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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.


GO functional classification of A. chrysochlorus unigenes.
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pone.0135677.g003: GO functional classification of A. chrysochlorus unigenes.

Mentions: We also compared the transcriptome similarity between A. chrysochlorus and other closely-related plant species. A total of 43.1% of A. chrysochlorus transcriptome were matched to Glycine max (43.1%) followed by Medicago truncatula (39.7%) and Lotus corniculatus var. japonicus (9.6%), respectively. For the COG classification, a total of 35,175 genes were categorized into 25 classes (Fig 2). According to the number of genes, the most significant ones were general function (6,278), replication, recombination and repair (3,846), transcription (3,101), posttranslational modification, protein turnover and chaperones (2,668) and signal transduction mechanisms (2,429). According to the Gene ontology analysis, unigenes were sorted into 55 categories (Fig 3). In biological process category, cellular process, metabolic process and single cell process ontologies were the top three gene ontology terms with the number of unigenes 25,641, 24,683 and 17,416, respectively. In the same category, biological adhesion, ryhtmic process and locomotion were the last three GO terms with the number of unigenes 324, 233 and 31, respectively. In cellular component category, cell, cell part and oganelle terms were the top three classes with 28,623, 28,622 and 23,094 unigenes. The last three categories were extracellular matrix part, extracellular region part and virion and virion part with the number of 26, 17, and 18, respectively. Lastly, for molecular function category, binding, catalytic activity and transporter activity were the top three GO terms with the number of unigenes 21,302, 20,560 and 2,578, respectively. The categories with the least three unigene numbers were metallochaperone activity (6), translation regulator activity (4) and protein tag (4), respectively. For KEGG analysis, 31,003 unigenes were annotated with the pathway analysis and it is determined that 3,549 of them were differentially expressed. These unigenes were annotated with 127 pathways according to KEGG analysis. The most significant unigene numbers that were detected, were listed in Fig 4. Metabolic pathways are the first category with 828 differentially expressed unigenes. Biosynthesis of secondary metabolites and plant-pathogen interaction are the second and third categories with 429 and 263 differentially expressed unigenes, 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)

GO functional classification of A. chrysochlorus unigenes.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0135677.g003: GO functional classification of A. chrysochlorus unigenes.
Mentions: We also compared the transcriptome similarity between A. chrysochlorus and other closely-related plant species. A total of 43.1% of A. chrysochlorus transcriptome were matched to Glycine max (43.1%) followed by Medicago truncatula (39.7%) and Lotus corniculatus var. japonicus (9.6%), respectively. For the COG classification, a total of 35,175 genes were categorized into 25 classes (Fig 2). According to the number of genes, the most significant ones were general function (6,278), replication, recombination and repair (3,846), transcription (3,101), posttranslational modification, protein turnover and chaperones (2,668) and signal transduction mechanisms (2,429). According to the Gene ontology analysis, unigenes were sorted into 55 categories (Fig 3). In biological process category, cellular process, metabolic process and single cell process ontologies were the top three gene ontology terms with the number of unigenes 25,641, 24,683 and 17,416, respectively. In the same category, biological adhesion, ryhtmic process and locomotion were the last three GO terms with the number of unigenes 324, 233 and 31, respectively. In cellular component category, cell, cell part and oganelle terms were the top three classes with 28,623, 28,622 and 23,094 unigenes. The last three categories were extracellular matrix part, extracellular region part and virion and virion part with the number of 26, 17, and 18, respectively. Lastly, for molecular function category, binding, catalytic activity and transporter activity were the top three GO terms with the number of unigenes 21,302, 20,560 and 2,578, respectively. The categories with the least three unigene numbers were metallochaperone activity (6), translation regulator activity (4) and protein tag (4), respectively. For KEGG analysis, 31,003 unigenes were annotated with the pathway analysis and it is determined that 3,549 of them were differentially expressed. These unigenes were annotated with 127 pathways according to KEGG analysis. The most significant unigene numbers that were detected, were listed in Fig 4. Metabolic pathways are the first category with 828 differentially expressed unigenes. Biosynthesis of secondary metabolites and plant-pathogen interaction are the second and third categories with 429 and 263 differentially expressed unigenes, 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.