Transcriptional Responses of Creeping Bentgrass to 2,3-Butanediol, a Bacterial Volatile Compound (BVC) Analogue
Abstract
:1. Introduction
2. Results
2.1. Disease Assessment of Creeping Bentgrass Treated with BD and the Antimicrobial Activity of BD
2.2. Transcriptome Sequencing and Read Statistics
2.3. Differentially Expressed Genes under the Treatment of BD
2.4. Gene Ontology Enrichment Analysis of Eight Clusters
2.5. Metabolic Pathway Analysis
2.6. BD Regulated Transcription Factors
2.7. BD-Regulated R-Gene of Creeping Bentgrass
2.8. BD-Induced DEGs Related with Plant Biotic Stress
3. Discussion
4. Materials and Methods
4.1. Plant Material and Treatment
4.2. Inoculation and Disease Assessments
4.3. Antimicrobial Activity Test
4.4. Sample Preparation and RNA Extraction
4.5. Library Preparation and Transcriptome Sequencing
4.6. Transcriptome Assembly and Annotation
4.7. Transcript Expression Analysis
4.8. Statistical Analysis of Data
5. Conclusions
Supplementary Materials
Acknowledgments
Author contributions
Conflicts of Interest
References
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Sample Availability: All samples are available from the authors. |
Items | Number of bp/Reads/Transcripts | |
---|---|---|
Sequencing and assembly | Total raw reads | 258,606,402 |
Total clean reads | 252,117,292 | |
Total transcripts | 466,761 | |
Total length of transcripts (bp) | 324,797,015 | |
Transcripts with N50 length (bp) | 1100 | |
Transcript mean length (bp) | 696 | |
Total unigenes | 334,212 | |
Total length of unigenes (bp) | 191,363,312 | |
Unigenes with N50 length (bp) | 791 | |
Unigenes mean length (bp) | 573 | |
Function annotation | NR database | 130,367 |
NT database | 72,777 | |
KO database | 41,963 |
Cluster | Biological Processes | Molecular Functions | Cellular Component |
---|---|---|---|
I | Translation | Catalytic activity | Intracellular |
Phosphorelay signal transduction system | RNA binding | Transcription factor | |
Metabolic process | Enzyme regulator activity | Membrane | |
DNA replication | Respiratory chain complex | ||
Oxidation-reduction process | |||
II | Lipopolysaccharide core region biosynthetic | Metal ion binding | Transcription factor complex |
Response to oxidative stress | Hydrolase activity | Component of membrane | |
Phospholipid catabolic process | Fructose-bisphosphate aldolase activity | ||
Diacylglycerol kinase activity | |||
III | Thiamine biosynthetic process | Transcription factor activity | Small-subunit processome |
Proteolysis | Ubiquitin binding | Peroxidase activity | |
RNA modification | |||
IV | Unsaturated fatty acid biosynthetic process | Terpene synthase activity | Fatty acid synthase complex |
Ferrous iron transport | Serine-type endopeptidase inhibitor activity | Chloroplast | |
Response to biotic stimulus | Malate synthase activity | Cell wall | |
Cellular aromatic compound metabolic | Xyloglucosyl transferase activity | ||
Peroxidase activity | |||
V | Pathogenesis | Calcium channel activity | Photosystem II oxygen evolving complex |
Chlorophyll biosynthetic process | Pheromone activity | Magnesium chelatase complex | |
Protein import into peroxisome matrix | |||
Nitrogen compound metabolic process | |||
FtsZ-dependent cytokinesis | |||
VI | Starch metabolic process | Chitinase activity | Cell junction |
Sucrose metabolic process | Calmodulin binding | Cell wall | |
Response to stress | ATPase activator activity | ||
Glycerolipid metabolic process | |||
Chitin catabolic process | |||
VII | Regulation of transcription, DNA-templated | Adenosylcobinamide kinase activity | U1 snRNP |
Pantothenate biosynthetic process | Aldehyde-lyase activity | Holliday junction helicase complex | |
Autophagy | |||
Cobalamin biosynthetic process | |||
Apoptotic process | |||
VIII | Cell adhesion | Enzyme inhibitor activity | Plasma membrane |
Photorespiration | Flavin adenine dinucleotide binding | ||
Oligosaccharide biosynthetic process | Nutrient reservoir activity | ||
Galactose metabolic process | |||
Benzoate metabolic process | |||
Pectin catabolic process |
Cluster | KEGG Pathway | q-Value |
---|---|---|
I | Ribosome | 4.59 × 10−36 |
Plant hormone signal transduction | 0.0251 | |
Glyoxylate and dicarboxylate metabolism | 0.0244 | |
II | Porphyrin and chlorophyll metabolism | 0.0100 |
Nitrogen metabolism | 0.0100 | |
Fructose and mannose metabolism | 0.0100 | |
Phenylalanine metabolism | 0.0100 | |
III | Thiamine metabolism | 0.0112 |
Circadian rhythm-plant | 0.0173 | |
Amino sugar and nucleotide sugar metabolism | 0.0251 | |
Carbon metabolism | 0.0453 | |
IV | Ribosome biogenesis in eukaryotes | 0.0181 |
Monoterpenoid biosynthesis | 0.0183 | |
alpha-Linolenic acid metabolism | 0.0181 | |
Pyruvate metabolism | 0.0181 | |
Sesquiterpenoid and triterpenoid biosynthesis | 0.0301 | |
Carotenoid biosynthesis | 0.0357 | |
V | Protein processing in endoplasmic reticulum | 1.23 × 10−17 |
Spliceosome | 0.0125 | |
Cutin, suberine and wax biosynthesis | 0.0485 | |
Metabolism of xenobiotics by cytochrome P450 | 0.0157 | |
MAPK signaling pathway | 0.0385 | |
Arachidonic acid metabolism | 0.0459 | |
Phenylalanine metabolism | 0.0732 | |
VI | NOD-like receptor signaling pathway | 8.38 × 10−6 |
Glutathione metabolism | 0.0304 | |
Ubiquinone and other terpenoid-quinone biosynthesis | 0.0304 | |
Phenylpropanoid biosynthesis | 0.0340 | |
Cyanoamino acid metabolism | 0.0484 | |
VII | Photosynthesis - antenna proteins | 5.97 × 10−7 |
NOD-like receptor signaling pathway | 6.25 × 10−5 | |
Carbon fixation in photosynthetic organisms | 0.0061 | |
VIII | NOD-like receptor signaling pathway | 9.69 × 10−5 |
Plant-pathogen interaction | 0.0012 | |
Photosynthesis | 0.0301 | |
Brassinosteroid biosynthesis | 0.0185 |
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Shi, Y.; Niu, K.; Huang, B.; Liu, W.; Ma, H. Transcriptional Responses of Creeping Bentgrass to 2,3-Butanediol, a Bacterial Volatile Compound (BVC) Analogue. Molecules 2017, 22, 1318. https://doi.org/10.3390/molecules22081318
Shi Y, Niu K, Huang B, Liu W, Ma H. Transcriptional Responses of Creeping Bentgrass to 2,3-Butanediol, a Bacterial Volatile Compound (BVC) Analogue. Molecules. 2017; 22(8):1318. https://doi.org/10.3390/molecules22081318
Chicago/Turabian StyleShi, Yi, Kuiju Niu, Bingru Huang, Wenhui Liu, and Huiling Ma. 2017. "Transcriptional Responses of Creeping Bentgrass to 2,3-Butanediol, a Bacterial Volatile Compound (BVC) Analogue" Molecules 22, no. 8: 1318. https://doi.org/10.3390/molecules22081318