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Differentially expressed gene analysis of Tamarix chinensis provides insights into NaCl-stress response

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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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Correspondence to Li-an Xu.

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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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