title: De novo assembly and characterization of Sophora japonica transcriptome using RNA-seq.
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.
authors: Institute of System Biology, Shanghai University, Shanghai 200444, China.
authors: Liucun
authors: L
authors: Zhu
authors: Yangzhou Breeding Biological Agriculture Technology Co. Ltd., Yangzhou 225200, China.
authors: Ying
authors: Y
authors: Zhang
authors: Institute of System Biology, Shanghai University, Shanghai 200444, China.
authors: Wenna
authors: W
authors: Guo
authors: Department of Mathematics, Shanghai University, Shanghai 200444, China.
authors: Xin-Jian
authors: XJ
authors: Xu
authors: State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210093, China.
authors: Qiang
authors: Q
authors: Wang
mesh_terms: D030541:Databases, Genetic; D020869:Gene Expression Profiling / Q000379:methods*; D017423:Sequence Analysis, RNA / Q000379:methods*; D029909:Sophora / Q000235:genetics* / Q000378:metabolism*; D059467:Transcriptome / Q000235:genetics*