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Open Access Highly Accessed Research article

De novo assembly and Characterisation of the Transcriptome during seed development, and generation of genic-SSR markers in Peanut (Arachis hypogaea L.)

Jianan Zhang12, Shan Liang3, Jialei Duan4, Jin Wang1, Silong Chen1, Zengshu Cheng1, Qiang Zhang1, Xuanqiang Liang5 and Yurong Li1*

Author Affiliations

1 Institute of Food and Oil Crops, Hebei Academy of Agriculture and Forestry Sciences/Laboratory of Crop Genetics and Breeding of Hebei Province, Shijiazhuang 050031, China

2 National Millet Improvement Center of China, Institute of Millet Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang 050031, China

3 Protein Science Laboratory of the Ministry of Education, School of Life Sciences, Tsinghua University, Beijing 100084, China

4 Key Laboratory of Crop Germplasm Resources and Utilization, Ministry of Agriculture/The National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China

5 Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong 510000, China

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BMC Genomics 2012, 13:90  doi:10.1186/1471-2164-13-90

Published: 12 March 2012

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.

Conclusion

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.