Biology subjects

Busby, P. E.

Publications and source records attributed to Busby, P. E..

6 recordsLinked to original sources

bioRxiv2025

Telomere-to-telomere assemblies reveal complex adaptive variation of 3-ketoacyl-CoA-synthases in Populus trichocarpa likely driven by helitrons

BackgroundThe model woody plant Populus trichocarpa displays an atypical alkene-diverse wax cuticle likely driven by copy number variation (CNV) of 3-ketoacyl-CoA synthases (KCS), which has been difficult to confirm based on short-read assemblies. New long-read sequencing provides opportunities to develop telomere-to-telomere resources to detect cryptic variation, including CNVs, which are currently missed in traditional analyses. Integrating this information can improve genomic prediction for breeding and provide insights into the evolutionary basis of important traits. ResultsOur analysis of 78 telomere-to-telomere long-read haplotypes identified more than twice as many KCS genes as previously reported, along with numerous intragenic non-synonymous substitutions. Random forest predictive models highlighted the importance of Potri.010G079500 in producing very long chain alkenes; however, its absence did not predict previously reported alkene-deficient phenotypes. Instead, alkene levels are best predicted by the combinations of KCS copies. Amino acid substitutions clustered around ligand and donor binding pockets, suggesting they contribute to differing wax cuticle composition. Finally, each KCS gene and copy was linked to a helitron transposon. A phylogenetic analysis indicates they are the evolutionary mechanism for generating KCS tandem arrays. ConclusionsLong-read sequencing and telomere-to-telomere assembles revealed large-effect loci critical to genetic studies that are unattainable from short-reads. These approaches also have the potential to reveal novel insights into genome structure and function, such as the helitrons identified here. Our results highlight that, given current challenges in annotation and assembly, detailed and focused long-read sequences are key to interpreting complex genomic regions that contain tandem copy number variants.

genomics↗

bioRxiv2025

Host specificity of fungal functional groups covaries with elevation: implications for intraspecific plant interactions

Plants of the same species can harbor shared enemies, resulting in indirect, intraspecific competition. When this competition is strong, there are fitness costs associated with growing near a same-species individual, termed Conspecific Negative Density Dependence (CNDD). Host-specific microbial pathogens are known mediators of this type of indirect, intraspecific plant competition, yet how these plant-microbe interactions vary with environmental context is less explored. Further, microbial pathogens and mutualists may jointly contribute to the relative strength of intraspecific competition, yet most studies focus only on pathogens. We use ITS metabarcoding to characterize soil and foliar fungal functional groups associated with individual trees of three dominant conifers in forests where the strength of CNDD is known to be greater at lower elevations relative to higher elevations. We hypothesize that plants found in the mesic low elevation forests accumulate more host-specific fungal pathogens compared to plants found in the more xeric high elevation forests. Conversely, we hypothesize that plants found in the high elevation forests accumulate more host-specific mutualists compared to those found at low elevations. We test these hypotheses by evaluating three metrics of plant-associated fungal functional groups - alpha diversity, relative abundance, and host specificity - that together address the degree to which a plant recruits particular groups. We find the diversity, relative abundance and host specificity of soil fungal pathogens to decrease with elevation. In contrast, we find ectomycorrhizal fungal host specificity, but not diversity or relative abundance, to increase with elevation. Aboveground, we find a key foliar pathogen Nothophaeocryptocus gaeumanii to support our hypotheses as a dominant, and highly host specific pathogen that is enriched at low elevation sites. Our results indicate that across a climate gradient known to negatively covary with CNDD strength, soil pathogens recruitment is most prevalent in the mesic climates and, to a lesser extent, ectomycorrhizal recruitment is most prevalent in the xeric climates. Together these findings suggest that both pathogenic and mutualistic fungal symbionts could contribute to landscape level variation in competitive, intraspecific plant interactions.

ecology↗

bioRxiv2021

Elevated CO2 reduces a common soybean leaf endophyte

Free-air CO2 enrichment (FACE) experiments have elucidated how climate change affects plant physiology and production. However, we lack a predictive understanding of how climate change alters interactions between plants and endophytes, critical microbial mediators of plant physiology and ecology. We leveraged the SoyFACE facility to examine how elevated [CO2] affected soybean (Glycine max) leaf endophyte communities in the field. Endophyte community composition changed under elevated [CO2], including a decrease in the abundance of a common endophyte, Methylobacterium sp. Moreover, Methylobacterium abundance was negatively correlated with co-occurring fungal endophytes. We then assessed how Methylobacterium affected the growth of co-occurring endophytic fungi in vitro. Methylobacterium antagonized most co-occurring fungal endophytes in vitro, particularly when it was more established in culture before fungal introduction. Variation in fungal response to Methylobacterium within a single fungal operational taxonomic unit (OTU) was comparable to inter-OTU variation. Finally, fungi isolated from elevated vs. ambient [CO2] plots differed in colony growth and response to Methylobacterium, suggesting that increasing [CO2] may affect fungal traits and interactions within the microbiome. By combining in situ and in vitro studies, we show that elevated [CO2] decreases the abundance of a common bacterial endophyte that interacts strongly with co-occurring fungal endophytes. We suggest that endophyte responses to global climate change will have important but largely unexplored implications for both agricultural and natural systems.

ecology↗

bioRxiv2020

Geographic variation in the seed mycobiome of Pseudotsuga menziesii var. menziesii across the Pacific Northwest, USA

Fungal symbionts occur in all plant tissues, and many aid their host plants with critical functions, including nutrient acquisition, defense against pathogens, and tolerance of abiotic stress. "Core" taxa in the plant mycobiome, defined as fungi present across individuals, populations, or time, may be particularly crucial to plant survival during the challenging seedling stage. However, studies on core seed fungi are limited to individual sampling sites, raising the question of whether core taxa exist across large geographic scales. We addressed this question using both culture-based and culture-free techniques to identify the fungi found in individual seeds collected from nine provenances across the range of Coastal Douglas-fir (Pseudotsuga menziesii var. menziesii), a foundation tree species in the Pacific Northwest and a globally important timber crop that is propagated commercially by seed. Two key findings emerged: 1) Seed mycobiome composition differed among seed provenances. 2) Despite spatial variation in the seed mycobiome, we detected four core members, none of which is a known pathogen of Douglas-fir: Trichoderma spp., Hormonema macrosporum, Mucor plumbeus and Talaromyces rugulosus. Our results support the concept of a core seed microbiome, yet additional work is needed to determine the functional consequences of core taxa for seedling germination, growth, survival and competition.

ecology↗

bioRxiv2020

Joint effects of host genotype and species arrival order govern plant microbiome composition and function

The composition of host-associated microbiomes can have important consequences for host health and fitness [1-3]. Yet, we still lack understanding of many fundamental processes that determine microbiome composition [4,5]. There is mounting evidence that historical contingency during microbiome assembly may overshadow more deterministic processes, such as the selective filters imposed by host traits [6-8]. More specifically, species arrival order has been frequently shown to affect microbiome composition [9-12], a phenomenon known as priority effects [13-15]. However, it is less clear whether priority effects during microbiome assembly are consequential for the host [16], or whether intraspecific variation in host traits can alter the trajectory of microbiome assembly under priority effects. In a greenhouse inoculation experiment using the black cottonwood (Populus trichocarpa) foliar microbiome, we manipulated host genotype and the colonization order of common foliar fungi. We quantified microbiome assembly outcomes using fungal marker-gene sequencing and measured susceptibility of the colonized host to a leaf rust pathogen, Melampsora x columbiana. We found that the effect of species arrival order on microbiome composition, and subsequent disease susceptibility, depended on the host genotype. Additionally, we found that microbiome assembly history can affect host disease susceptibility independent of microbiome composition at the time of pathogen exposure, suggesting that the interactive effects of species arrival order and host genotype can decouple community composition and function. Overall, these results highlight the importance of a key process underlying stochasticity in microbiome assembly while also revealing which hosts are most likely to experience these effects.

ecology↗

bioRxiv2019

Breeding for broad-spectrum disease resistance alters the maize leaf microbiome

O_LIPlant genotype strongly affects disease resistance, and also influences the composition of the leaf microbiome. However, these processes have not been studied and linked in the microevolutionary context of breeding for improved disease resistance. We hypothesized that broad-spectrum disease resistance alleles also affect colonization by non-pathogenic symbionts.\nC_LIO_LIQuantitative trait loci (QTL) conferring resistance to multiple fungal pathogens were introgressed into a disease-susceptible maize inbred line. Bacterial and fungal leaf microbiomes of the resulting near-isogenic lines were compared to the microbiome of the disease-susceptible parent line at two timepoints in multiple fields.\nC_LIO_LIIntrogression of QTL from disease-resistant lines strongly shifted the relative abundance of diverse fungal and bacterial taxa in both 3-week-old and 7-week-old plants. Nevertheless, the effects on overall community structure and diversity were minor and varied among fields and years. Contrary to our expectations, host genotype effects were not any stronger in fields with high disease pressure than in uninfected fields, and microbiome succession over time was similar in heavily infected plants and uninfected plants.\nC_LIO_LIThese results show that introgressed QTL can greatly improve broad-spectrum disease resistance while having only limited and inconsistent pleiotropic effects on the leaf microbiome in maize.\nC_LI

plant biology↗