between the green and red libraries, with 1,300 down-regulated and 1,214 up-regulated (Additional file 8). Of all the DEGs, 156 genes were found to be significantly differentially expressed among all three coloration stages (Figure 4B).Figure 4


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)

Differential gene expression profiles based on the library of the three coloration stages. (A) The numbers of up- and down-regulated genes in comparisons of the red-VS-yellow, red-VS-green, and yellow-VS-green fruit samples. (B) Venn diagram showing the comparison of differentially expressed genes between any two stages of the litchi pericarp.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Fig4: Differential gene expression profiles based on the library of the three coloration stages. (A) The numbers of up- and down-regulated genes in comparisons of the red-VS-yellow, red-VS-green, and yellow-VS-green fruit samples. (B) Venn diagram showing the comparison of differentially expressed genes between any two stages of the litchi pericarp.
Mentions: Differences in gene expression in the pericarp at three coloration stages (green-VS-yellow, yellow-VS-red, and green-VS-red) were assessed and DEGs were identified by pairwise comparisons of the three libraries with the expression fold (log2Ratio ≥ 1) and false discovery rate (FDR ≤ 10−3) as the thresholds (Figure 4A). A total of 3,649 genes were found to be significantly differentially expressed in the pair-wise comparisons between any two stages, with 1,800 DEGs (1,154 down-regulated and 646 up-regulated) between the green and yellow libraries (Additional file 6). A total of 1,241 DEGs were detected between the yellow and red libraries, with 371 down-regulated and 870 up-regulated (Additional file 7). Finally, the greatest number of differentially expressed genes occurred between the green and red libraries, with 1,300 down-regulated and 1,214 up-regulated (Additional file 8). Of all the DEGs, 156 genes were found to be significantly differentially expressed among all three coloration stages (Figure 4B).Figure 4

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