Phylogenomic challenges in polyploid-rich lineages: Insights from paralog processing and reticulation methods using the complex genus Packera (Asteraceae: Senecioneae)
Authors: Moore-Pollard, E. R., Ellestad, P., Mandel, J.
The study examined how polyploidy, hybridization, and incomplete lineage sorting affect phylogenetic reconstructions in the genus Packera, evaluating several published paralog‑processing pipelines. Results showed that the choice of orthology and paralog handling methods markedly altered tree topology, time‑calibrated phylogenies, biogeographic histories, and detection of ancient reticulation, underscoring the need for careful methodological selection alongside comprehensive taxon sampling.
The study examined how soil phosphorus and nitrogen availability influence wheat root-associated arbuscular mycorrhizal fungal (AMF) communities and the expression of mycorrhizal nutrient transporters. Field sampling across two years combined with controlled pot experiments showed that P and N jointly affect AMF colonisation, community composition (with Funneliformis dominance under high P), and regulation of phosphate, ammonium, and nitrate transporters. Integrating metabarcoding and RT‑qPCR provides a framework to assess AMF contributions to crop nutrition.
The study examined how white lupin (Lupinus albus) cotyledons mobilize nitrogen and minerals during early seedling growth under nitrogen‑deficient conditions, revealing that 60 % of stored proteins degrade within eight days and are redirected to support development. Proteomic analyses showed dynamic shifts in nutrient transport, amino acid metabolism, and stress responses, and premature cotyledon removal markedly impaired growth, highlighting the cotyledon's essential role in nutrient supply and transient photosynthetic activity.
The study investigated unexpected leaf spot symptoms in Psa3‑resistant kiwifruit (Actinidia) germplasm, finding that Psa3 was detectable by qPCR and metabarcoding despite poor culturing. Metabarcoding revealed distinct bacterial community shifts in lesions versus healthy tissue, and whole‑genome sequencing identified diverse Pseudomonas spp. that, while not individually more pathogenic, could enhance Psa3 growth, suggesting pathogenic consortia on resistant hosts.