De NovoAssembly and Characterization ofSophora japonicaTranscriptome Using RNA-seq

Liucun Zhu,Qiang Wang,Xin-Jian Xu,Ying Zhang,Wenna Guo

doi:10.1155/2014/750961

Liucun Zhu, Qiang Wang + Show 3 more

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https://doi.org/10.1155/2014/750961

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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.

Highlights

Sophora japonica Linn (Chinese Scholar Tree) is a shrub of the pea family Fabaceae
The synthesis of the second strand was performed in a solution containing the reaction buffer, dNTP, RNaseH, and DNA polymerase I using Truseq RNA sample preparation Kit
About 86.1 million reads assembled into 57614 unigenes were generated with an average length of 1321 bps

Summary

Introduction

Sophora japonica Linn (Chinese Scholar Tree) is a shrub of the pea family Fabaceae. It grows into a lofty tree 10–20 m tall that produces a fine, dark brown timber. It is a kind of popular ornamental tree, and a valuable nectar tree, offering delicious and healthy food. In spite of its medicinal and economic value, not much genomic or transcriptomic information is available for S. japonica. As of September 2013, only 74 nucleotide sequences and 35 proteins from S. japonica were available in GenBank. Generation of genomic and transcriptome data is necessary to help further studies on S. japonica

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