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BioMed Research International
Volume 2014 (2014), Article ID 750961, 9 pages
http://dx.doi.org/10.1155/2014/750961
Research Article

De Novo Assembly and Characterization of Sophora japonica Transcriptome Using RNA-seq

1Institute of System Biology, Shanghai University, Shanghai 200444, China
2Yangzhou Breeding Biological Agriculture Technology Co. Ltd., Yangzhou 225200, China
3Department of Mathematics, Shanghai University, Shanghai 200444, China
4State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210093, China

Received 25 September 2013; Revised 22 November 2013; Accepted 25 November 2013; Published 2 January 2014

Academic Editor: Tao Huang

Copyright © 2014 Liucun Zhu et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Abstract

Sophora japonica Linn (Chinese Scholar Tree) is a shrub species belonging to the subfamily Faboideae of the pea family Fabaceae. In this study, RNA sequencing of S. japonica transcriptome was performed to produce large expression datasets for functional genomic analysis. Approximate 86.1 million high-quality clean reads were generated and assembled de novo into 143010 unique transcripts and 57614 unigenes. The average length of unigenes was 901 bps with an N50 of 545 bps. Four public databases, including the NCBI nonredundant protein (NR), Swiss-Prot, Kyoto Encyclopedia of Genes and Genomes (KEGG), and the Cluster of Orthologous Groups (COG), were used to annotate unigenes through NCBI BLAST procedure. A total of 27541 of 57614 unigenes (47.8%) were annotated for gene descriptions, conserved protein domains, or gene ontology. Moreover, an interaction network of unigenes in S. japonica was predicted based on known protein-protein interactions of putative orthologs of well-studied plant genomes. The transcriptome data of S. japonica reported here represents first genome-scale investigation of gene expressions in Faboideae plants. We expect that our study will provide a useful resource for further studies on gene expression, genomics, functional genomics, and protein-protein interaction in S. japonica.