Transcriptomic changes during maize roots development responsive to Cadmium (Cd) pollution using comparative RNAseq-based approach

Peng, Hua; He, Xiujing; Gao, Junying; Ma, Hui; Zhang, Zhiming; Shen, Yaou; Pan, Guangtang; Lin, Hung-Ching

doi:10.1016/j.bbrc.2015.07.064

Cited by 40 publications

(39 citation statements)

References 23 publications

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“…The proportion of total reads that mapped to N. benthamiana genome of each sample was more than 96.09%, and that of uniquely mapped was above 72.69%. More than 95.58% of the clean reads had quality scores at the Q30 (an error probability for base calling of 0.1%) level [30]. Furthermore, the GC content ranges from 43.58 to 44.38%.…”

Section: Resultsmentioning

confidence: 99%

Transcriptome analysis of Nicotiana benthamiana infected by Tobacco curly shoot virus

et al. 2018

Virol J

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BackgroundTobacco curly shoot virus (TbCSV) is a monopartite begomovirus associated with betasatellite (Tobacco curly shoot betasatellite, TbCSB), which causes serious leaf curl disease on tomato and tobacco in China. It is interesting that TbCSV induced severe upward leaf curling in Nicotiana benthamiana, but in the presence of TbCSB, symptoms changed to be downward leaf curling. However, the mechanism of interactions between viral pathogenicity, host defense, viral-betasatellite interactions and virus-host interactions remains unclear.MethodsIn this study, RNA-seq was used to analyze differentially expressed genes (DEGs) in N. benthamiana plants infected by TbCSV (Y35A) and TbCSV together with TbCSB (Y35AB) respectively.ResultsThrough mapping to N. benthamiana reference genome, 59,814 unigenes were identified. Transcriptome analysis revealed that a total of 4081 and 3196 DEGs were identified in Y35AB vs CK (control check) and Y35A vs CK, respectively. Both GO and KEGG analyses were conducted to classify the DEGs. Ten of the top 15 GO terms were enriched in both DEGs of Y35AB vs CK and Y35A vs CK, and these enriched GO terms mainly classified into three categories including biological process, cellular component and molecular function. KEGG pathway analysis indicated that 118 and 111 pathways were identified in Y35AB vs CK and Y35A vs CK, respectively, of which nine and six pathways were significantly enriched. Three major pathways in Y35AB vs CK involved in metabolic pathways, carbon metabolism and photosynthesis, while those in Y35A vs CK were related to Ribosome, Glyoxylate and dicarboxylate metabolism and DNA replication. We observed that 8 PR genes were significantly up-regulated and 44 LRR-RLK genes were significantly differentially expressed in Y35A treatment or in Y35AB treatment. In addition, 7 and 13 genes were identified to be significantly changed in biosynthesis and signal transduction pathway of brassinosteroid (BR) and jasmonic acid (JA) respectively.ConclusionsThese results presented here would be particularly useful to further elucidate the response of the host plant against virus infection.Electronic supplementary materialThe online version of this article (10.1186/s12985-018-1044-1) contains supplementary material, which is available to authorized users.

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Section: Resultsmentioning

confidence: 99%

Transcriptome analysis of Nicotiana benthamiana infected by Tobacco curly shoot virus

et al. 2018

Virol J

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“…From each library >67% of reads mapped to the release-31 version of wheat reference genome, including >58% with unique mapping and <9% multiple mapping (Supplementary Table S1). Furthermore, >98% and >95% of the clean reads had quality scores at the Q20 or Q30 (an error probability for base calling of 1% or 0.1%) 37 level, respectively. The density of reads was equally distributed across all chromosomes of the wheat reference genome (Supplementary Fig.…”

Section: Resultsmentioning

confidence: 99%

RNAseq analysis reveals pathways and candidate genes associated with salinity tolerance in a spaceflight-induced wheat mutant

Xiong

Guo

Xie

et al. 2017

Sci Rep

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Salinity stress has become an increasing threat to food security worldwide and elucidation of the mechanism for salinity tolerance is of great significance. Induced mutation, especially spaceflight mutagenesis, is one important method for crop breeding. In this study, we show that a spaceflight-induced wheat mutant, named salinity tolerance 1 (st1), is a salinity-tolerant line. We report the characteristics of transcriptomic sequence variation induced by spaceflight, and show that mutations in genes associated with sodium ion transport may directly contribute to salinity tolerance in st1. Furthermore, GO and KEGG enrichment analysis of differentially expressed genes (DEGs) between salinity-treated st1 and wild type suggested that the homeostasis of oxidation-reduction process is important for salt tolerance in st1. Through KEGG pathway analysis, “Butanoate metabolism” was identified as a new pathway for salinity responses. Additionally, key genes for salinity tolerance, such as genes encoding arginine decarboxylase, polyamine oxidase, hormones-related, were not only salt-induced in st1 but also showed higher expression in salt-treated st1 compared with salt-treated WT, indicating that these genes may play important roles in salinity tolerance in st1. This study presents valuable genetic resources for studies on transcriptome variation caused by induced mutation and the identification of salt tolerance genes in crops.

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“…et al, 2015; Gao et al, 2015; Oono et al, 2016). A transcriptome data of maize roots response to Cd pollution has been already published by Peng et al (2015). Zea mays L. inbred line Zheng 58, a RBSDV (rice black-streaked dwarf virus)-resistant inbred line widely planted in central China, was used in our study.…”

Section: Introductionmentioning

confidence: 99%

Transcriptome Analysis of Cadmium-Treated Roots in Maize (Zea mays L.)

et al. 2016

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Cadmium (Cd) is a heavy metal and is highly toxic to all plant species. However, the underlying molecular mechanism controlling the effects of auxin on the Cd stress response in maize is largely unknown. In this study, the transcriptome produced by maize ‘Zheng 58’ root responses to Cd stress was sequenced using Illumina sequencing technology. In our study, six RNA-seq libraries yielded a total of 244 million clean short reads and 30.37 Gb of sequence data. A total of 6342 differentially expressed genes (DEGs) were grouped into 908 Gene Ontology (GO) categories and 198 Kyoto Encyclopedia of Genes and Genomes terms. GO term enrichment analysis indicated that various auxin signaling pathway-related GO terms were significantly enriched in DEGs. Comparison of the transcript abundances for auxin biosynthesis, transport, and downstream response genes revealed a universal expression response under Cd treatment. Furthermore, our data showed that free indole-3-acetic acid (IAA) levels were significantly reduced; but IAA oxidase activity was up-regulated after Cd treatment in maize roots. The analysis of Cd activity in maize roots under different Cd and auxin conditions confirmed that auxin affected Cd accumulation in maize seedlings. These results will improve our understanding of the complex molecular mechanisms underlying the response to Cd stress in maize roots.

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Transcriptomic changes during maize roots development responsive to Cadmium (Cd) pollution using comparative RNAseq-based approach

Cited by 40 publications

References 23 publications

Transcriptome analysis of Nicotiana benthamiana infected by Tobacco curly shoot virus

Transcriptome analysis of Nicotiana benthamiana infected by Tobacco curly shoot virus

RNAseq analysis reveals pathways and candidate genes associated with salinity tolerance in a spaceflight-induced wheat mutant

Transcriptome Analysis of Cadmium-Treated Roots in Maize (Zea mays L.)

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