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

Haiyue Sun,Jinman Geng,Hongdi Liu,Yuzhuo Gai,Li Chen,Yadong Li,Yushan Liu,Limin Kang,Youwen Tian

doi:10.1186/s12864-015-1842-4

Abstract

BackgroundCranberries (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.ResultsIn 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.ConclusionsOur 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.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1842-4) contains supplementary material, which is available to authorized users.

Highlights

Cranberries (Vaccinium macrocarpon Ait.), renowned for their excellent health benefits, are an important berry crop
Results and discussion cDNA sequence generation, de novo assembly and mapping to the cranberry genome To obtain a complete profile of the cranberry transcriptome during fruit development, two cDNA libraries were built for two fruit developmental stages: white fruit (W) and red fruit (R). 59,986,374 and 59,690,570 raw reads were generated from the W and R libraries, respectively
These results suggest that the sequencing data have sufficient quantity and quality to ensure accurate sequence assembly and adequate transcriptome coverage

Summary

Introduction

Cranberries (Vaccinium macrocarpon Ait.), renowned for their excellent health benefits, are an important berry crop. 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. The American, or large cranberries (Vaccinium macrocarpon Ait), renowned for their health benefits, are an important berry crop [1]. Most commercial cranberries produce round and red fruits, which are useful for fresh and frozen products, juice, wine, fruit beverages, jelly and jam. The bioactive compounds of V. macrocarpon have been analyzed previously in fresh fruit and cranberry juice by high-performance liquid chromatography (HPLC), ultraviolet–visible (UV/Vis) and mass spectrometer (MS) detection [4,5,6]. The major bioactive compounds in cranberries are flavonoids, Sun et al BMC Genomics (2015) 16:652

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