Genome-Wide Analysis and Evolutionary History of the Necrosis- and Ethylene-Inducing Peptide 1-Like Protein (NLP) Superfamily Across the Dothideomycetes Class of Fungi

Dal’Sasso, Thaís Carolina da Silva; Rody, Hugo Vianna Silva; Oliveira, Luiz Orlando de

doi:10.1007/s00284-022-03125-8

Cited by 3 publications

(9 citation statements)

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“…We found that the closer the evolutionary relationship, the closer the number of effector proteins; e.g., the number of effector proteins of N. dimidiatum , N. parvum , and B. dothidea were 121, 124, and 152, respectively. The annotation results of N. dimidiatum effector proteins showed that these proteins include pectate lyases, cutinases, necrosis and ethylene-inducing proteins, and cysteine-rich secretory proteins, which are known to be virulence factors in other fungi ( 10 , 26 , 32 , 33 ). These findings suggest that the pathogenicity of these fungi may be related to their ability to interact with host plants through the production of specific effector proteins.…”

Section: Discussionmentioning

confidence: 99%

Whole-genome sequencing and comparative genomics reveal the potential pathogenic mechanism of Neoscytalidium dimidiatum on pitaya

Wang,

Xu,

Wang

et al. 2023

Microbiol Spectr

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Neoscytalidium dimidiatum (class Dothideomycetes ) is a fungus responsible for canker disease in pitaya stems and fruits, leading to significant economic losses. However, little is known about the pathogenesis, family evolution, and genetic variants of this species. In this study, we report a high-quality genome sequence of N. dimidiatum based on the Nanopore sequencing technology platform for sequencing and Hi-C assembly technology for genome assembly. The genome contains 12 chromosomes (2 n = 2× = 12; diploid), with a sequencing depth of 186.1×, encoding 12,349 proteins. Molecular phylogenetic analysis showed that N. dimidiatum is evolutionarily close to Botryosphaeria dothidea . Compared to other fungi, the N. dimidiatum genome contains many carbohydrate-active enzymes and secondary metabolites. Additionally, we predict that N. dimidiatum contains 121 candidate effectors that may play important roles in infection and colonization, promoting pathogenicity in pitaya. Nine of these effectors were confirmed to contain signal peptides and inhibit BAX/INF1-induced necrosis in Nicotiana benthamiana , demonstrating their importance during infection. Finally, we also confirm that N. dimidiatum does not form an appressorium or infection thread but instead infects pitaya via open stomata. In conclusion, the results provide a foundation for future research on N. dimidiatum and the control of pitaya canker. IMPORTANCE Pitaya canker is a significant disease in the pitaya industry in China, causing significant economic losses. Therefore, systematic research on Neoscytalidium dimidiatum , the fungus implicated in pitaya canker, is essential for comprehending the pathogenesis of this disease and developing effective control strategies. We applied comparative genomics to reveal the genetic evolution, metabolic diversity, environmental adaptation, and pathogenicity of N. dimidiatum , providing ideal targets for studies of pathogenesis and molecular targets for fungicide development. Moreover, the systematic study of the N. dimidiatum growth cycle, morphological characteristics, and molecular phylogenetic analysis can promote a comprehensive understanding of its genetic basis.

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Section: Discussionmentioning

confidence: 99%

Whole-genome sequencing and comparative genomics reveal the potential pathogenic mechanism of Neoscytalidium dimidiatum on pitaya

Wang,

Xu,

Wang

et al. 2023

Microbiol Spectr

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“…Our data collection strategy aimed to encompass a broad range of species within the Dothideomycetes class of fungi, including Corynespora cassiicola, a polyphagous plant pathogenic fungus with a cosmopolitan distribution. The protein sequences utilized in this study were obtained from MycoCosm , and consisted of 79 species of Dothideomycetes representing 15 orders (Supplementary Table S1), previously employed in a recent phylogenomic study (Dal'Sasso et al, 2023). Additionally, protein sequences from two species of Eurotiomycetes (Aspergillus nidulans and Aspergillus fumigatus) were included to enhance the taxonomic diversity of the analyses.…”

Section: Data Assembly and Gene Predictionmentioning

confidence: 99%

“…Under relaxing selection, redundant copies of the duplicated gene can also be kept in the genome (Lynch and Conery, 2000). These alternative fates have been observed throughout the evolutionary history of other gene families in the Dothideomycetes (Dal'Sasso et al, 2023). Similarly, gene loss and retention have also played important roles in shaping the evolution of gene families in land plants (Rody and Oliveira, 2018).…”

Section: Evolutionary Patterns Of the Pme Gene Family In The Dothideo...mentioning

confidence: 99%

“…Recently, we have studied the interesting Dothideomycetes class of fungi, which encompasses a diverse array of plant-pathogenic species (Dal'Sasso et al, 2023, Rocha et al, 2023. The Dothideomycetes is a species-rich class within the phylum Ascomycota.…”

Section: Figure S2 Relative Expression Levels Of Five Pectin Methylte...mentioning

confidence: 99%

“…Together with the Capnodiales and the Botryosphaeriales, the Pleosporales harbor many genera capable of causing devastating diseases in important crops worldwide . High-quality genomic resources for Dothideomycetes are readily available in public repositories, with a majority of them derived from plant pathogens and plant-associated species (Dal'Sasso et al, 2023). Moreover, a robust molecular phylogenetic framework based on a set of 1,851 single-copy orthologs has been established to determine the genealogical relationships among 79 species across the Dothideomycetes (Dal'Sasso et al, 2023).…”

Section: Introductionmentioning

confidence: 99%

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Molecular evolution of two pathogenicity-associated gene families across the Dothideomycetes class of fungi

Rocha

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The Dothideomycetes class of fungi comprises over 19,000 described species, which are distributed into 23 orders. Generally, Dothideomycetes species have a cosmopolitan distribution and exhibit high ecological diversity, with distinct trophic modes (saprotrophic, pathogenic, endophytic, and mycorrhizal). Within the Dothideomycetes, one notable feature is the presence of many plant-pathogenic species, such as Corynespora cassiicola (Pleosporales) that causes diseases in economically important crops. Using data genomic data from 79 Dothideomycetes species (15 orders) and 61 C. cassiicola isolates, we investigated the evolutionary history of two pathogenicity-associated gene families: Pectin methylesterase (PME) and Deuterolysin metalloprotease (M35). We conducted phylogenic reconstructions and gene genealogies to uncover evolutionary patterns in both PME and M35. In C. cassiicola (isolate CC_29), we assessed gene expression patterns of members of each family, PME and M35, during the process of soybean infection. For the PME family, we recovered three major clades across the Dothideomycetes. Among these three clades, two (PME1 and PME2) have experienced duplications and sequent gene retention events, whereas the other clade (PME3) likely has evolved through biased gene loss. Each C. cassiicola isolate displayed five PME genes. The five PME haplogroups in C. cassiicola showed varying levels of genetic diversity and may have undergone distinct selective pressures. For the M35 family, the number of genes varied from zero to seven per genome across the Dothideomycetes. Specifically, some species within the order Botryophaeriales exhibited a higher numbergenesM35 genes. The majority of C. cassiicola isolates display three M35 genes per genome. In C. cassiicola, either gene retention episodes or gene loss characterized each of the four sub-clades within the M35 family. All genes of each family, PME and M35, were expressed in C. cassiicola during the interaction with soybean plants, suggesting that they are functional and may contribute to fungal infection. Keywords: Corynespora. Genomics. Gene duplication. Molecular phylogeny. Plant- pathogens

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Genome-wide survey and evolutionary history of the pectin methylesterase (PME) gene family in the Dothideomycetes class of fungi

Rocha,

Dal'Sasso,

Dal-Bianco

et al. 2023

Fungal Genetics and Biology

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Genome-Wide Analysis and Evolutionary History of the Necrosis- and Ethylene-Inducing Peptide 1-Like Protein (NLP) Superfamily Across the Dothideomycetes Class of Fungi

Cited by 3 publications

References 42 publications

Whole-genome sequencing and comparative genomics reveal the potential pathogenic mechanism of Neoscytalidium dimidiatum on pitaya

Whole-genome sequencing and comparative genomics reveal the potential pathogenic mechanism of Neoscytalidium dimidiatum on pitaya

Molecular evolution of two pathogenicity-associated gene families across the Dothideomycetes class of fungi

Genome-wide survey and evolutionary history of the pectin methylesterase (PME) gene family in the Dothideomycetes class of fungi

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