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

BMC Genomics
Haiyue SunYadong Li

Abstract

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. 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...Continue Reading

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Citations

Jun 1, 2016·Frontiers in Plant Science·Katja KarppinenLaura Jaakola
Apr 17, 2018·Genome Génome / Conseil National De Recherches Canada·Shruti ChoudharyPankaj Bhardwaj
Jun 3, 2021·Cells·Deepu PanditaHosam O Elansary
Dec 20, 2018·Journal of Agricultural and Food Chemistry·Chengcai ZhangKailiang Wang
Nov 13, 2021·Critical Reviews in Food Science and Nutrition·Yifan YanSimone Diego Castellarin

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Datasets Mentioned

BETA
SRX1140359
SRX1140360

Methods Mentioned

BETA
Illumina sequencing
RNA-Seq
glycosylation
PCR
electrophoresis

Software Mentioned

PRIMER
Trinity tool
Butterfly
finder
filter
fq
Blast2GO
Chrysalis
ssr
ESTScan

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