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De Novo Transcriptome Assembly and Comparative Analysis Elucidate Complicated Mechanism Regulating Astragalus chrysochlorus Response to Selenium Stimuli.

Çakır Ö, Turgut-Kara N, Arı Ş, Zhang B - PLoS ONE (2015)

Bottom Line: Annotated unigenes were also used for gene ontology enrichment and pathway enrichment analysis.The most significant genes and pathways were ABC transporters, plant pathogen interaction, biosynthesis of secondary metabolites and carbohydrate metabolism.Our results will help to enlighten the selenium accumulation and tolerance mechanisms, respectively in plants.

View Article: PubMed Central - PubMed

Affiliation: Department of Molecular Biology and Genetics, Faculty of Science, Istanbul University, 34134 Vezneciler Istanbul, Turkey; Department of Biology, East Carolina University, Greenville, NC 27858, United States of America.

ABSTRACT
Astragalus species are medicinal plants that are used in the world for years. Some Astragalus species are known for selenium accumulation and tolerance and one of them is Astragalus chrysochlorus, a secondary selenium accumulator. In this study, we employed Illumina deep sequencing technology for the first time to de novo assemble A. chrysochlorus transcriptome and identify the differentially expressed genes after selenate treatment. Totally, 59,656 unigenes were annotated with different databases and 53,960 unigenes were detected in NR database. Transcriptome in A. chrysochlorus is closer to Glycine max than other plant species with 43,1 percentage of similarity. Annotated unigenes were also used for gene ontology enrichment and pathway enrichment analysis. The most significant genes and pathways were ABC transporters, plant pathogen interaction, biosynthesis of secondary metabolites and carbohydrate metabolism. Our results will help to enlighten the selenium accumulation and tolerance mechanisms, respectively in plants.

No MeSH data available.


Related in: MedlinePlus

Se affected miRNAs and their targets in A. chrysochlorus calli based on the degradome data.ARF8 like: auxin response factor 8-like [Glycine max], HOX32-like protein: homeobox-leucine zipper protein HOX32-like [Glycine max], Class III HD Zip protein: Class III HD-Zip protein [Medicago truncatula], CMT-3 like protein: DNA (cytosine-5)-methyltransferase CMT3-like [Glycine max], F-Box: F-box protein SKIP2-like [Glycine max], Damage DNA Binding 2: protein DAMAGED DNA-BINDING 2 [Glycine max], RGA2: Disease resistance protein RGA2 [Medicago truncatula], AGO-2: protein argonaute 2-like [Glycine max], TIR- NBS-LRR: TIR-NBS-LRR RCT1 resistance protein [Medicago truncatula]. Blue color: upregulated, red color: downregulated.
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pone.0135677.g008: Se affected miRNAs and their targets in A. chrysochlorus calli based on the degradome data.ARF8 like: auxin response factor 8-like [Glycine max], HOX32-like protein: homeobox-leucine zipper protein HOX32-like [Glycine max], Class III HD Zip protein: Class III HD-Zip protein [Medicago truncatula], CMT-3 like protein: DNA (cytosine-5)-methyltransferase CMT3-like [Glycine max], F-Box: F-box protein SKIP2-like [Glycine max], Damage DNA Binding 2: protein DAMAGED DNA-BINDING 2 [Glycine max], RGA2: Disease resistance protein RGA2 [Medicago truncatula], AGO-2: protein argonaute 2-like [Glycine max], TIR- NBS-LRR: TIR-NBS-LRR RCT1 resistance protein [Medicago truncatula]. Blue color: upregulated, red color: downregulated.

Mentions: In our previous study, we found that miRNAs, an important gene regulator, play a potential role in A. chrysochlorus during Se treatment [9]. In this study, we compared the expression of miRNAs, identified in our previous study and miRNA expression, we found the adverse relationship between the expression of miRNAs and their targets (Fig 8). During Se treatment, auxin response factor 8-like was upregulated while miR167 was downregulated; The expression of omeobox-leucine zipper protein HOX32-like, Class III HD-Zip protein, DNA (cytosine-5)-methyltransferase CMT3-like, F-box protein SKIP2-like protein was up-regulated by Se exposure but based on the degradome data, their targeting miRNAs, miR166, miR166i, miR399k, miR399h-5p, were down-regulated, respectively. In this study, we found that DAMAGED DNA-BINDING 2, Disease resistance protein RGA2, protein argonaute 2-like, TIR-NBS-LRR RCT1 resistance protein were repressed by Se exposure; in our previous study, we found their targeting miRNAs; miR7767-3p, miR1507, miR7122b-5p and miR3633a-3p were induced by Se treatment, respectively.


De Novo Transcriptome Assembly and Comparative Analysis Elucidate Complicated Mechanism Regulating Astragalus chrysochlorus Response to Selenium Stimuli.

Çakır Ö, Turgut-Kara N, Arı Ş, Zhang B - PLoS ONE (2015)

Se affected miRNAs and their targets in A. chrysochlorus calli based on the degradome data.ARF8 like: auxin response factor 8-like [Glycine max], HOX32-like protein: homeobox-leucine zipper protein HOX32-like [Glycine max], Class III HD Zip protein: Class III HD-Zip protein [Medicago truncatula], CMT-3 like protein: DNA (cytosine-5)-methyltransferase CMT3-like [Glycine max], F-Box: F-box protein SKIP2-like [Glycine max], Damage DNA Binding 2: protein DAMAGED DNA-BINDING 2 [Glycine max], RGA2: Disease resistance protein RGA2 [Medicago truncatula], AGO-2: protein argonaute 2-like [Glycine max], TIR- NBS-LRR: TIR-NBS-LRR RCT1 resistance protein [Medicago truncatula]. Blue color: upregulated, red color: downregulated.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4592229&req=5

pone.0135677.g008: Se affected miRNAs and their targets in A. chrysochlorus calli based on the degradome data.ARF8 like: auxin response factor 8-like [Glycine max], HOX32-like protein: homeobox-leucine zipper protein HOX32-like [Glycine max], Class III HD Zip protein: Class III HD-Zip protein [Medicago truncatula], CMT-3 like protein: DNA (cytosine-5)-methyltransferase CMT3-like [Glycine max], F-Box: F-box protein SKIP2-like [Glycine max], Damage DNA Binding 2: protein DAMAGED DNA-BINDING 2 [Glycine max], RGA2: Disease resistance protein RGA2 [Medicago truncatula], AGO-2: protein argonaute 2-like [Glycine max], TIR- NBS-LRR: TIR-NBS-LRR RCT1 resistance protein [Medicago truncatula]. Blue color: upregulated, red color: downregulated.
Mentions: In our previous study, we found that miRNAs, an important gene regulator, play a potential role in A. chrysochlorus during Se treatment [9]. In this study, we compared the expression of miRNAs, identified in our previous study and miRNA expression, we found the adverse relationship between the expression of miRNAs and their targets (Fig 8). During Se treatment, auxin response factor 8-like was upregulated while miR167 was downregulated; The expression of omeobox-leucine zipper protein HOX32-like, Class III HD-Zip protein, DNA (cytosine-5)-methyltransferase CMT3-like, F-box protein SKIP2-like protein was up-regulated by Se exposure but based on the degradome data, their targeting miRNAs, miR166, miR166i, miR399k, miR399h-5p, were down-regulated, respectively. In this study, we found that DAMAGED DNA-BINDING 2, Disease resistance protein RGA2, protein argonaute 2-like, TIR-NBS-LRR RCT1 resistance protein were repressed by Se exposure; in our previous study, we found their targeting miRNAs; miR7767-3p, miR1507, miR7122b-5p and miR3633a-3p were induced by Se treatment, respectively.

Bottom Line: Annotated unigenes were also used for gene ontology enrichment and pathway enrichment analysis.The most significant genes and pathways were ABC transporters, plant pathogen interaction, biosynthesis of secondary metabolites and carbohydrate metabolism.Our results will help to enlighten the selenium accumulation and tolerance mechanisms, respectively in plants.

View Article: PubMed Central - PubMed

Affiliation: Department of Molecular Biology and Genetics, Faculty of Science, Istanbul University, 34134 Vezneciler Istanbul, Turkey; Department of Biology, East Carolina University, Greenville, NC 27858, United States of America.

ABSTRACT
Astragalus species are medicinal plants that are used in the world for years. Some Astragalus species are known for selenium accumulation and tolerance and one of them is Astragalus chrysochlorus, a secondary selenium accumulator. In this study, we employed Illumina deep sequencing technology for the first time to de novo assemble A. chrysochlorus transcriptome and identify the differentially expressed genes after selenate treatment. Totally, 59,656 unigenes were annotated with different databases and 53,960 unigenes were detected in NR database. Transcriptome in A. chrysochlorus is closer to Glycine max than other plant species with 43,1 percentage of similarity. Annotated unigenes were also used for gene ontology enrichment and pathway enrichment analysis. The most significant genes and pathways were ABC transporters, plant pathogen interaction, biosynthesis of secondary metabolites and carbohydrate metabolism. Our results will help to enlighten the selenium accumulation and tolerance mechanisms, respectively in plants.

No MeSH data available.


Related in: MedlinePlus