Transcriptome differences between two sister desert poplar species under salt stressReport as inadecuate




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BMC Genomics

, 15:337

Plant genomics

Abstract

BackgroundPopulus euphratica Oliv and P. pruinosa Schrenk Salicaceae both grow in dry desert areas with high summer temperatures. However, P. euphratica is distributed in dry deserts with deep underground water whereas P. pruinosa occurs in deserts in which there is underground water close to the surface. We therefore hypothesized that these two sister species may have evolved divergent regulatory and metabolic pathways during their interaction with different salt habitats and other stresses. To test this hypothesis, we compared transcriptomes from callus exposed to 24 h of salt stress and control callus samples from both species and identified differentially expressed genes DEGs and alternative splicing AS events that had occurred under salt stress.

ResultsA total of 36,144 transcripts were identified and 1430 genes were found to be differentially expressed in at least one species in response to salt stress. Of these DEGs, 884 and 860 were identified in P. euphratica and P. pruinosa, respectively, while 314 DEGs were common to both species. On the basis of parametric analysis of gene set enrichment, GO enrichment in P. euphratica was found to be significantly different from that in P. pruinosa. Numerous genes involved in hormone biosynthesis, transporters and transcription factors showed clear differences between the two species in response to salt stress. We also identified 26,560 AS events which were mapped to 8380 poplar genomic loci from four libraries. GO enrichments for genes undergoing AS events in P. euphratica differed significantly from those in P. pruinosa.

ConclusionsA number of salt-responsive genes in both P. euphratica and P. pruinosa were identified and candidate genes with potential roles in the salinity adaptation were proposed. Transcriptome comparisons of two sister desert poplar species under salt stress suggest that these two species may have developed different genetic pathways in order to adapt to different desert salt habitats. The DEGs that were found to be common to both species under salt stress may be especially important for future genetic improvement of cultivated poplars or other crops through transgenic approaches in order to increase tolerance of saline soil conditions.

KeywordsP. euphratica P. pruinosa Salt tolerance Salinity stress Transcriptome Differentially expressed genes Alternative splicing AbbreviationsDGEDigital gene expression

GOGene ontology

KEGGKyoto Encyclopedia of Genes and Genomes

FPKMNumber of fragments per kilobase of exon per million fragments mapped

DEGsDifferentially expressed genes

PAGEParametric analysis of gene set enrichment

SEASingular enrichment analysis

FDRFalse discovery rate

qRT-PCRQuantitative real-time polymerase chain reaction.

Electronic supplementary materialThe online version of this article doi:10.1186-1471-2164-15-337 contains supplementary material, which is available to authorized users.

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Author: Jian Zhang - Jianju Feng - Jing Lu - Yongzhi Yang - Xu Zhang - Dongshi Wan - Jianquan Liu

Source: https://link.springer.com/







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