Publications by authors named "Javier Tabima"
Article Synopsis
- The text discusses a new species of mushroom from the Boletales order, found in temperate forests, specifically at Marys Peak in Oregon, which is unique for being hypogeous (growing underground) unlike other related species.
- This species has distinctive features, such as a white peridium that turns pink to purple when bruised and a gleba that changes color from pale yellow to purple as it matures.
- Molecular analysis confirms this mushroom’s classification within a specific group, indicating a unique evolutionary development in the Boletales, demonstrating an independent origin for its underground growth and a shift to its current host environment.
Article Synopsis
- Wild organisms face various parasites, necessitating a balance between an effective immune response and avoiding harmful overreactions.
- Research on immune responses mostly comes from lab studies, overlooking the genetic and environmental factors in wild populations.
- A study on two Alaskan stickleback populations showed different immune gene expression patterns in response to the same parasite, revealing how wild populations uniquely adapt to infections.
Article Synopsis
- Herptiles, including reptiles and amphibians, are facing significant endangerment, prompting various conservation efforts to ensure their recovery, yet little is known about their gut microbiomes and how it impacts their health.
- This study examines the gut microbiome of various herptiles, revealing that bacterial communities differ based on host species and are influenced by geographical factors, with fungi also significantly present in these microbiomes.
- The findings suggest that interactions between fungi and bacteria could play a role in shaping the gut microbiome, potentially driven by unique metabolic functions resulting from horizontal gene transfer, highlighting the importance of these microbial relationships in herptile conservation efforts.
Article Synopsis
- Fungal effectors are crucial in affecting plant immune responses, particularly in the context of the heterothallic ascomycete fungus that causes diseases in poplar trees, leading to significant plantation issues.
- In this study, 19 out of 142 identified candidate secreted effector proteins were analyzed, revealing that while some (like SmCSEP3) can induce cell death, others can suppress it and assist in promoting infection.
- The research shows that these effector proteins influence various plant immune responses and target different parts of the plant cell, underscoring the complex interaction between the fungus and its host.
Article Synopsis
- Sudden oak death (SOD) is an invasive disease caused by an oomycete pathogen, which poses significant threats to nurseries, horticulture, and forestry across the U.S. and worldwide.
- The study aimed to create diagnostic tools using loop-mediated isothermal amplification (LAMP) assays to quickly identify and differentiate four common lineages of the SOD pathogen.
- The developed assays are highly sensitive, effective on various sample types, and have successfully identified 190 out of 200 field samples, aiding forest managers in responding to new outbreaks.
Article Synopsis
- DNA methylation is an important epigenetic marker in eukaryotes, influencing transcription, chromatin organization, and development, but its role in the social amoeba remains unclear.
- This study investigates the DNA methylation profile of the amoeba using advanced sequencing techniques, revealing a very low occurrence of methylation at only 303-3432 cytosines in a genome of approximately 7.5 million.
- Knockout experiments of the DNMA enzyme showed no significant change in DNA methylation levels, and the few detected methylated sites were likely false positives due to specific DNA sequence structures, indicating minimal DNA methylation before fruiting body formation.
Comparative Genomic Analysis of 31 Genomes Reveals Genome Plasticity and Horizontal Gene Transfer.
Mol Plant Microbe Interact
January 2023
Article Synopsis
- Oomycete plant pathogens, which encompass over 180 species, significantly affect various plants, including important crops, leading to substantial economic and ecological consequences.
- The study sequenced genomes and transcriptomes of 31 species, revealing differences in genome size, gene counts, and the types of effector genes linked to their ability to infect various plant hosts.
- Using machine learning, researchers identified 44 horizontally transferred genes from bacteria or fungi across 36 species, suggesting these genetic exchanges are key to understanding the evolution and adaptability of oomycetes.
Marine spp. are unicellular cyanobacteria widely distributed in the world's oceans. We report the complete genome sequence of sp.
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- The genome of the fungus Gams has 43 potential biosynthetic gene clusters for specialized metabolites, but connections between its genes and traits have only been confirmed for cyclosporins and fumonisins.
- The study cultured the fungus in minimal media with various amino acids and used techniques like LC-MS/MS for molecular networking and analysis, which helped in identifying known and novel metabolites.
- Researchers isolated and characterized a peptaibol called tolypocladamide H, which showed some antibacterial effects and toxicity towards mammalian cells, while also identifying it as containing a unique structural motif associated with cyclosporins.
Article Synopsis
- - Sudden death syndrome (SDS) in soybeans is caused by a fungus that first appeared in Arkansas in 1971 and has since spread throughout the Midwest, primarily affecting roots and leaves through toxins.
- - Research shows that while the pathogen has limited genetic diversity in North America, it exhibits varying levels of virulence, indicating different isolates can impact plants differently.
- - Three distinct genetic population clusters of the fungus were identified across the Midwest, with different clusters showing varying levels of genetic diversity and virulence, highlighting their roles in the disease's spread.
Winter squash ( cultivar Golden Delicious) produced in Oregon's Willamette Valley for edible seed production has experienced significant yield losses because of a soilborne disease. The symptoms associated with this disease problem include root rot, crown rot, and vascular discoloration in the stems, leading to a severe late season wilt and plant collapse. Through field surveys, , , like fungi, , and were identified to be associated with diseased tissues, and each produced symptoms of root rot, crown rot, or stem discoloration in preliminary pathogenicity trials.
View Article and Find Full Text PDFStripe rust, caused by the fungus f. sp. , is a worldwide disease of wheat that causes devastating crop losses.
View Article and Find Full Text PDFBackground: The type VI protein secretion system (T6SS) is important in diverse cellular processes in Gram-negative bacteria, including interactions with other bacteria and with eukaryotic hosts. In this study we analyze the evolution of the T6SS in the genus Xanthomonas and evaluate its importance of the T6SS for virulence and in vitro motility in Xanthomonas phaseoli pv. manihotis (Xpm), the causal agent of bacterial blight in cassava (Manihot esculenta).
View Article and Find Full Text PDFis an oomycete that was first isolated from soil, water, and tree foliage in mixed Douglas-fir-tanoak forests of the U.S. Pacific Northwest (PNW).
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- - Research shows that fungi produce a variety of biologically active compounds with medicinal uses, primarily in the Dikarya subkingdom, which includes the Ascomycota and Basidiomycota phyla.
- - The study investigates the potential for secondary metabolism (SM) in two other phyla, Mucoromycota and Zoopagomycota, and identifies core genes related to SM production.
- - Findings reveal that some non-Dikarya fungi, particularly amphibian gut symbionts, possess a greater number of SM genes due to horizontal gene transfer from bacteria, leading to the production of compounds like siderophores.
Article Synopsis
- - The plant pathogen responsible for the Irish potato famine is reappearing globally through clonal reproduction, while sexual reproduction occurs in its origin in Mexico.
- - A genomic analysis of 47 genomes revealed that sexual populations in Mexico are diploid and show no instances of tetraploidy, contradicting previous reports.
- - The study suggests that the emergence of dominant clonal lineages is driven by increased gene copy number, which enhances their fitness and leads to the replacement of older clones.
The accelerated evolution and spread of pathogens are threats to host species. Agrobacteria require an oncogenic Ti or Ri plasmid to transfer genes into plants and cause disease. We developed a strategy to characterize virulence plasmids and applied it to analyze hundreds of strains collected between 1927 and 2017, on six continents and from more than 50 host species.
View Article and Find Full Text PDFThe oomycete is a highly destructive pathogen of cultivated strawberry ( × ), causing the root rotting disease, "red core". The host-pathogen interaction has a well described gene-for-gene resistance relationship, but to date neither candidate avirulence nor resistance genes have been identified. We sequenced a set of American, Canadian, and United Kingdom isolates of known race type, along with three representatives of the closely related pathogen of the raspberry (), , and found a clear population structure, with a high degree of nucleotide divergence seen between some race types and abundant private variation associated with race types 4 and 5.
View Article and Find Full Text PDF: An Expandable R Package to Predict Candidate RxLR and CRN Effectors in Oomycetes Using Motif Searches.
Mol Plant Microbe Interact
September 2019
Article Synopsis
- Effectors are proteins that help plant pathogens infect their hosts, and finding these proteins in oomycetes (a type of fungus-like microorganism) typically involves identifying specific amino acid patterns in their genetic code.
- Researchers developed an R package that simplifies the identification of these effector proteins, allowing for quick and reproducible analysis of oomycete genomes and other genomes through the use of pattern recognition techniques.
- The package supports the addition of new effector motifs and has been validated against existing oomycete genome data, making it a useful tool for researchers in the lab.
Invasive alien species often have reduced genetic diversity and must adapt to new environments. Given the success of many invasions, this is sometimes called the genetic paradox of invasion. is invasive, limited to asexual reproduction within four lineages, and presumed clonal.
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- A species of Gram-positive bacteria, known for producing corynetoxin, causes a fatal condition called annual ryegrass toxicity in grazing animals and has shown low genetic diversity over 30 years of sampling in Australia.
- Phylogenomic analysis revealed that the bacteria form nine distinct species groups, with one species displaying a significantly reduced genome and minimal genetic diversity, which may have resulted from a key evolutionary event.
- The unique features of this species include the presence of a CRISPR system, which helps it defend against bacteriophages, and the findings suggest a three-stage process that highlights the role of bacteriophage interactions in shaping the bacteria's genome and genetic characteristics.
Article Synopsis
- Population genetics helps us understand how plant diseases, like Phytophthora root rot in raspberries, emerge and adapt in agricultural settings.
- Research on Phytophthora rubi shows low genetic diversity across the western U.S., suggesting it might be the main source of pathogen migration to Europe.
- Findings indicate that human activity could be influencing the spread of P. rubi, as genetic evidence shows migration patterns from California and Oregon to Washington.
Whole Genome Sequences of the Raspberry and Strawberry Pathogens Phytophthora rubi and P. fragariae.
Mol Plant Microbe Interact
October 2017
Phytophthora rubi and P. fragariae are two closely related oomycete plant pathogens that exhibit strong morphological and physiological similarities but are specialized to infect different hosts of economic importance, namely, raspberry and strawberry. Here, we report the draft genome sequences of these two Phytophthora species as a first step toward understanding the genomic processes underlying plant host adaptation in these pathogens.
View Article and Find Full Text PDFPhytopathogens have mastered the ability to evade plant innate immunity. In this issue of Cell Host & Microbe, Zhou and colleagues (Li et al., 2016) uncover a strategy whereby a bacterial pathogen disables the plant immune system with such precision as to avoid triggering alarms that could potentially reveal its presence.
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- * Microbe-ID includes two main components: Sequence-ID for species identification using sequence queries against a reference database, and Genotype-ID for placing multilocus markers into networks to identify genetic relationships.
- * The public website, microbe-id.org, offers tools specifically for the genus Phytophthora, allowing users to identify strains and species based on genetic markers, with all code provided openly for accessibility.