PRGdb 4.0: an updated database dedicated to genes involved in plant disease resistance process

García, Joan Calle; Guadagno, Anna; Paytuví-Gallart, Andreu; Saera-Vila, Alfonso; Amoroso, Ciro Gianmaria; D’Esposito, Daniela; Andolfo, Giuseppe; Cigliano, Riccardo Aiese; Sanseverino, Walter; Ercolano, Maria Raffaella

doi:10.1093/nar/gkab1087

Cited by 51 publications

(37 citation statements)

References 65 publications

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“…The domains included coiled-coil (CC), kinase (KIN), Toll/interleukin-1 receptor/resistance protein (TIR), nucleotide-binding site (NBS) and leucine-rich repeat (LRR). Non-canonical R-genes (which lack most conserved motifs but are nevertheless potential R-genes) were determined by BLAST searchers using manually curated R-genes from the PRGdb (v4.0) 90 database as reference sequences. Results with e-values of less than 1E-5 and top-hits with at least 30% query and subject coverage were considered to be the putative R-gene candidates.…”

Section: Methodsmentioning

confidence: 99%

Reference genome assemblies reveal the origin and evolution of allohexaploid oat

et al. 2022

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Common oat (Avena sativa) is an important cereal crop serving as a valuable source of forage and human food. Although reference genomes of many important crops have been generated, such work in oat has lagged behind, primarily owing to its large, repeat-rich polyploid genome. Here, using Oxford Nanopore ultralong sequencing and Hi-C technologies, we have generated a reference-quality genome assembly of hulless common oat, comprising 21 pseudomolecules with a total length of 10.76 Gb and contig N50 of 75.27 Mb. We also produced genome assemblies for diploid and tetraploid Avena ancestors, which enabled the identification of oat subgenomes and provided insights into oat chromosomal evolution. The origin of hexaploid oat is inferred from whole-genome sequencing, chloroplast genomes and transcriptome assemblies of different Avena species. These findings and the high-quality reference genomes presented here will facilitate the full use of crop genetic resources to accelerate oat improvement.

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Section: Methodsmentioning

confidence: 99%

Reference genome assemblies reveal the origin and evolution of allohexaploid oat

et al. 2022

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“…All of the protein domains of the detected genes were predicted by Pfam, and six typical disease resistance-related protein domains, including the coiled-coil (CC) domain, Tollinterleukin 1 receptor (TIR) domain, leucine-rich repeat (LRR) domain, nucleotide binding site (NBS) domain, and transmembrane (TM) domain and kinase domain were analyzed according to the previous reports [ 22 , 23 , 24 ]. These domains play a significant role in R protein interactions with effector proteins from pathogens and in activating signal transduction pathways involved in innate immunity.…”

Section: Resultsmentioning

confidence: 99%

Transcriptome Analysis Reveals a Comprehensive Virus Resistance Response Mechanism in Pecan Infected by a Novel Badnavirus Pecan Virus

Zhang¹,

Wang²,

Jia³

et al. 2022

IJMS

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Pecan leaf-variegated plant, which was infected with a novel badnavirus named pecan mosaic virus (PMV) detected by small RNA deep sequencing, is a vital model plant for studying the molecular mechanism of retaining green or chlorosis of virus-infected leaves. In this report, PMV infection in pecan leaves induced PAMP-triggered immunity (PTI) and effector-triggered immunity (ETI). PMV infection suppressed the expressions of key genes of fatty acid, oleic acid (C18:1), and very-long-chain fatty acids (VLCFA) biosynthesis, indicating that fatty acids-derived signaling was one of the important defense pathways in response to PMV infection in pecan. PMV infection in pecans enhanced the expressions of pathogenesis-related protein 1 (PR1). However, the transcripts of phenylalanine ammonia-lyase (PAL) and isochorismate synthase (ICS) were downregulated, indicating that salicylic acid (SA) biosynthesis was blocked in pecan infected with PMV. Meanwhile, disruption of auxin signaling affected the activation of the jasmonic acid (JA) pathway. Thus, C18:1 and JA signals are involved in response to PMV infection in pecan. In PMV-infected yellow leaves, damaged chloroplast structure and activation of mitogen-activated protein kinase 3 (MPK3) inhibited photosynthesis. Cytokinin and SA biosynthesis was blocked, leading to plants losing immune responses and systemic acquired resistance (SAR). The repression of photosynthesis and the induction of sink metabolism in the infected tissue led to dramatic changes in carbohydrate partitioning. On the contrary, the green leaves of PMV infection in pecan plants had whole cell tissue structure and chloroplast clustering, establishing a strong antiviral immunity system. Cytokinin biosynthesis and signaling transductions were remarkably strengthened, activating plant immune responses. Meanwhile, cytokinin accumulation in green leaves induced partial SA biosynthesis and gained comparatively higher SAR compared to that of yellow leaves. Disturbance of the ribosome biogenesis might enhance the resistance to PMV infection in pecan and lead to leaves staying green.

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“…PRGdb is a database of PRGs that provide constant updates on plant resistance genes ( Calle García et al, 2021 ). In this analysis, we found 73 transcripts having homology with reference PRGs in PRGdb.…”

Section: Discussionmentioning

confidence: 99%

Comparative Transcriptome Analysis of Onion in Response to Infection by Alternaria porri (Ellis) Cifferi

Khandagale

Roylawar²,

Kulkarni

et al. 2022

Front. Plant Sci.

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Purple blotch (PB) is one of the most destructive foliar diseases of onion and other alliums, caused by a necrotrophic fungal pathogen Alternaria porri. There are no reports on the molecular response of onion to PB infection. To elucidate the response of onion to A. porri infection, we consequently carried out an RNAseq analysis of the resistant (Arka Kalyan; AK) and susceptible (Agrifound rose; AFR) genotype after an artificial infection. Through differential expression analyses between control and pathogen-treated plants, we identified 8,064 upregulated and 248 downregulated genes in AFR, while 832 upregulated and 564 downregulated genes were identified in AK. A further significant reprogramming in the gene expression profile was also demonstrated by a functional annotation analysis. Gene ontology (GO) terms, which are particularly involved in defense responses and signaling, are overrepresented in current analyses such as “oxidoreductase activity,” “chitin catabolic processes,” and “defense response.” Several key plant defense genes were differentially expressed on A. porri infection, which includes pathogenesis-related (PR) proteins, receptor-like kinases, phytohormone signaling, cell-wall integrity, cytochrome P450 monooxygenases, and transcription factors. Some of the genes were exclusively overexpressed in resistant genotype, namely, GABA transporter1, ankyrin repeat domain-containing protein, xyloglucan endotransglucosylase/hydrolase, and PR-5 (thaumatin-like). Antioxidant enzyme activities were observed to be increased after infection in both genotypes but higher activity was found in the resistant genotype, AK. This is the first report of transcriptome profiling in onion in response to PB infection and will serve as a resource for future studies to elucidate the molecular mechanism of onion-A. porri interaction and to improve PB resistance in onions.

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PRGdb 4.0: an updated database dedicated to genes involved in plant disease resistance process

Cited by 51 publications

References 65 publications

Reference genome assemblies reveal the origin and evolution of allohexaploid oat

Reference genome assemblies reveal the origin and evolution of allohexaploid oat

Transcriptome Analysis Reveals a Comprehensive Virus Resistance Response Mechanism in Pecan Infected by a Novel Badnavirus Pecan Virus

Comparative Transcriptome Analysis of Onion in Response to Infection by Alternaria porri (Ellis) Cifferi

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