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De Novo Assembly and Characterization of Sophora japonica Transcriptome Using RNA-seq
Joint Authors
Guo, Wenna
Zhu, Liucun
Xu, Xin-Jian
Zhang, Ying
Wang, Qiang
Source
Issue
Vol. 2014, Issue 2014 (31 Dec. 2014), pp.1-9, 9 p.
Publisher
Hindawi Publishing Corporation
Publication Date
2014-01-02
Country of Publication
Egypt
No. of Pages
9
Main Subjects
Abstract EN
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.
American Psychological Association (APA)
Zhu, Liucun& Zhang, Ying& Guo, Wenna& Xu, Xin-Jian& Wang, Qiang. 2014. De Novo Assembly and Characterization of Sophora japonica Transcriptome Using RNA-seq. BioMed Research International،Vol. 2014, no. 2014, pp.1-9.
https://search.emarefa.net/detail/BIM-495827
Modern Language Association (MLA)
Zhu, Liucun…[et al.]. De Novo Assembly and Characterization of Sophora japonica Transcriptome Using RNA-seq. BioMed Research International No. 2014 (2014), pp.1-9.
https://search.emarefa.net/detail/BIM-495827
American Medical Association (AMA)
Zhu, Liucun& Zhang, Ying& Guo, Wenna& Xu, Xin-Jian& Wang, Qiang. De Novo Assembly and Characterization of Sophora japonica Transcriptome Using RNA-seq. BioMed Research International. 2014. Vol. 2014, no. 2014, pp.1-9.
https://search.emarefa.net/detail/BIM-495827
Data Type
Journal Articles
Language
English
Notes
Includes bibliographical references
Record ID
BIM-495827