Sugarcane transcriptome analysis in response to infection caused by Acidovorax avenae subsp. avenae

Autor: Cristian A. Alvarez Rojas, Sérgio Lifschitz, Elvismary Molina de Armas, Marcelo de Freitas Lima, Paulo Cavalcanti Gomes Ferreira, Flávia Thiebaut, Ailton B. Santa Brigida, Adriana Silva Hemerly, Clícia Grativol, Júlio O. P. Entenza, Laurent Farrinelli
Jazyk: angličtina
Rok vydání: 2016
Předmět:
0106 biological sciences
0301 basic medicine
De novo transcriptome assembly
Gene Expression
lcsh:Medicine
01 natural sciences
Biochemistry
Transcriptome
Database and Informatics Methods
Gene Expression Regulation
Plant
Gene expression
lcsh:Science
Genetics
Multidisciplinary
Acidovorax
Reverse Transcriptase Polymerase Chain Reaction
Agriculture
Genomics
Plants
Saccharum
Host-Pathogen Interactions
Carbohydrate Metabolism
Metabolic Pathways
Sequence Analysis
Transcriptome Analysis
Research Article
Sequence Databases
Crops
Plant disease resistance
Biology
Biosynthesis
Research and Analysis Methods
Comamonadaceae
03 medical and health sciences
Protein Domains
Botany
Grasses
KEGG
Molecular Biology Techniques
Sequencing Techniques
Gene
Molecular Biology
Plant Diseases
Sequence Analysis
RNA
Gene Expression Profiling
lcsh:R
Organisms
Biology and Life Sciences
Proteins
Computational Biology
Molecular Sequence Annotation
Sugarcane
biology.organism_classification
Genome Analysis
Metabolic pathway
030104 developmental biology
Gene Ontology
Metabolism
Biological Databases
lcsh:Q
010606 plant biology & botany
Crop Science
Zdroj: PLoS ONE, Vol 11, Iss 12, p e0166473 (2016)
PLoS ONE
ISSN: 1932-6203
Popis: Sugarcane is an important tropical crop mainly cultivated to produce ethanol and sugar. Crop productivity is negatively affected by Acidovorax avenae subsp avenae (Aaa), which causes the red stripe disease. Little is known about the molecular mechanisms triggered in response to the infection. We have investigated the molecular mechanism activated in sugarcane using a RNA-seq approach. We have produced a de novo transcriptome assembly (TR7) from sugarcane RNA-seq libraries submitted to drought and infection with Aaa. Together, these libraries present 247 million of raw reads and resulted in 168,767 reference transcripts. Mapping in TR7 of reads obtained from infected libraries, revealed 798 differentially expressed transcripts, of which 723 were annotated, corresponding to 467 genes. GO and KEGG enrichment analysis showed that several metabolic pathways, such as code for proteins response to stress, metabolism of carbohydrates, processes of transcription and translation of proteins, amino acid metabolism and biosynthesis of secondary metabolites were significantly regulated in sugarcane. Differential analysis revealed that genes in the biosynthetic pathways of ET and JA PRRs, oxidative burst genes, NBS-LRR genes, cell wall fortification genes, SAR induced genes and pathogenesis-related genes (PR) were upregulated. In addition, 20 genes were validated by RT-qPCR. Together, these data contribute to a better understanding of the molecular mechanisms triggered by the Aaa in sugarcane and opens the opportunity for the development of molecular markers associated with disease tolerance in breeding programs.
Databáze: OpenAIRE
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