Alien domains shaped the modular structure of plant NLR proteins

Andolfo, Giuseppe; Donato, Antimo Di; Chiaiese, Pasquale; Natale, Antonino De; Pollio, Antonino; Jones, Jonathan D. G.; Frusciante, Luigi; Ercolano, Maria Raffaella

doi:10.1093/gbe/evz248

Cited by 26 publications

(54 citation statements)

References 70 publications

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“…Indeed, large gene expansions (more than 15 copies), involving unknown NB-LRRs-as well as Prf /R1, Hero/Mi 1.2, Gro1-4/N members-were observed. genes have been amplified, thus resulting in species-specific sub-families [16]. The diversification of tomato R-gene arsenal was mediated by duplication events of distinct NB-LRR paralogs (Figure 1).…”

Section: The Genome-wide Arrangement Of Tomato Nb-lrr Genesmentioning

confidence: 99%

“…Generally, NB-LRR-encoding genes are clustered, as result of both segmental and tandem duplications [ 12 , 16 ]. Over 65% of tomato NB-LRRs are gathered in small genomic regions spanning 200 kb or less.…”

Section: The Genome-wide Arrangement Of Tomato Nb-lrr Genesmentioning

confidence: 99%

“…The innate immunity system of plants has evolved in two recognition layers (PTI: PAMP (pathogen-associated molecular pattern)-triggered immunity and ETI: effector-triggered immunity). Plants’ own numerous non-self-recognition receptors are able to identify enemy molecules and induce a set of pathways and signaling cascades to repel attacks [ 15 , 16 ]. In ETI, immunity is mainly activated through the recognition of pathogen effectors via plant disease R-proteins.…”

Section: Introductionmentioning

confidence: 99%

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The Tomato Interspecific NB-LRR Gene Arsenal and Its Impact on Breeding Strategies

Andolfo

D’Agostino

Frusciante

et al. 2021

Genes

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Tomato (Solanum lycopersicum L.) is a model system for studying the molecular basis of resistance in plants. The investigation of evolutionary dynamics of tomato resistance (R)-loci provides unique opportunities for identifying factors that promote or constrain genome evolution. Nucleotide-binding domain and leucine-rich repeat (NB-LRR) receptors belong to one of the most plastic and diversified families. The vast amount of genomic data available for Solanaceae and wild tomato relatives provides unprecedented insights into the patterns and mechanisms of evolution of NB-LRR genes. Comparative analysis remarked a reshuffling of R-islands on chromosomes and a high degree of adaptive diversification in key R-loci induced by species-specific pathogen pressure. Unveiling NB-LRR natural variation in tomato and in other Solanaceae species offers the opportunity to effectively exploit genetic diversity in genomic-driven breeding programs with the aim of identifying and introducing new resistances in tomato cultivars. Within this motivating context, we reviewed the repertoire of NB-LRR genes available for tomato improvement with a special focus on signatures of adaptive processes. This issue is still relevant and not thoroughly investigated. We believe that the discovery of mechanisms involved in the generation of a gene with new resistance functions will bring great benefits to future breeding strategies.

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Section: The Genome-wide Arrangement Of Tomato Nb-lrr Genesmentioning

confidence: 99%

Section: The Genome-wide Arrangement Of Tomato Nb-lrr Genesmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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The Tomato Interspecific NB-LRR Gene Arsenal and Its Impact on Breeding Strategies

Andolfo

D’Agostino

Frusciante

et al. 2021

Genes

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“…Additionally, Lee et al (2020) have recently proposed that the G10-subclade of NLRs is a monophyletic group containing a distinct type of CC (CCG10; CCG10-NLR). NLRs also occur in non-flowering plants where they carry additional types of N-terminal domains such as kinases and a/b hydrolases (Andolfo et al, 2019).…”

Section: Introductionmentioning

confidence: 99%

RefPlantNLR: a comprehensive collection of experimentally validated plant NLRs

Kourelis

Sakai

Adachi

et al. 2020

Preprint

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Reference datasets are critical in computational biology. They help define canonical biological features and are essential for benchmarking studies. Here, we describe a comprehensive reference dataset of experimentally validated plant NLR immune receptors. RefPlantNLR consists of 415 NLRs from 31 genera belonging to 11 orders of flowering plants. We used RefPlantNLR to determine the canonical features of functionally validated plant NLRs. This reference dataset should prove useful for benchmarking NLR annotation tools, guiding comparative analyses of NLRs across the wide spectrum of plant diversity and identifying under-studied taxa. We hope that the RefPlantNLR resource will contribute to moving the field beyond a uniform view of NLR structure and function.

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“…Symptom recovery is generally accompanied by activation of pathogen receptor genes and other defencerelated genes during the plant-pathogen interaction [23,36,37]. In particular, we found a resistance protein (CNL) annotated by Andolfo et al, [19] and located on linkage group 8 scaffold 3 (Cup000003g003423.1) up regulated and privately expressed (LogFC 1.51) in 381e [19,38,39]. It is interesting to note that in such transcript we found a variant that could lead to functional modification.…”

Section: Discussionmentioning

confidence: 65%

Transcriptomic and genomic analysis highlights the basis of ZYMV tolerance in zucchini

Amoroso

Andolfo

Capuozzo

et al. 2021

Preprint

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Background: Cucurbita pepo is high susceptible to Zucchini yellow mosaic virus (ZYMV) and the resistance found in several wild species does not provide complete or broad-spectrum resistance. In this study, a source of tolerance introgressed in C. pepo (381e) from C. moschata, in True French (TF) background, was investigated 12 days post inoculation (DPI) at transcriptomic and genomic levels. Results: A comparative RNA-seq experiment on TF (susceptible to ZYMV) and 381e (tolerant to ZYMV), allowed to evaluate 33,000 expressed transcripts and to identify 146 differentially expressed genes (DEGs) in 381e, mainly involved in photosynthesis, transcription, cytoskeleton organization and callose synthesis. By contrast, the susceptible line True French triggered oxidative processes related to response to biotic stimulus, and key regulators of plant virus intercellular movement. Moreover, the genome mapping of transcripts allowed the identification of two chromosome regions rich in SNPs (Single Nucleotide Polymorphisms), putatively introgressed from C. moschata, containing genes exclusively expressed in 381e. Conclusion: The transcriptome reprogramming of 381e ZYMV challenged revealed a globally restoring of cellular activities and a reduced virus movement and replication. Furthermore, genes putatively involved in ZYMV tolerance were detected in C. moschata introgressed genomic regions. Our work provides new insight into the plant virus recovery process and a better understanding of the molecular basis of 381e tolerance.

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Alien domains shaped the modular structure of plant NLR proteins

Cited by 26 publications

References 70 publications

The Tomato Interspecific NB-LRR Gene Arsenal and Its Impact on Breeding Strategies

The Tomato Interspecific NB-LRR Gene Arsenal and Its Impact on Breeding Strategies

RefPlantNLR: a comprehensive collection of experimentally validated plant NLRs

Transcriptomic and genomic analysis highlights the basis of ZYMV tolerance in zucchini

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