Limits...
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.


Histogram of GO analysis of DEGs
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

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

Fig9: Histogram of GO analysis of DEGs

Mentions: We identified 1,246 DEGs that were assigned to 49 significantly enriched GO terms. The most abundant GO terms were “metabolic process”, “cell and cell part” and “catalytic activity” in the biological process, cellular component and molecular function categories, respectively (Fig. 9). Moreover, there are some interesting biological processes which are associated with fruit development, such as “developmental process”, “growth”, “reproduction”, “reproductive process”, “antioxidant activity” and “transporter activity”.Fig. 9


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)

Histogram of GO analysis of DEGs
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

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

Fig9: Histogram of GO analysis of DEGs
Mentions: We identified 1,246 DEGs that were assigned to 49 significantly enriched GO terms. The most abundant GO terms were “metabolic process”, “cell and cell part” and “catalytic activity” in the biological process, cellular component and molecular function categories, respectively (Fig. 9). Moreover, there are some interesting biological processes which are associated with fruit development, such as “developmental process”, “growth”, “reproduction”, “reproductive process”, “antioxidant activity” and “transporter activity”.Fig. 9

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.