De novo sequencing and analysis of the cranberry fruit transcriptome to identify putative genes involved in flavonoid biosynthesis, transport and regulation.
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.
College of Horticulture, Jilin Agricultural University, Changchun, Jilin, China. haiyue-sun@hotmail.com.
Haiyue
H
Sun
College of Horticulture, Jilin Agricultural University, Changchun, Jilin, China. crazy4321@sina.cn.
Yushan
Y
Liu
College of Horticulture, Jilin Agricultural University, Changchun, Jilin, China. gallia@qq.com.
Yuzhuo
Y
Gai
College of Horticulture, Jilin Agricultural University, Changchun, Jilin, China. gengjinman@2008.sina.com.
Jinman
J
Geng
College of Horticulture, Jilin Agricultural University, Changchun, Jilin, China. chenlixx@yeah.net.
Li
L
Chen
College of Horticulture, Jilin Agricultural University, Changchun, Jilin, China. tang_tang1234@126.com.
Hongdi
H
Liu
College of Horticulture, Jilin Agricultural University, Changchun, Jilin, China. kang15543270828@126.com.
Limin
L
Kang
College of Horticulture, Jilin Agricultural University, Changchun, Jilin, China. tyw5219@163.com.
Youwen
Y
Tian
College of Horticulture, Jilin Agricultural University, Changchun, Jilin, China. blueberryli@163.com.
Yadong
Y
Li
D000872:Anthocyanins / Q000096:biosynthesis; D001483:Base Sequence; D001692:Biological Transport / Q000235:genetics; D053898:Biosynthetic Pathways / Q000235:genetics*; D002874:Chromosome Mapping; D018076:DNA, Complementary / Q000235:genetics; D030541:Databases, Genetic; D015536:Down-Regulation / Q000235:genetics; D005419:Flavonoids / Q000096:biosynthesis*; D005638:Fruit / Q000235:genetics*; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D063990:Gene Ontology; D017343:Genes, Plant; D056726:Genetic Association Studies; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D018895:Microsatellite Repeats / Q000235:genetics; D058977:Molecular Sequence Annotation; D059372:Nucleotide Motifs / Q000235:genetics; D060888:Real-Time Polymerase Chain Reaction; D015203:Reproducibility of Results; D016622:Silver Staining; D014157:Transcription Factors / Q000378:metabolism; D059467:Transcriptome / Q000235:genetics*; D015854:Up-Regulation / Q000235:genetics; D029799:Vaccinium macrocarpon / Q000235:genetics*
D000872:Anthocyanins; D018076:DNA, Complementary; D005419:Flavonoids; D014157:Transcription Factors