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De novo sequencing and analysis of the cranberry fruit transcriptome to identify putative genes involved in flavonoid biosynthesis, transport and regulation.

Sun H, Liu Y, Gai Y, Geng J, Chen L, Liu H, Kang L, Tian Y, Li Y - BMC Genomics (2015)

Bottom Line: In addition, 14,473 simple sequence repeats (SSRs) were detected.Our results present comprehensive gene expression information about the cranberry fruit transcriptome that could facilitate our understanding of the molecular mechanisms of fruit development in cranberries.Although it will be necessary to validate the functions carried out by these genes, these results could be used to improve the quality of breeding programs for the cranberry and related species.

View Article: PubMed Central - PubMed

Affiliation: College of Horticulture, Jilin Agricultural University, Changchun, Jilin, China. haiyue-sun@hotmail.com.

ABSTRACT

Background: Cranberries (Vaccinium macrocarpon Ait.), renowned for their excellent health benefits, are an important berry crop. Here, we performed transcriptome sequencing of one cranberry cultivar, from fruits at two different developmental stages, on the Illumina HiSeq 2000 platform. Our main goals were to identify putative genes for major metabolic pathways of bioactive compounds and compare the expression patterns between white fruit (W) and red fruit (R) in cranberry.

Results: In this study, two cDNA libraries of W and R were constructed. Approximately 119 million raw sequencing reads were generated and assembled de novo, yielding 57,331 high quality unigenes with an average length of 739 bp. Using BLASTx, 38,460 unigenes were identified as putative homologs of annotated sequences in public protein databases, including NCBI NR, NT, Swiss-Prot, KEGG, COG and GO. Of these, 21,898 unigenes mapped to 128 KEGG pathways, with the metabolic pathways, secondary metabolites, glycerophospholipid metabolism, ether lipid metabolism, starch and sucrose metabolism, purine metabolism, and pyrimidine metabolism being well represented. Among them, many candidate genes were involved in flavonoid biosynthesis, transport and regulation. Furthermore, digital gene expression (DEG) analysis identified 3,257 unigenes that were differentially expressed between the two fruit developmental stages. In addition, 14,473 simple sequence repeats (SSRs) were detected.

Conclusions: Our results present comprehensive gene expression information about the cranberry fruit transcriptome that could facilitate our understanding of the molecular mechanisms of fruit development in cranberries. Although it will be necessary to validate the functions carried out by these genes, these results could be used to improve the quality of breeding programs for the cranberry and related species.

No MeSH data available.


The expression profiles of 10 unigenes between W and R libraries in cranberry
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Fig10: The expression profiles of 10 unigenes between W and R libraries in cranberry

Mentions: To validate the data from our digital expression analysis, quantitative Real Time PCR (qRT-PCR) assays were performed on 10 DEGs involved in the phenylpropanoid biosynthesis, flavone and flavonol biosynthesis, and flavonoid biosynthetic pathways (Table 6). The qRT-PCR expression pattern of these unigenes is shown in Fig. 10. Except for the unigenes encoding UDP-glycosyltransferase (CL754.Contig1_All), cytochrome P450 (CL1200.Contig1_All, CL1200.Contig2_All, CL3597.Contig3_All, CL3597.Contig4_All, CL3597.Contig5_All and Unigene7973_All), flavonoid 3′ hydroxylase (Unigene20161_All), carboxylesterase (CL1068.Contig2_All), and UDP-glycosyltransferase (Unigene 24441_All), the unigenes were up-regulated in the red fruit stage. The results of the qRT-PCR are consistent with our digital expression data (Table 6). This also showed an association with flavonoid production, and it is likely that these genes are involved in the fruit development stage. Plant cytochrome P450s are a large superfamily of heme-containing monooxygenases, which are involved in a wide range of secondary metabolite biosynthetic reactions, such as terpenoids, phenylpropanoids, and nitrogen-containing compounds, including alkaloids, cyanogenic glucosides, and glucosinolates [77]. Therefore, the selected unigenes encoding cytochrome P450s may play important roles in flavonoid accumulation in cranberry fruit.Table 6


De novo sequencing and analysis of the cranberry fruit transcriptome to identify putative genes involved in flavonoid biosynthesis, transport and regulation.

Sun H, Liu Y, Gai Y, Geng J, Chen L, Liu H, Kang L, Tian Y, Li Y - BMC Genomics (2015)

The expression profiles of 10 unigenes between W and R libraries in cranberry
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4556307&req=5

Fig10: The expression profiles of 10 unigenes between W and R libraries in cranberry
Mentions: To validate the data from our digital expression analysis, quantitative Real Time PCR (qRT-PCR) assays were performed on 10 DEGs involved in the phenylpropanoid biosynthesis, flavone and flavonol biosynthesis, and flavonoid biosynthetic pathways (Table 6). The qRT-PCR expression pattern of these unigenes is shown in Fig. 10. Except for the unigenes encoding UDP-glycosyltransferase (CL754.Contig1_All), cytochrome P450 (CL1200.Contig1_All, CL1200.Contig2_All, CL3597.Contig3_All, CL3597.Contig4_All, CL3597.Contig5_All and Unigene7973_All), flavonoid 3′ hydroxylase (Unigene20161_All), carboxylesterase (CL1068.Contig2_All), and UDP-glycosyltransferase (Unigene 24441_All), the unigenes were up-regulated in the red fruit stage. The results of the qRT-PCR are consistent with our digital expression data (Table 6). This also showed an association with flavonoid production, and it is likely that these genes are involved in the fruit development stage. Plant cytochrome P450s are a large superfamily of heme-containing monooxygenases, which are involved in a wide range of secondary metabolite biosynthetic reactions, such as terpenoids, phenylpropanoids, and nitrogen-containing compounds, including alkaloids, cyanogenic glucosides, and glucosinolates [77]. Therefore, the selected unigenes encoding cytochrome P450s may play important roles in flavonoid accumulation in cranberry fruit.Table 6

Bottom Line: In addition, 14,473 simple sequence repeats (SSRs) were detected.Our results present comprehensive gene expression information about the cranberry fruit transcriptome that could facilitate our understanding of the molecular mechanisms of fruit development in cranberries.Although it will be necessary to validate the functions carried out by these genes, these results could be used to improve the quality of breeding programs for the cranberry and related species.

View Article: PubMed Central - PubMed

Affiliation: College of Horticulture, Jilin Agricultural University, Changchun, Jilin, China. haiyue-sun@hotmail.com.

ABSTRACT

Background: Cranberries (Vaccinium macrocarpon Ait.), renowned for their excellent health benefits, are an important berry crop. Here, we performed transcriptome sequencing of one cranberry cultivar, from fruits at two different developmental stages, on the Illumina HiSeq 2000 platform. Our main goals were to identify putative genes for major metabolic pathways of bioactive compounds and compare the expression patterns between white fruit (W) and red fruit (R) in cranberry.

Results: In this study, two cDNA libraries of W and R were constructed. Approximately 119 million raw sequencing reads were generated and assembled de novo, yielding 57,331 high quality unigenes with an average length of 739 bp. Using BLASTx, 38,460 unigenes were identified as putative homologs of annotated sequences in public protein databases, including NCBI NR, NT, Swiss-Prot, KEGG, COG and GO. Of these, 21,898 unigenes mapped to 128 KEGG pathways, with the metabolic pathways, secondary metabolites, glycerophospholipid metabolism, ether lipid metabolism, starch and sucrose metabolism, purine metabolism, and pyrimidine metabolism being well represented. Among them, many candidate genes were involved in flavonoid biosynthesis, transport and regulation. Furthermore, digital gene expression (DEG) analysis identified 3,257 unigenes that were differentially expressed between the two fruit developmental stages. In addition, 14,473 simple sequence repeats (SSRs) were detected.

Conclusions: Our results present comprehensive gene expression information about the cranberry fruit transcriptome that could facilitate our understanding of the molecular mechanisms of fruit development in cranberries. Although it will be necessary to validate the functions carried out by these genes, these results could be used to improve the quality of breeding programs for the cranberry and related species.

No MeSH data available.