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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.


Related in: MedlinePlus

Gene transcription profile between W and R libraries. For comparing gene expression level between the two libraries, each library was normalized to 1 million tags. Red dots represent transcripts more prevalent in R library, green dots show those present at a lower frequency in W library and blue dots indicate transcripts that did not change significantly
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Fig7: Gene transcription profile between W and R libraries. For comparing gene expression level between the two libraries, each library was normalized to 1 million tags. Red dots represent transcripts more prevalent in R library, green dots show those present at a lower frequency in W library and blue dots indicate transcripts that did not change significantly

Mentions: To obtain a digital expression profile of the differentially expressed genes between the two fruit development stages in the cranberry, we used the FPKM (Fragments per kb per million fragments) method to perform gene expression analysis between the W and R libraries [76]. The transcripts with at least a two-fold difference between white and red fruits are shown in Fig. 7. A total of 3,257 unigenes were identified as differentially expressed genes (DEGs) between the two developmental stages of cranberry fruit (Fig. 8). Among them, 2,125 and 1,132 unigenes were highly expressed in the red and white fruits, respectively. More genes were highly expressed in red fruits, suggesting that more genes were involved in complex metabolites during the full ripening stage of the fruit. Moreover, 3,010 and 1,328 unigenes were only expressed in red and white fruits, respectively. This indicates that the unigenes may be specifically expressed in the different development stages of cranberry fruits.Fig. 7


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)

Gene transcription profile between W and R libraries. For comparing gene expression level between the two libraries, each library was normalized to 1 million tags. Red dots represent transcripts more prevalent in R library, green dots show those present at a lower frequency in W library and blue dots indicate transcripts that did not change significantly
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

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

Fig7: Gene transcription profile between W and R libraries. For comparing gene expression level between the two libraries, each library was normalized to 1 million tags. Red dots represent transcripts more prevalent in R library, green dots show those present at a lower frequency in W library and blue dots indicate transcripts that did not change significantly
Mentions: To obtain a digital expression profile of the differentially expressed genes between the two fruit development stages in the cranberry, we used the FPKM (Fragments per kb per million fragments) method to perform gene expression analysis between the W and R libraries [76]. The transcripts with at least a two-fold difference between white and red fruits are shown in Fig. 7. A total of 3,257 unigenes were identified as differentially expressed genes (DEGs) between the two developmental stages of cranberry fruit (Fig. 8). Among them, 2,125 and 1,132 unigenes were highly expressed in the red and white fruits, respectively. More genes were highly expressed in red fruits, suggesting that more genes were involved in complex metabolites during the full ripening stage of the fruit. Moreover, 3,010 and 1,328 unigenes were only expressed in red and white fruits, respectively. This indicates that the unigenes may be specifically expressed in the different development stages of cranberry fruits.Fig. 7

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.


Related in: MedlinePlus