The Arabidopsis Stress Responsive Gene Database

Borkotoky, Subhomoi; Vijayakumar, Saravanan; Jaiswal, Amit; Das, Bipul; Selvaraj, S.; Murali, Ayaluru; Lakshmi, P.T.V.

doi:10.1155/2013/949564

Cited by 37 publications

(20 citation statements)

References 9 publications

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“…To identify transcripts putatively involved in stress in A. donax , we used as reference the comprehensive resource provided by the Arabidopsis Stress Responsive Gene Database (ASRGDB; Borkotoky et al , 2013 ). For reliable identification of putative homologs, BLASTx searches were carried out with sequence identity >70% and sequence coverage >70%, which resulted in the identification of homologs for 148 of the abiotic stress genes in the ASRGDB.…”

Section: Resultsmentioning

confidence: 99%

“…To identify transcript homologs putatively involved in stress, customized databases were made by retrieving all the proteins corresponding to the HKT1, NHX, GST, metallothioneins and heavy metal-associated gene families from UniProt, NCBI, TrEMBL. In addition, we also retrieved the experimentally characterized stress response genes from the Arabidopsis Stress Responsive Gene Database available at http://srgdb.bicpu.edu.in/ ( Borkotoky et al , 2013 ). BLASTx searches were made with an e-value cut-off of 1 × 10 −3 , and all hits with at least 70% identity and coverage to the query were retained.…”

Section: Methodsmentioning

confidence: 99%

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Fuelling genetic and metabolic exploration of C₃ bioenergy crops through the first reference transcriptome of Arundo donax L.

Sablok

Bobbio

et al. 2014

Plant Biotechnology Journal

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The development of inexpensive and highly productive biomass sources of biofuel is a priority in global climate change biology. Arundo donax, also known as the giant reed, is recognized as one of the most promising nonfood bioenergy crops in Europe. Despite its relevance, to date no genomic resources are available to support the characterization of the developmental, adaptive and metabolic traits underlying the high productivity of this nonmodel species. We hereby present the first report on the de novo assembly of bud, culm, leaf and root transcriptomes of A. donax, which can be accessed through a customized BLAST server (http://ecogenomics.fmach.it/arundo/) for mining and exploring the genetic potential of this species. Based on functional annotation and homology comparison to 19 prospective biofuel Poaceae species, we provide the first genomic view of this so far unexplored crop and indicate the model species with highest potential for comparative genomics approaches. The analysis of the transcriptome reveals strong differences in the enrichment of the Gene Ontology categories and the relative expression among different organs, which can guide future efforts for functional genomics or genetic improvement of A. donax. A set of homologs to key genes involved in lignin, cellulose, starch, lipid metabolism and in the domestication of other crops is discussed to provide a platform for possible enhancement of productivity and saccharification efficiency in A. donax.

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Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Fuelling genetic and metabolic exploration of C₃ bioenergy crops through the first reference transcriptome of Arundo donax L.

Sablok

Bobbio

et al. 2014

Plant Biotechnology Journal

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“…To identify the potential stress-responsive genes in the P. vera transcriptome, all final assembled transcripts were searched against the genes involved in various abiotic stresses (salt, drought, and cold) [ 34 , 35 ] using BLASTX with the e-value cutoff of 1e-5.…”

Section: Methodsmentioning

confidence: 99%

A genome-wide transcriptome map of pistachio (Pistacia vera L.) provides novel insights into salinity-related genes and marker discovery

et al. 2017

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BackgroundPistachio (Pistacia vera L.) is one of the most important commercial nut crops worldwide. It is a salt-tolerant and long-lived tree, with the largest cultivation area in Iran. Climate change and subsequent increased soil salt content have adversely affected the pistachio yield in recent years. However, the lack of genomic/global transcriptomic sequences on P. vera impedes comprehensive researches at the molecular level. Hence, whole transcriptome sequencing is required to gain insight into functional genes and pathways in response to salt stress.ResultsRNA sequencing of a pooled sample representing 24 different tissues of two pistachio cultivars with contrasting salinity tolerance under control and salt treatment by Illumina Hiseq 2000 platform resulted in 368,953,262 clean 100 bp paired-ends reads (90 Gb). Following creating several assemblies and assessing their quality from multiple perspectives, we found that using the annotation-based metrics together with the length-based parameters allows an improved assessment of the transcriptome assembly quality, compared to the solely use of the length-based parameters. The generated assembly by Trinity was adopted for functional annotation and subsequent analyses. In total, 29,119 contigs annotated against all of five public databases, including NR, UniProt, TAIR10, KOG and InterProScan. Among 279 KEGG pathways supported by our assembly, we further examined the pathways involved in the plant hormone biosynthesis and signaling as well as those to be contributed to secondary metabolite biosynthesis due to their importance under salinity stress. In total, 11,337 SSRs were also identified, which the most abundant being dinucleotide repeats. Besides, 13,097 transcripts as candidate stress-responsive genes were identified. Expression of some of these genes experimentally validated through quantitative real-time PCR (qRT-PCR) that further confirmed the accuracy of the assembly. From this analysis, the contrasting expression pattern of NCED3 and SOS1 genes were observed between salt-sensitive and salt-tolerant cultivars.ConclusionThis study, as the first report on the whole transcriptome survey of P. vera, provides important resources and paves the way for functional and comparative genomic studies on this major tree to discover the salinity tolerance-related markers and stress response mechanisms for breeding of new pistachio cultivars with more salinity tolerance.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-017-3989-7) contains supplementary material, which is available to authorized users.

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“…Overall, we found different sets of deregulated genes involved in transcriptional regulation, carbohydrate metabolism, protein synthesis, transport, detoxification signalling, osmolite production, hormone metabolism and nucleic acid metabolism. All these functional categories have been widely described through transcriptomic analyses as drought stress genes in many plant species (Alter et al, 2015;Borkotoky et al, 2013;Xue et al, 2008).…”

Section: Network Of Genes Involved In Response To Abrupt or Gradual Wmentioning

confidence: 99%

Distinct gene networks drive differential response to abrupt or gradual water deficit in potato

Ambrosone

Batelli

Bostan

et al. 2017

Gene

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Water-limiting conditions affect dramatically plant growth and development and, ultimately, yield of potato plants (Solanum tuberosum L.). Therefore, understanding the mechanisms underlying the response to water deficit is of paramount interest to obtain drought tolerant potato varieties. Herein, potato 10K cDNA array slides were used to profile transcriptomic changes of two potato cell populations under abrupt (shocked cells) or gradual exposure (adapted cells) to polyethylene glycol (PEG)-mediated water stress. Data analysis identified >1000 differentially expressed genes (DEGs) in our experimental conditions. Noteworthy, our microarray study also suggests that distinct gene networks underlie the cellular response to shock or gradual water stress. On the basis of our experimental findings, it is possible to speculate that DEGs identified in shocked cells participate in early protective and sensing mechanisms to environmental insults, while the genes whose expression was modulated in adapted cells are directly involved in the acquisition of a new cellular homeostasis to cope with water stress conditions. To validate microarray data obtained for potato cells, the expression analysis of 21 selected genes of interest was performed by Real-Time Quantitative Reverse Transcription PCR (qRT-PCR). Intriguingly, the expression levels of these transcripts in 4-week old potato plants exposed to long-term water-deficit. qRT-PCR analysis showed that several genes were regulated similarly in potato cells cultures and tissues exposed to drought, thus confirming the efficacy of our simple experimental system to capture important genes involved in osmotic stress response. Highlighting the differences in gene expression between shock-like and adaptive response, our findings could contribute to the discussion on the biological function of distinct gene networks involved in the response to abrupt and gradual adaptation to water deficit.

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The Arabidopsis Stress Responsive Gene Database

Cited by 37 publications

References 9 publications

Fuelling genetic and metabolic exploration of C₃ bioenergy crops through the first reference transcriptome of Arundo donax L.

Fuelling genetic and metabolic exploration of C₃ bioenergy crops through the first reference transcriptome of Arundo donax L.

A genome-wide transcriptome map of pistachio (Pistacia vera L.) provides novel insights into salinity-related genes and marker discovery

Distinct gene networks drive differential response to abrupt or gradual water deficit in potato

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The Arabidopsis Stress Responsive Gene Database

Cited by 37 publications

References 9 publications

Fuelling genetic and metabolic exploration of C3 bioenergy crops through the first reference transcriptome of Arundo donax L.

Fuelling genetic and metabolic exploration of C3 bioenergy crops through the first reference transcriptome of Arundo donax L.

A genome-wide transcriptome map of pistachio (Pistacia vera L.) provides novel insights into salinity-related genes and marker discovery

Distinct gene networks drive differential response to abrupt or gradual water deficit in potato

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Fuelling genetic and metabolic exploration of C₃ bioenergy crops through the first reference transcriptome of Arundo donax L.

Fuelling genetic and metabolic exploration of C₃ bioenergy crops through the first reference transcriptome of Arundo donax L.