Population genetics of Hyaloperonospora arabidopsidis (Hpa), a natural oomycete pathogen of Arabidopsis thaliana

Many plant pathogens cause devastating diseases, continually threatening food security worldwide. Due to the antagonistic nature of hostpathogen interactions, the interaction partners pose high selection pressures on one another. In agricultural pathosystems, which are less genetically diverse compared to wild plant pathosystems, such interactions have been well-studied, but little is known about how they play out in natural plant-pathogen systems. In 2018, we sampled wild populations of the annual plant Arabidopsis thaliana infected with a natural obligate biotrophic oomycete pathogen Hyaloperonospora arabidopsidis (Hpa) throughout a large part of their natural range in Eurasia. After propagation on immune-compromised host plants in the lab, we whole-genome sequenced 137 Hpa isolates as well as host plants from 76 populations. We expect tight co-evolutionary dynamics between both partners because of the pathogen’s host-specificity and its dependency on host resources to complete its lifecycle. We will present first insights from studying genetic diversity and population structure of Hpa. By looking closer at genomic variation within and among pathogen isolates, we aim to understand how the pathogen adapts to its host. Additionally, combining knowledge about the pathogen with information about the host, we will be able to investigate co-evolutionary dynamics in this pathosystem to deepen our understanding of natural plant-pathogen interactions

Host-associated microbe PCR (hamPCR): accessing new biology through convenient measurement of both microbial load and community composition

The ratio of microbial population size relative to the amount of host tissue, or “microbial load”, is a fundamental metric of colonization and infection, but it cannot be directly deduced from microbial amplicon data such as 16S rRNA gene counts. Because conventional methods to determine load, such as serial dilution plating or quantitative PCR, add substantial experimental burden, they are only rarely paired with amplicon sequencing. Alternatively, whole metagenome sequencing of DNA contributed by host and microbes both reveals microbial community composition and enables determination of microbial load, but host DNA typically greatly outweighs microbial DNA, severely limiting the cost-effectiveness and scalability of this approach. We introduce host-associated microbe PCR (hamPCR), a robust amplicon sequencing strategy to quantify microbial load and describe interkingdom microbial community composition in a single, cost-effective library. We demonstrate its accuracy and flexibility across multiple host and microbe systems, including nematodes and major crops. We further present a technique that can be used, prior to sequencing, to optimize the host representation in a batch of libraries without loss of information. Because of its simplicity, and the fact that it provides an experimental solution to the well-known statistical challenges provided by compositional data, hamPCR will become a transformative approach throughout culture-independent microbiology

Cycles of satellite and transposon evolution in Arabidopsis centromeres

Centromeres are critical for cell division, loading CENH3 or CENPA histone variant nucleosomes, directing kinetochore formation and allowing chromosome segregation1,2. Despite their conserved function, centromere size and structure are diverse across species. To understand this centromere paradox3,4, it is necessary to know how centromeric diversity is generated and whether it reflects ancient trans-species variation or, instead, rapid post-speciation divergence. To address these questions, we assembled 346 centromeres from 66 Arabidopsis thaliana and 2 Arabidopsis lyrata accessions, which exhibited a remarkable degree of intra- and inter-species diversity. A. thaliana centromere repeat arrays are embedded in linkage blocks, despite ongoing internal satellite turnover, consistent with roles for unidirectional gene conversion or unequal crossover between sister chromatids in sequence diversification. Additionally, centrophilic ATHILA transposons have recently invaded the satellite arrays. To counter ATHILA invasion, chromosome-specific bursts of satellite homogenization generate higher-order repeats and purge transposons, in line with cycles of repeat evolution. Centromeric sequence changes are even more extreme in comparison between A. thaliana and A. lyrata. Together, our findings identify rapid cycles of transposon invasion and purging through satellite homogenization, which drive centromere evolution and ultimately contribute to speciation