Ignazio Carbone
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View article: Seasonal assembly of the phyllosphere fungal microbiome of a perennial grass is robust to nutrient addition
Seasonal assembly of the phyllosphere fungal microbiome of a perennial grass is robust to nutrient addition Open
The leaf microbiome plays an important role in plant health and defense. Despite its importance, how the assembly of the leaf microbial community is modified by environmental conditions such as nutrient availability remains relatively unin…
View article: Rhs-toxin Abundance, Diversity, and Function in Four Genera of Plant Pathogenic Bacteria: <i>Xanthomonas, Ralstonia, Pectobacterium,</i> and <i>Dickeya</i>
Rhs-toxin Abundance, Diversity, and Function in Four Genera of Plant Pathogenic Bacteria: <i>Xanthomonas, Ralstonia, Pectobacterium,</i> and <i>Dickeya</i> Open
Rearrangement hotspot (Rhs) toxins are polymorphic bacterial toxins that inhibit competitor microbes, playing a critical role in interbacterial competition. Each toxin comprises a conserved N-terminal region for translocation and a hyperva…
View article: Preserving the Biologically Coherent Generic Concept of <i>Phytophthora</i>, “Plant Destroyer”
Preserving the Biologically Coherent Generic Concept of <i>Phytophthora</i>, “Plant Destroyer” Open
Phytophthora is a long-established, well-known, and globally important genus of plant pathogens. Phylogenetic evidence has shown that the biologically distinct, obligate biotrophic downy mildews evolved from Phytophthora at least twice. Be…
View article: A pangenome analysis reveals the center of origin and evolutionary history of Phytophthora infestans and 1c clade species
A pangenome analysis reveals the center of origin and evolutionary history of Phytophthora infestans and 1c clade species Open
We examined the evolutionary history of Phytophthora infestans and its close relatives in the 1c clade. We used whole genome sequence data from 69 isolates of Phytophthora species in the 1c clade and conducted a range of genomic analyses i…
View article: Eco‐phylogenetic study of <i>Trebouxia</i> in southern Africa reveals interbiome connectivity and potential endemism in a green algal lichen photobiont
Eco‐phylogenetic study of <i>Trebouxia</i> in southern Africa reveals interbiome connectivity and potential endemism in a green algal lichen photobiont Open
Premise Southern Africa is a biodiversity hotspot rich in endemic plants and lichen‐forming fungi. However, species‐level data about lichen photobionts in this region are minimal. We focused on Trebouxia (Chlorophyta), the most common lich…
View article: Parasites, niche modification and the host microbiome: A field survey of multiple parasites
Parasites, niche modification and the host microbiome: A field survey of multiple parasites Open
Parasites can affect and be affected by the host's microbiome, with consequences for host susceptibility, parasite transmission, and host and parasite fitness. Yet, two aspects of the relationship between parasite infection and host microb…
View article: Towards a nomenclatural clarification of the <i>Peltigera ponojensis/monticola</i> clade including metagenomic sequencing of type material and the introduction of <i>P. globulata</i> Miadl. & Magain sp. nov.
Towards a nomenclatural clarification of the <i>Peltigera ponojensis/monticola</i> clade including metagenomic sequencing of type material and the introduction of <i>P. globulata</i> Miadl. & Magain sp. nov. Open
Peltigera globulata Miadl. & Magain, a new species in the P. ponojensis/monticola species complex of section Peltigera , is formally described. This clade was previously given the interim designation Peltigera sp. 17. It is found in sun-ex…
View article: Cassava begomovirus species diversity changes during plant vegetative cycles
Cassava begomovirus species diversity changes during plant vegetative cycles Open
Cassava is a root crop important for global food security and the third biggest source of calories on the African continent. Cassava production is threatened by Cassava mosaic disease (CMD), which is caused by a complex of single-stranded …
View article: An open-access T-BAS phylogeny for emerging Phytophthora species
An open-access T-BAS phylogeny for emerging Phytophthora species Open
Phytophthora species cause severe diseases on food, forest, and ornamental crops. Since the genus was described in 1876, it has expanded to comprise over 190 formally described species. There is a need for an open access phylogenetic tool …
View article: Ancient Rapid Radiation Explains Most Conflicts Among Gene Trees and Well-Supported Phylogenomic Trees of Nostocalean Cyanobacteria
Ancient Rapid Radiation Explains Most Conflicts Among Gene Trees and Well-Supported Phylogenomic Trees of Nostocalean Cyanobacteria Open
Prokaryotic genomes are often considered to be mosaics of genes that do not necessarily share the same evolutionary history due to widespread horizontal gene transfers (HGTs). Consequently, representing evolutionary relationships of prokar…
View article: Asymmetrical lineage introgression and recombination in populations of Aspergillus flavus: Implications for biological control
Asymmetrical lineage introgression and recombination in populations of Aspergillus flavus: Implications for biological control Open
Aspergillus flavus is an agriculturally important fungus that causes ear rot of maize and produces aflatoxins, of which B 1 is the most carcinogenic naturally-produced compound. In the US, the management of aflatoxins includes the deployme…
View article: Microbial Diversity in Four Rhizocompartments (Bulk Soil, Rhizosphere, Rhizoplane, and Endosphere) of Four Winter Wheat Varieties at the Fully Emerged Flag Leaf Growth Stage
Microbial Diversity in Four Rhizocompartments (Bulk Soil, Rhizosphere, Rhizoplane, and Endosphere) of Four Winter Wheat Varieties at the Fully Emerged Flag Leaf Growth Stage Open
Community composition and recruitment are important elements of plant-microbe interactions and may provide insights for plant development and resilience. The results of 16S rRNA amplicon sequencing from four rhizocompartments for four whea…
View article: Recombination-aware phylogeographic inference using the structured coalescent with ancestral recombination
Recombination-aware phylogeographic inference using the structured coalescent with ancestral recombination Open
Movement of individuals between populations or demes is often restricted, especially between geographically isolated populations. The structured coalescent provides an elegant theoretical framework for describing how movement between popul…
View article: An open-access T-BAS phylogeny for Emerging<i>Phytophthora</i>species
An open-access T-BAS phylogeny for Emerging<i>Phytophthora</i>species Open
Phytophthora species cause severe diseases on food, forest, and ornamental crops. Since the genus was described in 1875, it has expanded to comprise over 190 formally described species. There is a need for an open access bioinformatic tool…
View article: Rapid Multilocus Adaptation of Clonal Cabbage Leaf Curl Virus Populations to <i>Arabidopsis thaliana</i>
Rapid Multilocus Adaptation of Clonal Cabbage Leaf Curl Virus Populations to <i>Arabidopsis thaliana</i> Open
Cabbage leaf curl virus (CabLCV) has a bipartite single-stranded DNA genome and infects the model plant Arabidopsis thaliana. CabLCV serves as a model for the genus Begomovirus, members of which cause tremendous crop losses worldwide. We h…
View article: Asymmetrical lineage introgression and recombination in populations of<i>Aspergillus flavus</i>: implications for biological control
Asymmetrical lineage introgression and recombination in populations of<i>Aspergillus flavus</i>: implications for biological control Open
Aspergillus flavus is an agriculturally important fungus that causes ear rot of maize and produces aflatoxins (AFs), of which B 1 is the most potent carcinogen known. In the US, the management of AFs includes the deployment of biological c…
View article: Recombination-aware Phylogeographic Inference Using the Structured Coalescent with Ancestral Recombination
Recombination-aware Phylogeographic Inference Using the Structured Coalescent with Ancestral Recombination Open
Movement of individuals between populations or demes is often restricted, especially between geographically isolated populations. The structured coalescent provides an elegant theoretical framework for describing how movement between popul…
View article: Development of sexual structures influences metabolomic and transcriptomic profiles in Aspergillus flavus
Development of sexual structures influences metabolomic and transcriptomic profiles in Aspergillus flavus Open
Sclerotium (female) fertility, the ability of a strain to produce ascocarps, influences internal morphological changes during sexual reproduction in Aspergillus flavus. Although sclerotial morphogenesis has been linked to secondary metabol…
View article: An experimental strategy for preparing circular ssDNA virus genomes for next-generation sequencing
An experimental strategy for preparing circular ssDNA virus genomes for next-generation sequencing Open
The ability of begomoviruses to evolve rapidly threatens many crops and underscores the importance of detecting these viruses quickly and to understand their genome diversity. This study presents an improved protocol for the enhanced ampli…
View article: Rapid multilocus adaptation of clonal cabbage leaf curl virus populations to<i>Arabidopsis thaliana</i>
Rapid multilocus adaptation of clonal cabbage leaf curl virus populations to<i>Arabidopsis thaliana</i> Open
Cabbage leaf curl virus (CabLCV) has a bipartite single-stranded DNA genome and infects the model plant Arabidopsis thaliana . CabLCV serves as a model for the genus Begomovirus , members of which cause tremendous crop losses worldwide. We…
View article: Population diversity of cassava mosaic begomoviruses increases over the course of serial vegetative propagation
Population diversity of cassava mosaic begomoviruses increases over the course of serial vegetative propagation Open
Cassava mosaic disease (CMD) represents a serious threat to cassava, a major root crop for more than 300 million Africans. CMD is caused by single-stranded DNA begomoviruses that evolve rapidly, making it challenging to develop durable dis…
View article: Population diversity of cassava mosaic begomoviruses increases over the course of serial vegetative propagation
Population diversity of cassava mosaic begomoviruses increases over the course of serial vegetative propagation Open
Cassava mosaic disease (CMD) represents a serious threat to cassava, a major root crop for more than 300 million Africans. CMD is caused by single-stranded DNA begomoviruses that evolve rapidly, making it challenging to develop durable dis…
View article: Parasites, niche modification and the host microbiome: A field survey of multiple parasites
Parasites, niche modification and the host microbiome: A field survey of multiple parasites Open
Parasites can affect and be affected by the host's microbiome, with consequences for host susceptibility, parasite transmission, and host and parasite fitness. Yet, two aspects of the relationship between parasite infection and host microb…
View article: An improved experimental pipeline for preparing circular ssDNA viruses for next-generation sequencing
An improved experimental pipeline for preparing circular ssDNA viruses for next-generation sequencing Open
We present an optimized protocol for enhanced amplification and enrichment of viral DNA for Next Generation Sequencing of begomovirus genomes. The rapid ability of these viruses to evolve threatens many crops and underscores the importance…
View article: Genome Resources for Seven Fungal Isolates That Cause Dollar Spot Disease in Turfgrass, Including <i>Clarireedia jacksonii</i> and <i>C. monteithiana</i>
Genome Resources for Seven Fungal Isolates That Cause Dollar Spot Disease in Turfgrass, Including <i>Clarireedia jacksonii</i> and <i>C. monteithiana</i> Open
Fungi in the genus Clarireedia are widespread and destructive pathogens of grasses worldwide, and are best known as the causal agents of dollar spot disease in turfgrass. Here, we report genome assemblies of seven Clarireedia isolates, inc…
View article: Parasites as niche modifiers for the microbiome: A field test with multiple parasites
Parasites as niche modifiers for the microbiome: A field test with multiple parasites Open
Parasites can affect and be affected by the host’s microbiome, with consequences for host susceptibility, parasite transmission, and host and parasite fitness. Yet, there are two aspects of the relationship between parasite infection and t…