Biology subjects

Clarke, C. R.

Publications and source records attributed to Clarke, C. R..

4 recordsLinked to original sources

bioRxiv2026

Improved genome assemblies of plant-associated Streptomyces spp. as a resource for understanding plant pathogenicity in the genus

Common scab disease on potato is caused by members of more than 10 pathogenic Streptomyces species. Genome-enabled methods are being increasingly deployed to characterize Streptomyces that cause common scab disease of potato and other tuber and root crops. However, the study of phytopathogenic Streptomyces is constrained by the limited availability of high-quality genome sequences. Here we report improvements to the quality and completeness of genome assemblies for 12 pathogenic type strains of Streptomyces and six closely related non-pathogenic type strains. These assemblies have an average N50 of 7.4 Mbp and with BUSCO scores all greater than 98.5%. Analyses showed that the genomes of phytopathogenic Streptomyces are consistently among the largest Streptomyces genomes sequenced and, relative to those of non-pathogenic strains, are more enriched in genes involved in carbohydrate and amino acid metabolism. Plasmids were not consistently detected across assemblies, suggesting that they are not conserved across species and are not necessary for pathogenicity. Furthermore, comparisons of genome assemblies among both closely and distantly related strains revealed multiple rearrangements within linear chromosomes and reduced synteny near telomeric regions. These improved genome assemblies, many of which correspond to type strains, provide valuable resources for advancing our understanding of the pathogenicity in the genus.

genomics↗

bioRxiv2024

Thiamin priming to control early blight in potato: investigation of its effectiveness and molecular mechanisms

BackgroundPrevious reports in several plant species have shown that thiamin applied on foliage primes plant immunity and is effective in controlling fungal, bacterial, and viral diseases. However, the effectiveness of thiamin against potato (Solanum tuberosum) pathogens has seldom been investigated. Additionally, the transcriptomics and metabolomics of immune priming by thiamin have not previously been investigated. Here, we tested the effect of thiamin application against Alternaria solani, a necrotrophic fungus that causes early blight disease on potato foliage, and identified associated changes in gene expression and metabolite content. ResultsFoliar applications of thiamin reduced lesion size by approximately 33% when applied at an optimal concentration of 10 mM. However, the effect of thiamin on preventing lesion growth was temporally limited, as we observed a reduction of lesion size when leaves were inoculated 4 h, but not 24 h, following thiamin treatment. Additionally, we found that the effect of thiamin on lesion size was restricted to the site of application and was not systemic. Gene expression analysis via RNA-seq showed that thiamin induced the expression of genes involved in the synthesis of salicylic acid (SA) and phenylpropanoids to higher levels than the pathogen alone, as well as fatty acid metabolism genes that may be related to jasmonic acid biosynthesis. Thiamin also delayed the downregulation of photosynthesis-associated genes in plants inoculated with A. solani, which is a typical plant response to pathogens, but could also induce a similar repression of primary metabolic pathways in non-infected leaves. Metabolite analyses revealed that thiamin treatment in the absence of pathogen decreased the amounts of several organic compounds involved in the citric acid cycle as well as sugars, sugar alcohols, and amino acids. ConclusionsOur study indicates that thiamin priming of plant defenses may occur through perturbation of primary metabolic pathways and a re-allocation of energy resources towards defense activities.

plant biology↗

bioRxiv2022

Steroidal glycoalkaloids contribute to anthracnose resistance in Solanum lycopersicum

Anthracnose is a widespread plant disease caused by various species of the fungal pathogen Colletotrichum. In solanaceous plants such as tomato (Solanum lycoperiscum), Colletotrichum infections exhibit a quiescent, asymptomatic state in developing fruit, followed by a transition to necrotrophic infections in ripe fruit. Through analysis of fruit tissue extracts of 95L368, a tomato breeding line that yields fruit with enhanced anthracnose resistance, we identified a role for steroidal glycoalkaloids (SGAs) in anthracnose resistance. The SGA -tomatine and several of its derivatives accumulated at higher levels, in comparison to fruit of the susceptible tomato cultivar US28, 95L368 fruit extracts with fungistatic activity against Colletotrichum. Correspondingly, ripe and unripe 95L368 fruit displayed enhanced expression of glycoalkaloid metabolic enzyme (GAME) genes, which encode key enzymes in SGA biosynthesis. Metabolomics analysis incorporating recombinant inbred lines (RILs) generated from 95L368 and US28 yielded strong positive correlations between anthracnose resistance and accumulation of -tomatine and several derivatives. Lastly, transient silencing of expression of the GAME genes GAME31 and GAME5 in anthracnose-susceptible tomato fruit yielded enhancements to anthracnose resistance. Together, our data support a role for SGAs in anthracnose defense in tomato, with a distinct SGA metabolomic profile conferring resistance to virulent Colletotrichum infections in ripe fruit. HighlightThis work describes an important role for steroidal glycoalkaloids (SGAs), abundant secondary metabolites in tomato fruit, in defense against anthracnose, a widespread fungal disease that impacts diverse crop species.

plant biology↗

bioRxiv2021

Experimental evidence pointing to rain as a reservoir of tomato phyllosphere microbiota

Plant microbiota play essential roles in plant health and crop productivity. Comparisons of community composition have suggested seeds, soil, and the atmosphere as reservoirs of phyllosphere microbiota. After finding that leaves of tomato (Solanum lycopersicum) plants exposed to rain carried a higher microbial population size than leaves of tomato plants not exposed to rain, we experimentally tested the hypothesis that rain is a so far neglected reservoir of phyllosphere microbiota. Rain microbiota were thus compared with phyllosphere microbiota of tomato plants either treated with concentrated rain microbiota, filter-sterilized rain, or sterile water. Based on 16S rRNA amplicon sequencing, one-hundred and four operational taxonomic units (OTUs) significantly increased in relative abundance after inoculation with concentrated rain microbiota but no OTU significantly increased after treatment with either sterile water or filter-sterilized rain. Some of the genera to which these 104 OTUs belonged were also found at higher relative abundance on tomatoes exposed to rain outdoors than on tomatoes grown protected from rain in a commercial greenhouse. Taken together, these results point to precipitation as a reservoir of phyllosphere microbiota and show the potential of controlled experiments to investigate the role of different reservoirs in the assembly of phyllosphere microbiota.

microbiology↗