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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.

SUBMITTER: Zhu L

PROVIDER: S-EPMC4058233 | biostudies-literature | 2014

REPOSITORIES: biostudies-literature

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Gleditsia sinensis: transcriptome sequencing, construction, and application of its protein-protein interaction network.

Zhu Liucun L Zhang Ying Y Guo Wenna W Wang Qiang Q

BioMed research international 20140527

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 uni ...[more]

PMID: 24982878

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Project description:BackgroundGleditsia sinensis is a significant tree species from both ecological and economic perspectives. However, its growth is hampered by temporary droughts during the seedling stage, thereby impeding the development of the G. sinensis industry. Drought stress and rehydration of semi-annual potted seedlings using an artificial simulated water control method. RNA sequencing (RNA-seq) analyses were conducted on leaves collected from highly resistant (HR) and highly susceptible (HS) seedling families at five different stages during the process of drought stress and rehydration to investigate their gene expression patterns.ResultsThe differentially expressed genes (DEGs) were predominantly enriched in pathways related to "chloroplast" (GO:0009507), "photosynthesis" (GO:0015979), "plant hormone signal transduction" (map04075), "flavonoid biosynthesis" (map00941), "stress response", "response to reactive oxygen species (ROS)" (GO:0000302), "signal transduction" (GO:0007165) in G. sinensis HR and HS families exposed to mild and severe drought stress. Additionally, the pathways related to "plant hormone signal transduction" (map04075), and osmoregulation were also enriched. The difference in drought tolerance between the two families of G. sinensis may be associated with "transmembrane transporter activity" (GO:0022857), "stress response", "hormones and signal transduction" (GO:0007165), "cutin, suberine and wax biosynthesis" (map00073), "ribosome" (map03010), "photosynthesis" (map00195), "sugar metabolism", and others. An enrichment analysis of DEGs under severe drought stress suggests that the drought tolerance of both families may be related to "water-soluble vitamin metabolic process" (GO:0006767), "photosynthesis" (map00195), "plant hormone signal transduction" (map04075), "starch and sucrose metabolism" (map00500), and "galactose metabolism" (map00052). Osmoregulation-related genes such as delta-1-pyrroline-5-carboxylate synthase (P5CS), Amino acid permease (AAP), Amino acid permease 2 (AAP2) and Trehalose-phosphate synthase (TPS), as well as the antioxidant enzyme L-ascorbate peroxidase 6 (APX6), may be significant genes involved in drought tolerance in G. sinensis. Five genes were selected randomly to validate the RNA-seq results using quantitative real-time PCR (RT-qPCR) and they indicated that the transcriptome data were reliable.ConclusionsThe study presents information on the molecular regulation of the drought tolerance mechanism in G. sinensis and provides a reference for further research on the molecular mechanisms involved in drought tolerance breeding of G. sinensis.

Dataset Information

Gleditsia sinensis: transcriptome sequencing, construction, and application of its protein-protein interaction network.

Publications

Gleditsia sinensis: transcriptome sequencing, construction, and application of its protein-protein interaction network.

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