title: Gleditsia sinensis: transcriptome sequencing, construction, and application of its protein-protein interaction network.
abstract: Gleditsia sinensis is a genus of deciduous tree in the family Caesalpinioideae, native to China, and is of great economic importance. However, despite its economic value, gene sequence information is strongly lacking. In the present study, transcriptome sequencing of G. sinensis was performed resulting in approximately 75.5 million clean reads assembled into 142155 unique transcripts generating 58583 unigenes. The average length of the unigenes was 900 bp, with an N50 of 549 bp. The obtained unigene sequences were then compared to four protein databases to include NCBI nonredundant protein (NRDB), Swiss-prot, Kyoto Encyclopedia of Genes and Genomes (KEGG), and the Cluster of Orthologous Groups (COG). Using BLAST procedure, 31385 unigenes (53.6%) were generated to have functional annotations. Additionally, sequence homologies between identified unigenes and genes of known species in a protein-protein interaction (PPI) network facilitated G. sinensis PPI network construction. Based on this network construction, new stress resistance genes (including cold, drought, and high salinity) were predicted. The present study is the first investigation of genome-wide gene expression in G. sinensis with the results providing a basis for future functional genomic studies relating to this species.
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: State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210093, China.
authors: Qiang
authors: Q
authors: Wang
mesh_terms: D018506:Gene Expression Regulation, Plant; D063990:Gene Ontology; D017343:Genes, Plant; D031501:Gleditsia / Q000235:genetics*; D058977:Molecular Sequence Annotation; D060066:Protein Interaction Maps / Q000235:genetics*; D017423:Sequence Analysis, RNA; D059467:Transcriptome / Q000235:genetics*