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Identification and characterization of potato long noncoding RNAs responsive to Pectobacterium carotovorum subspecies brasiliense infection

ABSTRACT: Identification and characterization of potato long noncoding RNAs responsive to Pectobacterium carotovorum subspecies brasiliense infection

PROVIDER: PRJNA301698 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR2932300_1.fastq.gz	Fastqsanger.gz
	SRR2932300_2.fastq.gz	Fastqsanger.gz
	SRR2932310_1.fastq.gz	Fastqsanger.gz
	SRR2932310_2.fastq.gz	Fastqsanger.gz
	SRR2932320_1.fastq.gz	Fastqsanger.gz

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Identification and characterization of potato long noncoding RNAs responsive to Pectobacterium carotovorum subspecies brasiliense infection [Time-course RNAseq]

Project description:Long noncoding RNAs (lncRNAs) represent a class of RNA molecules that are implicated in regulation of gene expression, both in mammals and plants. While much progress has been made in determining the biological functions of lncRNAs in mammals, the functional roles of lncRNAs in plants are still poorly understood. Specifically, the roles of lncRNAs in plant defense responses are yet to be fully explored. Here, we used strand-specific RNA sequencing to identify 1649 lncRNAs in potato (Solanum tuberosum) from stem tissues. The lncRNAs are expressed from all 12 potato chromosomes and generally smaller in size compared to protein-coding genes. Like in other plants, most potato lncRNAs (86%) are transcribed from intergenic regions and possess single exons. A time-course RNA-seq analysis between a tolerant and susceptible potato cultivar challenged with Pectobacterium carotovorum subsp. brasilience revealed that 227 of these lncRNAs could be associated with response to this pathogen. These results suggest that lncRNAs have potential functional roles in potato defense responses. This work provides the foundation for further functional studies in understanding potato defense mechanisms.

2016-12-31 | GSE74870 | GEO

Identification and characterization of potato long noncoding RNAs responsive to Pectobacterium carotovorum subspecies brasiliense infection [Strand-specific RNA-seq]

2016-11-23 | GSE74869 | GEO

Genome-wide identification of potato long intergenic noncoding RNAs responsive to Pectobacterium carotovorum subspecies brasiliense infection.

Project description:Long noncoding RNAs (lncRNAs) represent a class of RNA molecules that are implicated in regulation of gene expression in both mammals and plants. While much progress has been made in determining the biological functions of lncRNAs in mammals, the functional roles of lncRNAs in plants are still poorly understood. Specifically, the roles of long intergenic nocoding RNAs (lincRNAs) in plant defence responses are yet to be fully explored.In this study, we used strand-specific RNA sequencing to identify 1113 lincRNAs in potato (Solanum tuberosum) from stem tissues. The lincRNAs are expressed from all 12 potato chromosomes and generally smaller in size compared to protein-coding genes. Like in other plants, most potato lincRNAs possess single exons. A time-course RNA-seq analysis between a tolerant and a susceptible potato cultivar showed that 559 lincRNAs are responsive to Pectobacterium carotovorum subsp. brasiliense challenge compared to mock-inoculated controls. Moreover, coexpression analysis revealed that 17 of these lincRNAs are highly associated with 12 potato defence-related genes.Together, these results suggest that lincRNAs have potential functional roles in potato defence responses. Furthermore, this work provides the first library of potato lincRNAs and a set of novel lincRNAs implicated in potato defences against P. carotovorum subsp. brasiliense, a member of the soft rot Enterobacteriaceae phytopathogens.

| S-EPMC4982125 | biostudies-literature

Identification and characterization of potato long noncoding RNAs responsive to Pectobacterium carotovorum subspecies brasiliense infection

Project description:This SuperSeries is composed of the SubSeries listed below.

2016-11-29 | GSE74871 | GEO

RNA-seq of Pectobacterium carotovorum subsp. carotovorum and P. polaris infecting potato at 24, 48 and 72 hpi, and grown on M9 solid minimal medium at 24 hpi

Project description:Importance: Pectobacterium species cause soft rot in potato and other host plants primarily by secreting a battery of plant cell wall degrading enzymes. In addition, several different secretion systems are mobilized during infection. Previous studies of gene expression and regulation thereof primarily focused on the onset of infection. This work investigated transcriptome changes in Pectobacterium during the infection of potato tubers up to 72 hours post inoculation to elucidate biological processes during a longer infection period. Methods: The transcriptomes of aggressive strains of the two species P. carotovorum subsp. carotovorum and P. polaris were investigated during infection of potato minitubers (cv. 'Asterix') at 24, 48 and 72 hours after inoculation by RNA sequencing. The transcriptomes were compared to that of bacteria grown on minimal M9 medium, and transcriptomes from later infection time points (48 and 72 hours after inoculation) were compared to early infection (24 hours after inoculation). Results: Plant cell wall degrading enzymes and secretion system associated genes were largely upregulated during infection compared to in vitro growth, but downregulated in the later phases of infection compared to the early infection phase. The downregulation was not sufficiently explained by the expression of known virulence regulators such as the RsmA/B or the ExpA/S systems.

2022-04-01 | E-MTAB-7921 | biostudies-arrayexpress

Transcriptome-Wide Identification and Characterization of Potato Circular RNAs in Response to Pectobacterium carotovorum Subspecies brasiliense Infection.

Project description:Little information about the roles of circular RNAs (circRNAs) during potato-Pectobacterium carotovorum subsp. brasiliense (Pcb) interaction is currently available. In this study, we conducted the systematic identification of circRNAs from time series samples of potato cultivars Valor (susceptible) and BP1 (disease tolerant) infected by Pcb. A total of 2098 circRNAs were detected and about half (931, 44.38%) were intergenic circRNAs. And differential expression analysis detected 429 significantly regulated circRNAs. circRNAs play roles by regulating parental genes and sponging miRNAs. Gene Ontology (GO) enrichment of parental genes and miRNAs targeted mRNAs revealed that these differentially expressed (DE) circRNAs were involved in defense response (GO:0006952), cell wall (GO:0005199), ADP binding (GO:0043531), phosphorylation (GO:0016310), and kinase activity (GO:0016301), suggesting the roles of circRNAs in regulating potato immune response. Furthermore, weighted gene co-expression network analysis (WGCNA) found that circRNAs were closely related with coding-genes and long intergenic noncoding RNAs (lincRNAs). And together they were cultivar-specifically regulated to strengthen immune response of potato to Pcb infection, implying the roles of circRNAs in reprogramming disease responsive transcriptome. Our results will provide new insights into the potato-Pcb interaction and may lead to novel disease control strategy in the future.

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Pectobacterium brasiliense strain:CFIA1009

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Pectobacterium brasiliense strain:CFIA1001

Project description:Pectobacterium carotovorum subsp. brasiliense CFIA1001

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Pectobacterium brasiliense strain:CFIA1033

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