Abstract
Key message
Based on the transcriptome sequencing of Tamarix chinensis roots under NaCl stress, the differentially expressed gene analysis provides insights into NaCl-stress response.
Abstract
Salinity is an environmental stress that limits plants’ growth and crop yield. High salinity evokes multiple abiotic stresses on plants and affects plants’ life almost in all respects. To avoid the grain yield reduction induced by global increases in soil salinization, Tamarix chinensis, being a salt-tolerant tree species, is an appropriate material for plants’ salt-tolerance genes examining and tolerance mechanisms investigating. 59,331 unigenes were assembled by transcriptome sequencing of T. chinensis roots under sodium chloride (NaCl) stress, using Illumina HiSeq 2000. Of these unigenes, 45.58% had significant hits in seven databases. 9886, 8153, and 19,938 unigenes were subdivided into 28 KOG (EuKaryotic Orthologous Groups) groups, 29 KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways, and 47 GO (Gene ontology) terms, respectively. A gene expression profile was built, and 1251 DEGs (differentially expressed genes) were identified and classified into ten expression patterns. From the 59,331 unigenes, we predicted about 3000 general NaCl-stress responsive genes. Especially, we predicted several specific salt-tolerance candidate genes by comprehensive analysis of DEGs. Given that all the responsive genes were potential salt-tolerance determinants, we described their roles on the frame of salt-signaling pathway and this could be a systematic guide for following salt-tolerance studies.
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Abbreviations
- DEGs:
-
Differentially expressed genes
- DGE:
-
Digital gene expression profile
- RNA-Seq:
-
High-throughput transcriptome sequencing
- Nr:
-
NCBI non-redundant protein sequences
- Nt:
-
NCBI non-redundant nucleotide sequences
- Pfam:
-
Protein family
- KOG/COG:
-
Clusters of orthologous groups of proteins
- Swiss-Prot:
-
A manually annotated and reviewed protein sequence database
- KO:
-
KEGG ortholog database
- GO:
-
Gene ontology
- ROS:
-
Reactive oxygen species
- MF:
-
Molecular function
- CC:
-
Cellular component
- BP:
-
Biological process
- KOG:
-
EuKaryotic Orthologous Groups
- KEGG:
-
Kyoto encyclopedia of genes and genomes
- FPKM:
-
Fragments per kilobase of exon per million fragments mapped
- ABA:
-
Abscisic acid
- ETH:
-
Ethylene
- ETR:
-
ETH receptor
- BR:
-
Brassinolide
- JA:
-
Jasmonic acid
- SA:
-
Salicylic acid
- MAPK:
-
Mitogen-activated protein kinase
- SOS:
-
Salt overly senstive
- LEA:
-
Late embryogenesis abundant protein
- SOD/POD:
-
Superoxidase dismutase/peroxidase
- Bzip:
-
Basic region-leucine zipper motif
- MYB:
-
V-MYB avian myeloblastosis viral oncogene homolog
- AP2/ERF:
-
APETALA2/ETH-responsive factor
- DRE/CRT:
-
Dehydration-responsive element/C-repeat
- PP2C:
-
Protein phosphatase 2C
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Acknowledgements
This research was financially supported by the Science and Technology Support Program of Jiangsu Province (CN), BE2011321, the Doctorate Fellowship Foundation of Nanjing Forestry University and the Priority Academic Program Development of Jiangsu Higher Education Institutions (PAPD). We are grateful to Xin Guo for assisting with sample collection and preservation. The authors also thank Novogene Bioinformatics Technology (Beijing, China) for assisting with transcriptome sequencing and Vazyme Biotech (Nanjing, China) for assisting with the real-time quantitative analysis.
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Wang, J., Xu, M., Gu, Y. et al. Differentially expressed gene analysis of Tamarix chinensis provides insights into NaCl-stress response. Trees 31, 645–658 (2017). https://doi.org/10.1007/s00468-016-1497-z
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DOI: https://doi.org/10.1007/s00468-016-1497-z