title: De novo assembly and characterisation of the transcriptome during seed development, and generation of genic-SSR markers in peanut (Arachis hypogaea L.).
abstract: BACKGROUND
  The peanut (Arachis hypogaea L.) is an important oilseed crop in tropical and subtropical regions of the world. However, little about the molecular biology of the peanut is currently known. Recently, next-generation sequencing technology, termed RNA-seq, has provided a powerful approach for analysing the transcriptome, and for shedding light on the molecular biology of peanut.
  
  
  RESULTS
  In this study, we employed RNA-seq to analyse the transcriptomes of the immature seeds of three different peanut varieties with different oil contents. A total of 26.1-27.2 million paired-end reads with lengths of 100 bp were generated from the three varieties and 59,077 unigenes were assembled with N50 of 823 bp. Based on sequence similarity search with known proteins, a total of 40,100 genes were identified. Among these unigenes, only 8,252 unigenes were annotated with 42 gene ontology (GO) functional categories. And 18,028 unigenes mapped to 125 pathways by searching against the Kyoto Encyclopedia of Genes and Genomes pathway database (KEGG). In addition, 3,919 microsatellite markers were developed in the unigene library, and 160 PCR primers of SSR loci were used for validation of the amplification and the polymorphism.
  
  
  CONCLUSIONS
  We completed a successful global analysis of the peanut transcriptome using RNA-seq, a large number of unigenes were assembled, and almost four thousand SSR primers were developed. These data will facilitate gene discovery and functional genomic studies of the peanut plant. In addition, this study provides insight into the complex transcriptome of the peanut and established a biotechnological platform for future research.
authors.affiliation: Institute of Food and Oil Crops, Hebei Academy of Agriculture and Forestry Sciences/Laboratory of Crop Genetics and Breeding of Hebei Province, Shijiazhuang, China.
authors.forename: Jianan
authors.initials: J
authors.lastname: Zhang
authors.forename: Shan
authors.initials: S
authors.lastname: Liang
authors.forename: Jialei
authors.initials: J
authors.lastname: Duan
authors.forename: Jin
authors.initials: J
authors.lastname: Wang
authors.forename: Silong
authors.initials: S
authors.lastname: Chen
authors.forename: Zengshu
authors.initials: Z
authors.lastname: Cheng
authors.forename: Qiang
authors.initials: Q
authors.lastname: Zhang
authors.forename: Xuanqiang
authors.initials: X
authors.lastname: Liang
authors.forename: Yurong
authors.initials: Y
authors.lastname: Li
mesh_terms: D010367:Arachis / Q000235:genetics*; D020869:Gene Expression Profiling; D018895:Microsatellite Repeats; D058977:Molecular Sequence Annotation; D008969:Molecular Sequence Data; D012639:Seeds / Q000235:genetics*; D059467:Transcriptome